List of supported software

Note

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EasyBuild supports 3470 different software packages (incl. toolchains, bundles):

a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z

3

3d-dna - 3to2

3d-dna

3D de novo assembly (3D DNA) pipeline

homepage: https://github.com/theaidenlab/3d-dna

version	versionsuffix	toolchain
180922	-Python-2.7.15	GCCcore/8.2.0

3to2

lib3to2 is a set of fixers that are intended to backport code written for Python version 3.x into Python version 2.x.

homepage: https://pypi.python.org/pypi/3to2

version	versionsuffix	toolchain
1.1.1	-Python-2.7.12	foss/2016b, intel/2016b
1.1.1	-Python-2.7.13	intel/2017a

4

4ti2

4ti2

A software package for algebraic, geometric and combinatorial problems on linear spaces

homepage: https://4ti2.github.io/

version	toolchain
1.6.9	GCC/11.3.0, GCC/8.2.0-2.31.1, intel/2018b

A

ABAQUS - ABINIT - ABRA2 - ABRicate - Abseil - abTEM - ABySS - ack - ACTC - ada - AdapterRemoval - ADDA - ADF - ADIOS - adjustText - ADMIXTURE - ADOL-C - Advisor - affinity - AFNI - AGAT - AGeNT - AGFusion - AICSImageIO - AIMAll - aiohttp - ALADIN - ALAMODE - Albacore - Albumentations - alevin-fry - ALFA - Alfred - ALL - alleleCount - alleleIntegrator - Allinea - ALLPATHS-LG - almosthere - Alpha - AlphaFold - AlphaPulldown - ALPS - alsa-lib - AMAPVox - Amara - amask - Amber - AmberMini - AmberTools - AMD-LibM - AMD-RNG - AMD-SecureRNG - AMD-uProf - AMICA - AMOS - AMPHORA2 - AMPL-MP - amplimap - AMPtk - AMRFinderPlus - AmrPlusPlus - AMS - Anaconda2 - Anaconda3 - anadama2 - aNCI - andi - ANGEL - angsd - ANIcalculator - anndata - Annif - Annocript - annovar - ANSYS - ANSYS_CFD - ant - ANTIC - antiSMASH - ANTLR - ANTs - anvio - any2fasta - AOCC - AOFlagger - AOMP - APBS - apex - APR - APR-util - AptaSUITE - ARAGORN - Arb - Arcade-Learning-Environment - arcasHLA - ARCH - Archive-Zip - ArchR - archspec - AreTomo2 - ARGoS - argtable - aria2 - Arlequin - Armadillo - arosics - ARPACK++ - arpack-ng - ArrayFire - Arriba - Arrow - arrow-R - ART - Artemis - artic-ncov2019 - ARTS - ArviZ - ARWEN - ASAP - ASAP3 - ASCAT - ASE - ASF-SearchAPI - ASHS - Aspera-CLI - Aspera-Connect - assimp - Assimulo - ASTRID - astro-tulips - astropy - at-spi2-atk - at-spi2-core - ATAT - ATK - ATLAS - atomate - AtomPAW - atools - atropos - ATSAS - attr - attrdict - attrdict3 - augur - AUGUSTUS - Austin - AUTO-07p - Autoconf - Autoconf-archive - AutoDock - AutoDock-GPU - AutoDock-Vina - AutoDockSuite - AutoGeneS - AutoGrid - Automake - AutoMap - autopep8 - Autotools - Avogadro2 - avro-cpp - awscli - Ax - axel

ABAQUS

Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA.

homepage: http://www.simulia.com/products/abaqus_fea.html

version	versionsuffix	toolchain
6.12.1	-linux-x86_64	system
6.13.5	-linux-x86_64	system
6.14.1	-linux-x86_64	system
2017	-hotfix-1721	system
2018	-hotfix-1806	system
2020		system
2021	-hotfix-2132	system
2022		system
2022	-hotfix-2214	system
2022	-hotfix-2223	system

ABINIT

ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.

homepage: https://www.abinit.org/

version	versionsuffix	toolchain
7.0.3	-x86_64_linux_gnu4.5	system
7.0.5	-x86_64_linux_gnu4.5	system
7.2.1	-x86_64_linux_gnu4.5	system
7.10.5		intel/2016.02-GCC-4.9
7.10.5	-libxc	intel/2016.02-GCC-4.9
8.0.8		intel/2016a
8.0.8b		foss/2016b, intel/2016b
8.2.2		foss/2016b, intel/2016b
8.4.4		intel/2017b
8.6.3		intel/2018a
8.10.2		intel/2018b
8.10.3		intel/2018b
9.2.1		foss/2019b, intel/2019b, intel/2020a
9.4.1		foss/2020b, intel/2020a, intel/2020b
9.4.2		foss/2021a, intel/2021a
9.6.2		foss/2022a, intel/2021a, intel/2021b, intel/2022a
9.10.3		intel/2022a

ABRA2

Assembly Based ReAligner

homepage: https://github.com/mozack/abra2

version	toolchain
2.22	iccifort/2019.5.281
2.23	GCC/10.2.0, GCC/9.3.0

ABRicate

Mass screening of contigs for antimicrobial and virulence genes

homepage: https://github.com/tseemann/abricate

version	versionsuffix	toolchain
0.9.9		gompi/2019b
0.9.9	-Perl-5.28.1	gompi/2019a
1.0.0		gompi/2021a

Abseil

Abseil is an open-source collection of C++ library code designed to augment the C++ standard library. The Abseil library code is collected from Google's own C++ code base, has been extensively tested and used in production, and is the same code we depend on in our daily coding lives.

homepage: https://abseil.io/

version	toolchain
20210324.2	GCCcore/11.2.0
20230125.2	GCCcore/11.3.0, GCCcore/12.2.0
20230125.3	GCCcore/12.3.0
20240116.1	GCCcore/13.2.0

abTEM

abTEM provides a Python API for running simulations of Transmission Electron Microscopy images.

homepage: https://github.com/jacobjma/abTEM

version	versionsuffix	toolchain
1.0.0b24	-ASE-3.22.0	fosscuda/2020b
1.0.0b26	-ASE-3.22.0	foss/2020b, fosscuda/2020b

ABySS

Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

homepage: https://www.bcgsc.ca/platform/bioinfo/software/abyss

version	toolchain
1.9.0	foss/2016a
2.0.2	foss/2016b, foss/2018a, gompi/2019a, intel/2016b
2.0.3	foss/2017b, intel/2017b
2.1.5	foss/2019b
2.2.5	foss/2020b
2.3.7	foss/2023a

ack

ack is a tool like grep, optimized for programmers

homepage: https://beyondgrep.com

version	toolchain
2.14	system
3.4.0	GCCcore/10.2.0
3.5.0	GCCcore/10.3.0

ACTC

ACTC converts independent triangles into triangle strips or fans.

homepage: https://sourceforge.net/projects/actc

version	toolchain
1.1	GCCcore/10.2.0, GCCcore/11.3.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.3.0, GCCcore/9.3.0, intel/2016b

ada

Performs discrete, real, and gentle boost under both exponential and logistic loss on a given data set.

homepage: https://cran.r-project.org/web/packages/ada/index.html

version	versionsuffix	toolchain
2.0-5	-R-3.4.0	intel/2017a

AdapterRemoval

AdapterRemoval searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal.

homepage: https://github.com/MikkelSchubert/adapterremoval

version	toolchain
2.2.0	foss/2016b
2.2.2	foss/2018b
2.3.1	foss/2018b
2.3.2	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0
2.3.3	GCC/11.3.0

ADDA

ADDA is an open-source parallel implementation of the discrete dipole approximation, capable to simulate light scattering by particles of arbitrary shape and composition in a wide range of particle sizes.

homepage: https://github.com/adda-team/adda/wiki

version	toolchain
1.3b4	foss/2019a

ADF

ADF is an accurate, parallelized, powerful computational chemistry program to understand and predict chemical structure and reactivity with density functional theory (DFT).

homepage: https://www.scm.com/ADF/

version	versionsuffix	toolchain
2009.01a.pc64_linux.intelmpi		system
2014.02		system
2014.11.r48287		intel/2016a
2016.101		system
2019.303	-intelmpi	system

ADIOS

The Adaptable IO System (ADIOS) provides a simple, flexible way for scientists to describe the data in their code that may need to be written, read, or processed outside of the running simulation.

homepage: https://www.olcf.ornl.gov/center-projects/adios/

version	versionsuffix	toolchain
1.13.1	-Python-2.7.15	foss/2019a
1.13.1	-Python-3.8.2	foss/2020a
20210804	-Python-3.8.2	foss/2020a

adjustText

A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps.

homepage: https://github.com/Phlya/adjustText

version	versionsuffix	toolchain
0.7.3		foss/2021b
0.7.3	-Python-3.6.6	foss/2018b
0.7.3	-Python-3.7.2	intel/2019a

ADMIXTURE

ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm.

homepage: https://dalexander.github.io/admixture/

version	toolchain
1.3.0	system

ADOL-C

The package ADOL-C (Automatic Differentiation by OverLoading in C++) facilitates the evaluation of first and higher derivatives of vector functions that are defined by computer programs written in C or C++. The resulting derivative evaluation routines may be called from C/C++, Fortran, or any other language that can be linked with C.

homepage: https://projects.coin-or.org/ADOL-C

version	toolchain
2.7.0	gompi/2019a
2.7.2	gompi/2020a

Advisor

Vectorization Optimization and Thread Prototyping - Vectorize & thread code or performance “dies” - Easy workflow + data + tips = faster code faster - Prioritize, Prototype & Predict performance gain

homepage: https://software.intel.com/intel-advisor-xe

version	toolchain
2016_update2	system
2017_update1	system
2018_update1	system
2018_update3	system
2019_update2	system
2019_update3	system
2019_update5	system
2021.2.0	system
2021.4.0	system
2022.1.0	system
2023.0.0	system
2023.2.0	system

affinity

A small C++ wrapper for managing Linux CPU sets and CPU affinity. It also includes a tool to report binding, which is useful for testing different binding options

homepage: https://github.com/vkarak/affinity

version	toolchain
20230524	foss/2022a, intel/2022a

AFNI

AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity.

homepage: http://afni.nimh.nih.gov/

version	versionsuffix	toolchain
18.1.09	-Python-3.6.4	intel/2018a
18.3.00	-Python-3.6.6	foss/2018b
19.0.01	-Python-2.7.14	foss/2017b, intel/2017b
20160329	-Python-2.7.11	intel/2016a

AGAT

AGAT: Another GTF/GFF Analysis Toolkit. Suite of tools to handle gene annotations in any GTF/GFF format.

homepage: https://agat.readthedocs.io/en/latest/

version	toolchain
0.9.2	GCC/11.2.0
1.1.0	GCC/12.2.0

AGeNT

The Agilent Genomics NextGen Toolkit (AGeNT) is a Java-based software module that processes the read sequences from targeted high-throughput sequencing data generated by sequencing Agilent SureSelect and HaloPlex libraries. The Trimmer utility of the AGeNT module processes the read sequences to identify and remove the adaptor sequences and extracts dual molecular barcodes (for SureSelect XT HS2). The LocatIt utility of the AGeNT module processes the Molecular Barcode (MBC) information from HaloPlex HS, SureSelect XT HS, and SureSelect XT HS2 Illumina sequencing runs with options to either mark or merge duplicate reads and output in BAM file format. The Illumina InterOp libraries are a set of common routines used for reading InterOp metric files produced by Illumina sequencers including NextSeq 1k/2k. These libraries are backwards compatible and capable of supporting prior releases of the software, with one exception: GA systems have been excluded.

homepage: https://www.agilent.com/en/product/next-generation-sequencing/hybridization-based-next-generation-sequencing-ngs/ngs-software/agent-232879

version	toolchain
3.0.6	system

AGFusion

AGFusion is a python package for annotating gene fusions from the human or mouse genomes.

homepage: https://github.com/murphycj/AGFusion

version	versionsuffix	toolchain
1.2	-Python-3.7.2	foss/2019a

AICSImageIO

Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python

homepage: https://github.com/AllenCellModeling/aicsimageio

version	toolchain
4.14.0	foss/2022a

AIMAll

AIMAll is an easy to use, accurate, reliable and efficient quantum chemistry software package for performing comprehensive, quantitative and visual QTAIM analyses of molecular systems - starting from molecular wavefunction data.

homepage: http://aim.tkgristmill.com

version	versionsuffix	toolchain
19.10.12	-linux_64bit	intel/2020b

aiohttp

Asynchronous HTTP client/server framework for asyncio and Python.

homepage: https://github.com/aio-libs/aiohttp

version	versionsuffix	toolchain
3.5.4	-Python-3.6.6	foss/2018b
3.8.1		GCCcore/10.3.0, GCCcore/11.2.0
3.8.3		GCCcore/11.3.0
3.8.5		GCCcore/12.2.0, GCCcore/12.3.0

ALADIN

ALADIN was entirely built on the notion of compatibility with its mother system, IFS/ARPEG. The latter, a joint development between the European Centre for Medium-Range Weather Forecasts (ECMWF) and Meteo-France, was only meant to consider global Numerical Weather Prediction applications; hence the idea, for ALADIN, to complement the IFS/ARPEGE project with a limited area model (LAM) version, while keeping the differences between the two softwares as small as possible.

homepage: http://www.cnrm.meteo.fr/aladin/

version	toolchain
36t1_op2bf1	intel/2016a

ALAMODE

ALAMODE is an open source software designed for analyzing lattice anharmonicity and lattice thermal conductivity of solids. By using an external DFT package such as VASP and Quantum ESPRESSO, you can extract harmonic and anharmonic force constants straightforwardly with ALAMODE. Using the calculated anharmonic force constants, you can also estimate lattice thermal conductivity, phonon linewidth, and other anharmonic phonon properties from first principles.

homepage: http://alamode.readthedocs.io/en/latest/index.html

version	toolchain
1.4.2	foss/2022b

Albacore

Albacore is a software project that provides an entry point to the Oxford Nanopore basecalling algorithms.

homepage: https://community.nanoporetech.com/protocols/albacore-offline-basecalli/v/abec_2003_v1_revz_29nov2016

version	versionsuffix	toolchain
2.0.2	-Python-3.6.1	intel/2017a

Albumentations

Albumentations is a Python library for fast and flexible image augmentations

homepage: https://albumentations.ai

version	versionsuffix	toolchain
1.1.0		foss/2021b
1.1.0	-CUDA-11.3.1	foss/2021a
1.3.0		foss/2022a
1.3.0	-CUDA-11.7.0	foss/2022a

alevin-fry

alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

homepage: https://github.com/COMBINE-lab/alevin-fry

version	toolchain
0.4.3	GCCcore/11.2.0
0.6.0	GCCcore/10.3.0

ALFA

ALFA provides a global overview of features distribution composing NGS dataset(s). Given a set of aligned reads (BAM files) and an annotation file (GTF format), the tool produces plots of the raw and normalized distributions of those reads among genomic categories (stop codon, 5'-UTR, CDS, intergenic, etc.) and biotypes (protein coding genes, miRNA, tRNA, etc.). Whatever the sequencing technique, whatever the organism.

homepage: https://github.com/biocompibens/ALFA

version	versionsuffix	toolchain
1.1.1	-Python-3.7.2	foss/2019a

Alfred

Alfred is an efficient and versatile command-line application that computes multi-sample quality control metrics in a read-group aware manner. Alfred supports read counting, feature annotation and haplotype-resolved consensus computation using multiple sequence alignments.

homepage: https://www.gear-genomics.com/alfred/

version	toolchain
0.2.6	GCC/11.2.0

ALL

A Load Balancing Library (ALL) aims to provide an easy way to include dynamic domain-based load balancing into particle based simulation codes. The library is developed in the Simulation Laboratory Molecular Systems of the Jülich Supercomputing Centre at Forschungszentrum Jülich.

homepage: https://gitlab.jsc.fz-juelich.de/SLMS/loadbalancing

version	toolchain
0.9.2	foss/2022b, foss/2023a

alleleCount

The alleleCount package primarily exists to prevent code duplication between some other projects, specifically AscatNGS and Battenberg. As of v4 the perl code wraps the C implementation of allele counting code for BAM/CRAM processing.

homepage: http://cancerit.github.io/alleleCount/

version	toolchain
4.0.0	GCCcore/6.4.0
4.2.1	GCC/11.3.0
4.3.0	GCC/12.2.0

alleleIntegrator

R package to generate allele specific counts for scRNA data and use it to identify cancer cells

homepage: https://github.com/constantAmateur/alleleIntegrator

version	versionsuffix	toolchain
0.8.8	-R-4.2.1	foss/2022a
0.8.8	-R-4.2.2	foss/2022b

Allinea

The Allinea environment is an essential toolkit for developers and computational scientists looking to get results faster.

homepage: http://www.allinea.com

version	toolchain
4.1-32834-Redhat-5.7-x86_64	system
4.1-32834-Redhat-6.0-x86_64	system
6.1.1-Ubuntu-14.04-x86_64	system

ALLPATHS-LG

ALLPATHS-LG, the new short read genome assembler.

homepage: http://www.broadinstitute.org/software/allpaths-lg/blog/

version	toolchain
52488	foss/2016a

almosthere

Progress indicator C library. ATHR is a simple yet powerful progress indicator library that works on Windows, Linux, and macOS. It is non-blocking as the progress update is done via a dedicated, lightweight thread, as to not impair the performance of the calling program.

homepage: https://github.com/horta/almosthere

version	toolchain
1.0.1	GCCcore/7.3.0
1.0.10	GCCcore/9.3.0
2.0.2	GCCcore/10.2.0

Alpha

Alpha is a tool designed for detailed comparative study of bacteriophage genomes.

homepage: https://www.lirmm.fr/~swenson/alpha/alpha.htm

version	versionsuffix	toolchain
20200430	-Python-2.7.16	foss/2019b

AlphaFold

AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known. This package of AlphaFold contains patches for ColabFold.

homepage: https://github.com/sokrypton/alphafold

version	versionsuffix	toolchain
2.0.0		foss/2020b, fosscuda/2020b
2.0.1		foss/2020b, fosscuda/2020b
2.1.1		fosscuda/2020b
2.1.2		foss/2021a
2.1.2	-CUDA-11.3.1	foss/2021a
2.1.2	-TensorFlow-2.5.0	foss/2020b, fosscuda/2020b
2.2.2		foss/2021a
2.2.2	-CUDA-11.3.1	foss/2021a
2.3.0	-CUDA-11.4.1	foss/2021b
2.3.1		foss/2022a
2.3.1	-CUDA-11.7.0	foss/2022a
2.3.4	-CUDA-11.7.0-ColabFold	foss/2022a
2.3.4	-ColabFold	foss/2022a

AlphaPulldown

AlphaPulldown is a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer

homepage: https://github.com/KosinskiLab/AlphaPulldown

version	toolchain
0.30.4	foss/2020b, fosscuda/2020b

ALPS

The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as C++ libraries for simplifying the development of such code.

homepage: http://alps.comp-phys.org/

version	versionsuffix	toolchain
2.2.b4	-Python-2.7.11	intel/2016a
2.3.0	-Python-2.7.12	foss/2016b
2.3.0	-Python-3.5.2	foss/2016b

alsa-lib

The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality to the Linux operating system.

homepage: https://www.alsa-project.org

version	toolchain
1.2.4	GCCcore/9.3.0
1.2.8	GCCcore/10.2.0, GCCcore/11.2.0, GCCcore/11.3.0

AMAPVox

LiDAR data voxelisation software

homepage: https://amap-dev.cirad.fr/projects/amapvox

version	versionsuffix	toolchain
1.9.4	-Java-11	system

Amara

Library for XML processing in Python, designed to balance the native idioms of Python with the native character of XML.

homepage: https://pypi.org/project/Amara

version	versionsuffix	toolchain
1.2.0.2	-Python-2.7.15	foss/2019a, intel/2019a

amask

amask is a set of tools to to determine the affinity of MPI processes and OpenMP threads in a parallel environment.

homepage: https://github.com/TACC/amask

version	toolchain
20171106	foss/2018a
20190404	foss/2018b

Amber

Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction.

homepage: https://ambermd.org/amber.html

version	versionsuffix	toolchain
14	-AmberTools-15-patchlevel-13-13	intel/2016a
16	-AmberTools-16-patchlevel-5-14	iomkl/2016.07
16	-AmberTools-16-patchlevel-5-14-CUDA	iomkl/2016.09-GCC-4.9.3-2.25
16	-AmberTools-16-patchlevel-5-14-serial	iomkl/2016.07
16	-AmberTools-17-patchlevel-10-15	foss/2018b, fosscuda/2018b, intel/2018b
16	-AmberTools-17-patchlevel-10-15-Python-2.7.14	foss/2017b, fosscuda/2017b, intel/2017b, intelcuda/2017b
16	-AmberTools-17-patchlevel-8-12	intel/2017b
18	-AmberTools-18-patchlevel-10-8	foss/2018b, fosscuda/2018b, intel/2017b
18	-AmberTools-19-patchlevel-12-17-Python-2.7.16	foss/2019b, fosscuda/2019b
20.11	-AmberTools-20.15-Python-3.8.2	foss/2020a, fosscuda/2020a
20.11	-AmberTools-21.3	foss/2020b, fosscuda/2020b
22.0	-AmberTools-22.3	foss/2021b
22.0	-AmberTools-22.3-CUDA-11.4.1	foss/2021b
22.4	-AmberTools-22.5-CUDA-11.7.0	foss/2022a

AmberMini

A stripped-down set of just antechamber, sqm, and tleap.

homepage: https://github.com/choderalab/ambermini

version	toolchain
16.16.0	intel/2017b, intel/2020a

AmberTools

AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.

homepage: https://ambermd.org/

version	versionsuffix	toolchain
17		intel/2017b, intel/2018a
17	-Python-2.7.14	foss/2018a
20	-Python-3.8.2	intel/2020a
21		foss/2021a, intel/2021b
21.12		foss/2021b
22.3		foss/2021b

AMD-LibM

AMD LibM is a software library containing a collection of basic math functions optimized for x86-64 processor based machines.

homepage: https://developer.amd.com/amd-cpu-libraries/amd-math-library-libm/

version	toolchain
3.2.2	GCC/7.3.0-2.30
3.6.0-4	GCC/9.3.0

AMD-RNG

AMD Random Number Generator Library is a pseudorandom number generator library.

homepage: https://developer.amd.com/amd-cpu-libraries/rng-library/

version	toolchain
1.0	GCC/7.3.0-2.30
2.2-4	GCC/9.3.0

AMD-SecureRNG

The AMD Secure Random Number Generator (RNG) is a library that provides APIs to access the cryptographically secure random numbers generated by AMD’s hardware-based random number generator implementation.

homepage: https://developer.amd.com/amd-cpu-libraries/rng-library/

version	toolchain
1.0	GCC/7.3.0-2.30
2.2-4	GCC/9.3.0

AMD-uProf

AMD uProf is a performance analysis tool for applications running on Windows, Linux & FreeBSD operating systems. It allows developers to better understand the runtime performance of their application and to identify ways to improve its performance.

homepage: https://developer.amd.com/amd-uprof/

version	toolchain
3.4.502	system
3.5.671	system
4.1.424	system

AMICA

Code for AMICA: Adaptive Mixture ICA with shared components

homepage: https://github.com/sccn/amica

version	toolchain
2024.1.19	intel/2023a

AMOS

The AMOS consortium is committed to the development of open-source whole genome assembly software

homepage: http://amos.sourceforge.net

version	toolchain
3.1.0	foss/2018b, foss/2021b, foss/2023a

AMPHORA2

An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.

homepage: https://github.com/wu-lab-uva/AMPHORA2

version	versionsuffix	toolchain
20190730	-Java-13-pthreads-avx2	gompi/2020b

AMPL-MP

An open-source library for mathematical programming.

homepage: https://github.com/ampl/mp

version	toolchain
3.1.0	GCCcore/6.4.0

amplimap

amplimap is a command-line tool to automate the processing and analysis of data from targeted next-generation sequencing (NGS) experiments with PCR-based amplicons or capture-based enrichment systems.

homepage: https://amplimap.readthedocs.io/en/latest/

version	versionsuffix	toolchain
0.4.16	-Python-3.6.6	foss/2018b

AMPtk

AMPtk is a series of scripts to process NGS amplicon data using USEARCH and VSEARCH, it can also be used to process any NGS amplicon data and includes databases setup for analysis of fungal ITS, fungal LSU, bacterial 16S, and insect COI amplicons.

homepage: https://amptk.readthedocs.io

version	toolchain
1.5.4	foss/2021b

AMRFinderPlus

This software and the accompanying database are designed to find acquired antimicrobial resistance genes and some point mutations in protein or assembled nucleotide sequences.

homepage: https://github.com/ncbi/amr

version	toolchain
3.11.18	gompi/2021b, gompi/2022b

AmrPlusPlus

AmrPlusPlus v2.0 can process the raw data from the sequencer, identify the fragments of DNA, and count them. It also provides a count of the polymorphisms that occur in each DNA fragment with respect to the reference database.

homepage: https://megares.meglab.org/amrplusplus/latest/html/v2

version	toolchain
2.0-20200114	GCC/8.3.0

AMS

The Amsterdam Modeling Suite (AMS) provides a comprehensive set of modules for computational chemistry and materials science, from quantum mechanics to fluid thermodynamics.

homepage: https://www.scm.com/amsterdam-modeling-suite/

version	versionsuffix	toolchain
2020.102	-intelmpi	iimpi/2020b
2022.102	-intelmpi	iimpi/2021b
2023.101	-intelmpi	iimpi/2022a
2023.104	-intelmpi	iimpi/2022b

Anaconda2

Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.

homepage: https://www.anaconda.com

version	toolchain
4.0.0	system
4.2.0	system
4.4.0	system
5.0.1	system
5.1.0	system
5.3.0	system
2018.12	system
2019.03	system
2019.07	system
2019.10	system

Anaconda3

Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.

homepage: https://www.anaconda.com

version	toolchain
4.0.0	system
4.2.0	system
4.4.0	system
5.0.1	system
5.1.0	system
5.3.0	system
2018.12	system
2019.03	system
2019.07	system
2019.10	system
2020.02	system
2020.07	system
2020.11	system
2021.05	system
2021.11	system
2022.05	system
2022.10	system
2023.03-1	system
2023.07-2	system
2023.09-0	system
2024.02-1	system

anadama2

AnADAMA2 is the next generation of AnADAMA (Another Automated Data Analysis Management Application). AnADAMA is a tool to create reproducible workflows and execute them efficiently.

homepage: http://huttenhower.sph.harvard.edu/anadama2

version	toolchain
0.10.0	foss/2022a

aNCI

Non-covalent interaction (NCI) for MD trajectories

homepage: https://www.lct.jussieu.fr/pagesperso/contrera/nci-MD.html

version	toolchain
2.0	iccifort/2019.5.281

andi

This is the andi program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes.

homepage: https://github.com/evolbioinf/andi/

version	toolchain
0.13	foss/2018b

ANGEL

ANGEL: Robust Open Reading Frame prediction

homepage: https://github.com/PacificBiosciences/ANGEL

version	versionsuffix	toolchain
3.0	-Python-3.7.2	foss/2019a

angsd

Program for analysing NGS data.

homepage: http://www.popgen.dk/angsd

version	toolchain
0.910	foss/2016a
0.921	foss/2018a
0.925	foss/2018b
0.933	GCC/8.3.0, iccifort/2019.5.281
0.935	GCC/10.2.0
0.940	GCC/11.2.0, GCC/12.3.0

ANIcalculator

This tool will calculate the bidirectional average nucleotide identity (gANI) and Alignment Fraction (AF) between two genomes. Required input is the full path to the fna file (nucleotide sequence of genes in fasta format) of each query genome. Either the rRNA and tRNA genes can be excluded, or provided in a list with the -ignoreList option. This is necessary as the presence of tRNA and/or rRNA genes in the fna will artificially inflate the ANI.

homepage: https://ani.jgi.doe.gov/html/home.php

version	toolchain
1.0	GCCcore/10.3.0, GCCcore/11.3.0

anndata

anndata is a Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray

homepage: https://github.com/scverse/anndata

version	toolchain
0.8.0	foss/2022a
0.9.2	foss/2021a
0.10.5.post1	foss/2023a

Annif

Annif is a multi-algorithm automated subject indexing tool for libraries, archives and museums.

homepage: https://github.com/NatLibFi/Annif

version	versionsuffix	toolchain
0.40.0	-Python-3.7.2	foss/2019a, intel/2019a

Annocript

Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes blast analysis with UniProt, NCBI Conserved Domain Database and Nucleotide division adding also annotations from Gene Ontology, the Enzyme Commission and UniPathways. Annocript also gives information about the longest ORF and the non-coding potential using external software. Annocript is also capable to identify putative long non-coding RNAs by using an heuristic based on homology and sequence features.

homepage: https://github.com/frankMusacchia/Annocript

version	toolchain
2.0	foss/2022a

annovar

ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).

homepage: http://annovar.openbioinformatics.org/en/latest/

version	versionsuffix	toolchain
2016Feb01	-Perl-5.22.1	foss/2016a
20191024	-Perl-5.28.1	GCCcore/8.2.0
20200607	-Perl-5.34.0	GCCcore/11.2.0

ANSYS

ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater.

homepage: https://www.ansys.com

version	toolchain
15.0	system
2022R2	system
2023R1	system

ANSYS_CFD

ANSYS computational fluid dynamics (CFD) simulation software allows you to predict, with confidence, the impact of fluid flows on your product throughout design and manufacturing as well as during end use. ANSYS renowned CFD analysis tools include the widely used and well-validated ANSYS Fluent and ANSYS CFX.

homepage: http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics

version	toolchain
16.2	system
17.0	system

ant

Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.

homepage: http://ant.apache.org/

version	versionsuffix	toolchain
1.8.4	-Java-1.7.0_10	system
1.8.4	-Java-1.7.0_21	system
1.9.0	-Java-1.7.0_15	system
1.9.0	-Java-1.7.0_21	system
1.9.3	-Java-1.7.0_60	system
1.9.3	-Java-1.7.0_79	system
1.9.6	-Java-1.7.0_75	system
1.9.6	-Java-1.7.0_79	system
1.9.6	-Java-1.7.0_80	system
1.9.6	-Java-1.8.0_66	system
1.9.6	-Java-1.8.0_72	system
1.9.6	-Java-1.8.0_77	system
1.9.7	-Java-1.8.0_92	system
1.10.0	-Java-1.8.0_112	system
1.10.1	-Java-1.8	system
1.10.1	-Java-1.8.0_121	system
1.10.1	-Java-1.8.0_144	system
1.10.1	-Java-1.8.0_152	system
1.10.1	-Java-1.8.0_162	system
1.10.5	-Java-1.8	system
1.10.6	-Java-1.8	system
1.10.7	-Java-11	system
1.10.8	-Java-11	system
1.10.9	-Java-11	system
1.10.11	-Java-11	system
1.10.11	-Java-13	system
1.10.12	-Java-11	system
1.10.12	-Java-17	system
1.10.14	-Java-11	system
1.10.14	-Java-21	system

ANTIC

Antic is an algebraic number theory library.

homepage: https://github.com/flintlib/antic

version	toolchain
0.2.5	gfbf/2022a

antiSMASH

antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes.

homepage: https://github.com/antismash/antismash

version	versionsuffix	toolchain
5.1.2	-Python-3.7.4	foss/2019b
5.2.0		foss/2020b
6.0.1		foss/2020b

ANTLR

ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language tool that provides a framework for constructing recognizers, compilers, and translators from grammatical descriptions containing Java, C#, C++, or Python actions.

homepage: http://www.antlr2.org/

version	versionsuffix	toolchain
2.7.7		GCCcore/7.3.0, GCCcore/8.2.0, foss/2017b, foss/2018b, foss/2019a, intel/2017b
2.7.7	-Java-11	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/8.3.0, GCCcore/9.3.0
2.7.7	-Python-2.7.11	foss/2016a
2.7.7	-Python-2.7.13	intel/2017a
2.7.7	-Python-2.7.14	foss/2018a, intel/2017b
2.7.7	-Python-3.6.4	intel/2018a

ANTs

ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data.

homepage: https://stnava.github.io/ANTs/

version	versionsuffix	toolchain
2.2.0	-Python-2.7.12	foss/2016b
2.3.0	-Python-2.7.14	foss/2017b, intel/2017b
2.3.1	-Python-3.6.6	foss/2018b
2.3.2	-Python-3.7.4	foss/2019b
2.3.5		foss/2021a
2.5.0		foss/2022b

anvio

An analysis and visualization platform for 'omics data.

homepage: https://merenlab.org/software/anvio/

version	versionsuffix	toolchain
6.1	-Python-3.7.4	intel/2019b
8		foss/2022b

any2fasta

Convert various sequence formats to FASTA

homepage: https://github.com/tseemann/any2fasta

version	versionsuffix	toolchain
0.4.2		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/8.3.0, GCCcore/9.3.0
0.4.2	-Perl-5.28.1	GCCcore/8.2.0

AOCC

AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0

homepage: https://developer.amd.com/amd-aocc/

version	toolchain
2.3.0	GCCcore/10.2.0, GCCcore/9.3.0
3.0.0	GCCcore/10.2.0, GCCcore/10.3.0
3.1.0	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0
3.2.0	GCCcore/11.2.0, GCCcore/11.3.0
4.0.0	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0

AOFlagger

The AOFlagger is a tool that can find and remove radio-frequency interference (RFI) in radio astronomical observations. It can make use of Lua scripts to make flagging strategies flexible, and the tools are applicable to a wide set of telescopes.

homepage: https://aoflagger.readthedocs.io/

version	toolchain
3.4.0	foss/2022a, foss/2023b

AOMP

AMD fork of LLVM, setup for OpenMP offloading to Accelerators

homepage: https://github.com/ROCm-Developer-Tools/aomp

version	toolchain
13.0-2	GCCcore/10.2.0, gcccuda/2020a

APBS

APBS is a software package for modeling biomolecular solvation through solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media.

homepage: http://www.poissonboltzmann.org/apbs

version	versionsuffix	toolchain
1.4	-linux-static-x86_64	system

apex

A PyTorch Extension: Tools for easy mixed precision and distributed training in Pytorch

homepage: https://github.com/nvidia/apex

version	versionsuffix	toolchain
20200325	-Python-3.7.4	fosscuda/2019b
20210420		fosscuda/2020b

APR

Apache Portable Runtime (APR) libraries.

homepage: https://apr.apache.org/

version	toolchain
1.6.3	GCCcore/6.4.0, GCCcore/7.3.0, iomkl/2018a
1.7.0	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/8.2.0, GCCcore/9.3.0
1.7.4	GCCcore/12.3.0

APR-util

Apache Portable Runtime (APR) util libraries.

homepage: https://apr.apache.org/

version	toolchain
1.6.1	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/9.3.0, iomkl/2018a
1.6.3	GCCcore/12.3.0

AptaSUITE

A full-featured bioinformatics software collection for the comprehensive analysis of aptamers in HT-SELEX experiments

homepage: https://drivenbyentropy.github.io/

version	versionsuffix	toolchain
0.9.4	-Java-11	system

ARAGORN

a program to detect tRNA genes and tmRNA genes in nucleotide sequences

homepage: http://www.ansikte.se/ARAGORN/

version	toolchain
1.2.38	foss/2016b, iccifort/2019.5.281
1.2.41	foss/2021b

Arb

Arb is a C library for arbitrary-precision interval arithmetic. It has full support for both real and complex numbers. The library is thread-safe, portable, and extensively tested.

homepage: https://arblib.org/

version	toolchain
2.16.0	GCC/7.3.0-2.30, GCC/8.2.0-2.31.1, iccifort/2018.3.222-GCC-7.3.0-2.30
2.17.0	GCC/8.3.0
2.19.0	GCC/10.3.0
2.22.1	foss/2021b
2.23.0	gfbf/2022a

Arcade-Learning-Environment

The Arcade Learning Environment (ALE) is a simple framework that allows researchers and hobbyists to develop AI agents for Atari 2600 games. It is built on top of the Atari 2600 emulator Stella and separates the details of emulation from agent design. This video depicts over 50 games currently supported in the ALE.

homepage: https://github.com/mgbellemare/Arcade-Learning-Environment

version	toolchain
0.7.3	foss/2021b
0.8.1	foss/2022a

arcasHLA

arcasHLA performs high resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples.

homepage: https://github.com/RabadanLab/arcasHLA

version	versionsuffix	toolchain
0.2.0	-Python-3.7.4	foss/2019b

ARCH

Autoregressive Conditional Heteroskedasticity (ARCH) and other tools for financial econometrics, written in Python (with Cython and/or Numba used to improve performance).

homepage: https://pypi.org/project/arch

version	versionsuffix	toolchain
4.5.0	-Python-3.6.4	intel/2018a

Archive-Zip

Provide an interface to ZIP archive files.

homepage: https://metacpan.org/pod/Archive::Zip

version	toolchain
1.68	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0

ArchR

ArchR is a full-featured R package for processing and analyzing single-cell ATAC-seq data.

homepage: https://www.archrproject.com

version	versionsuffix	toolchain
1.0.1	-R-4.1.2	foss/2021b
1.0.2	-R-4.3.2	foss/2023a

archspec

A library for detecting, labeling, and reasoning about microarchitectures

homepage: https://github.com/archspec/archspec

version	versionsuffix	toolchain
0.1.0	-Python-3.7.4	GCCcore/8.3.0
0.1.0	-Python-3.8.2	GCCcore/9.3.0
0.1.2		GCCcore/10.2.0, GCCcore/10.3.0
0.1.3		GCCcore/11.2.0
0.1.4		GCCcore/11.3.0
0.2.0		GCCcore/12.2.0
0.2.1		GCCcore/12.3.0
0.2.2		GCCcore/13.2.0

AreTomo2

AreTomo2, a multi-GPU accelerated software package that fully automates motion- corrected marker-free tomographic alignment and reconstruction, now includes robust GPU-accelerated CTF (Contrast Transfer Function) estimation in a single package. AreTomo2 is part of our endeavor to build a fully-automated high- throughput processing pipeline that enables real-time reconstruction of tomograms in parallel with tomographic data collection. It strives to be fast and accurate, as well as provides for easy integration into subtomogram processing workflows by generating IMod compatible files containing alignment and CTF parameters needed to bootstrap subtomogram averaging. AreTomo2 can also be used for on-the-fly reconstruction of tomograms and CTF estimation in parallel with tilt series collection, enabling real-time assessment of sample quality and adjustment of collection parameters

homepage: https://github.com/czimaginginstitute/AreTomo2

version	versionsuffix	toolchain
1.0.0	-CUDA-12.1.1	GCCcore/12.3.0

ARGoS

A parallel, multi-engine simulator for heterogeneous swarm robotics

homepage: http://www.argos-sim.info

version	versionsuffix	toolchain
3.0.0-beta53	-Lua-5.2.4	foss/2018b
3.0.0-beta59		GCC/11.2.0

argtable

Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss.

homepage: https://argtable.sourceforge.io/

version	toolchain
2.13	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/8.2.0, GCCcore/8.3.0, foss/2016b, foss/2018b, intel/2018a, intel/2018b

aria2

aria2 is a lightweight multi-protocol & multi-source command-line download utility.

homepage: https://aria2.github.io

version	toolchain
1.35.0	GCCcore/10.3.0
1.36.0	GCCcore/11.3.0

Arlequin

Arlequin: An Integrated Software for Population Genetics Data Analysis

homepage: http://cmpg.unibe.ch/software/arlequin35/Arlequin35.html

version	toolchain
3.5.2.2	foss/2019b

Armadillo

Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions.

homepage: https://arma.sourceforge.net/

version	versionsuffix	toolchain
7.600.2	-Python-2.7.12	foss/2016b
7.800.0	-Python-2.7.12	intel/2016b
7.950.1	-Python-2.7.12	intel/2016b
8.300.1		foss/2017b, intel/2017b
8.400.0		foss/2018a
9.600.5		foss/2018b
9.700.2		foss/2019a
9.880.1		foss/2020a
9.900.1		foss/2019b, foss/2020a
10.5.3		foss/2020b
10.7.5		foss/2021a
11.4.3		foss/2022a, foss/2022b
12.6.2		foss/2023a
12.8.0		foss/2023b

arosics

AROSICS is a python package to perform automatic subpixel co-registration of two satellite image datasets based on an image matching approach working in the frequency domain, combined with a multistage workflow for effective detection of false-positives.

homepage: https://github.com/GFZ/arosics

version	toolchain
1.7.6	foss/2021a

ARPACK++

Arpackpp is a C++ interface to the ARPACK Fortran package, which implements the implicit restarted Arnoldi method for iteratively solving large-scale sparse eigenvalue problems.

homepage: https://github.com/m-reuter/arpackpp

version	toolchain
2018.03.26	foss/2017b

arpack-ng

ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.

homepage: https://github.com/opencollab/arpack-ng

version	toolchain
3.3.0	foss/2016a, intel/2016a
3.4.0	foss/2016b, foss/2017a, intel/2016b, intel/2017a
3.5.0	foss/2017b, foss/2018a, foss/2018b, intel/2017a, intel/2017b
3.6.2	intel/2018a
3.7.0	foss/2019a, foss/2019b, foss/2020a, intel/2019b, intel/2020a
3.8.0	foss/2020b, foss/2021a, foss/2021b, foss/2022a, foss/2022b
3.9.0	foss/2023a, foss/2023b
3.9.1	foss/2023b

ArrayFire

ArrayFire is a general-purpose library that simplifies the process of developing software that targets parallel and massively-parallel architectures including CPUs, GPUs, and other hardware acceleration devices.

homepage: https://arrayfire.com/

version	versionsuffix	toolchain
3.6.4		foss/2018b
3.6.4	-CUDA-9.2.88	foss/2018b

Arriba

Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for the use in a clinical research setting. Therefore, short runtimes and high sensitivity were important design criteria.

homepage: https://github.com/suhrig/arriba

version	toolchain
1.1.0	foss/2018b
2.1.0	GCC/10.2.0, GCC/10.3.0
2.2.1	GCC/11.2.0
2.3.0	GCC/11.2.0
2.4.0	GCC/12.2.0

Arrow

Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform for in-memory data.

homepage: https://arrow.apache.org

version	versionsuffix	toolchain
0.7.1	-Python-3.6.3	intel/2017b
0.12.0	-Python-2.7.15	foss/2018b, intel/2018b
0.12.0	-Python-3.6.6	intel/2018b
0.16.0	-Python-3.7.4	foss/2019b, intel/2019b
0.17.1		foss/2020b, fosscuda/2020b, intel/2020b
0.17.1	-Python-3.8.2	foss/2020a, intel/2020a
6.0.0		foss/2021a, foss/2021b
6.0.1		foss/2021a
8.0.0		foss/2021a, foss/2021b, foss/2022.05, foss/2022a
11.0.0		gfbf/2022b
14.0.1		gfbf/2023a

arrow-R

R interface to the Apache Arrow C++ library

homepage: https://cran.r-project.org/web/packages/arrow

version	versionsuffix	toolchain
0.17.1	-R-4.0.0	foss/2020a
6.0.0.2	-R-4.1.0	foss/2021a
6.0.0.2	-R-4.1.2	foss/2021b
6.0.0.2	-R-4.2.0	foss/2021b
8.0.0	-R-4.2.1	foss/2022a
11.0.0.3	-R-4.2.2	foss/2022b
14.0.0.2	-R-4.3.2	foss/2023a

ART

ART is a set of simulation tools to generate synthetic next-generation sequencing reads

homepage: http://www.niehs.nih.gov/research/resources/software/biostatistics/art/

version	toolchain
2016.06.05	GCCcore/6.4.0, intel/2016b

Artemis

The Artemis Software is a set of software tools for genome browsing and annotation. It includes: Artemis, Artemis Comparison Tool (ACT), BamView and DNAPlotter.

homepage: http://sanger-pathogens.github.io/Artemis/

version	versionsuffix	toolchain
18.0.2	-Java-11	system
18.0.3	-Java-11	system
18.2.0	-Java-11	system

artic-ncov2019

Initial implementation of an ARTIC bioinformatics platform for nanopore sequencing of nCoV2019 novel coronavirus.

homepage: https://github.com/artic-network/artic-ncov2019

version	versionsuffix	toolchain
2020.04.13	-Python-3.6.6	foss/2018b
2021.06.24		foss/2020b

ARTS

ARTS is a radiative transfer model for the millimeter and sub-millimeter spectral range. There are a number of models mostly developed explicitly for the different sensors.

homepage: http://www.radiativetransfer.org/

version	toolchain
2.2.64	gompi/2019a

ArviZ

Exploratory analysis of Bayesian models with Python

homepage: https://github.com/arviz-devs/arviz

version	versionsuffix	toolchain
0.7.0	-Python-3.7.4	foss/2019b, intel/2019b
0.11.1		intel/2020b
0.11.4		foss/2021b, intel/2021b
0.12.1		foss/2021a, foss/2022a, intel/2022a
0.16.1		foss/2023a

ARWEN

ARWEN, tRNA detection in metazoan mitochondrial sequences

homepage: http://mbio-serv2.mbioekol.lu.se/ARWEN

version	toolchain
1.2.3	GCCcore/7.3.0

ASAP

ASAP focuses on fast and fluid image viewing with an easy-to-use interface for making annotations. It consists of two main components: an IO library for reading and writing multi-resolution images and a viewer component for visualizing such images.

homepage: https://computationalpathologygroup.github.io/ASAP/

version	versionsuffix	toolchain
2.0	-CUDA-11.3.1	foss/2021a
2.1		foss/2022a

ASAP3

ASAP is a calculator for doing large-scale classical molecular dynamics within the Campos Atomic Simulation Environment (ASE).

homepage: https://wiki.fysik.dtu.dk/asap/

version	versionsuffix	toolchain
3.10.7	-Python-3.5.2	foss/2016b
3.10.7	-Python-3.6.2	foss/2017b
3.10.8	-Python-3.5.2	foss/2016b
3.10.8	-Python-3.6.2	foss/2017b
3.10.8	-Python-3.6.3	foss/2017b
3.10.10	-Python-3.6.6	foss/2018b, intel/2018b, iomkl/2018b
3.11.10	-Python-3.7.2	foss/2019a, intel/2019a
3.12.2	-ASE-3.21.1	foss/2020b, intel/2020b
3.12.7	-ASE-3.21.1	foss/2020b, intel/2020b
3.13.2		foss/2023a
3.13.3		foss/2023a, intel/2023a

ASCAT

ASCAT is a method to derive copy number profiles of tumor cells, accounting for normal cell admixture and tumor aneuploidy.

homepage: https://github.com/VanLoo-lab/ascat

version	versionsuffix	toolchain
3.1.2	-R-4.2.1	foss/2022a
3.1.2	-R-4.2.2	foss/2022b

ASE

ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language.

homepage: https://wiki.fysik.dtu.dk/ase/

version	versionsuffix	toolchain
3.9.1.4567	-Python-2.7.11	intel/2016a
3.10.0	-Python-2.7.11	intel/2016.02-GCC-4.9
3.11.0	-Python-2.7.12	intel/2016b
3.13.0	-Python-2.7.12	foss/2016b
3.13.0	-Python-2.7.13	intel/2017a
3.15.0	-Python-2.7.12	foss/2016b
3.15.0	-Python-2.7.14	intel/2017b
3.15.0	-Python-3.5.2	foss/2016b
3.15.0	-Python-3.6.2	foss/2017b
3.15.0	-Python-3.6.3	foss/2017b
3.16.2	-Python-3.6.4	iomkl/2018.02, iomkl/2018a
3.16.2	-Python-3.6.6	foss/2018b, intel/2018b, iomkl/2018b
3.17.0	-Python-3.6.6	foss/2018b, intel/2018b, iomkl/2018b
3.17.0	-Python-3.7.2	foss/2019a, intel/2019a
3.18.0	-Python-3.6.6	foss/2018b, intel/2018b
3.18.0	-Python-3.7.2	foss/2019a, intel/2019a
3.19.0	-Python-3.6.6	foss/2018b, intel/2018b
3.19.0	-Python-3.7.4	foss/2019b, fosscuda/2019b, intel/2019b
3.19.0	-Python-3.8.2	foss/2020a, intel/2020a
3.20.1		foss/2020b, fosscuda/2020b, intel/2020b
3.20.1	-Python-3.7.4	foss/2019b, intel/2019b
3.20.1	-Python-3.8.2	intel/2020a
3.21.1		foss/2020b, fosscuda/2020b, intel/2020b
3.21.1	-Python-3.8.2	foss/2020a
3.22.0		foss/2020b, foss/2021a, fosscuda/2020b, intel/2020b, intel/2021a
3.22.1		foss/2021b, foss/2022a, gfbf/2022b, gfbf/2023a, gomkl/2021a, iimkl/2023a, intel/2021b, intel/2022a

ASF-SearchAPI

asf_search is a Python module for performing searches of the ASF catalog. In addition, it offers baseline functionality and download support.

homepage: https://docs.asf.alaska.edu/

version	toolchain
6.5.0	foss/2022a

ASHS

Automatic Segmentation of Hippocampal Subfields (ASHS)

homepage: https://sites.google.com/site/hipposubfields/home

version	toolchain
rev103_20140612	system

Aspera-CLI

IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line. The Aspera CLI is for users and organizations who want to automate their transfer workflows.

homepage: https://asperasoft.com

version	versionsuffix	toolchain
3.7.2	.354.010c3b8	system
3.9.0	.1326.6985b21	system
3.9.6	.1467.159c5b1	system

Aspera-Connect

Connect is an install-on-demand Web browser plug-in that facilitates high-speed uploads and downloads with an Aspera transfer server.

homepage: http://downloads.asperasoft.com/connect2/

version	toolchain
3.6.1	system
3.9.6	system

assimp

Open Asset Import Library (assimp) is a library to import and export various 3d-model-formats including scene-post-processing to generate missing render data.

homepage: https://github.com/assimp/assimp

version	toolchain
5.0.1	GCCcore/8.3.0
5.2.5	GCCcore/12.3.0
5.3.1	GCCcore/13.2.0

Assimulo

Assimulo is a simulation package for solving ordinary differential equations.

homepage: https://jmodelica.org/assimulo/

version	versionsuffix	toolchain
2.9	-Python-2.7.15	intel/2018b

ASTRID

ASTRID-2 is a method for estimating species trees from gene trees.

homepage: https://github.com/pranjalv123/ASTRID

version	toolchain
2.2.1	gompi/2019a

astro-tulips

tulips creates diagrams of the structure and evolution of stars. It creates plots and movies based on output from the MESA stellar evolution code

homepage: https://astro-tulips.readthedocs.io/en/latest/installation.html

version	toolchain
1.0.1	foss/2022a

astropy

The Astropy Project is a community effort to develop a common core package for Astronomy in Python and foster an ecosystem of interoperable astronomy packages. The Astropy community is committed to supporting diversity and inclusion.

homepage: https://www.astropy.org/

version	versionsuffix	toolchain
2.0.12	-Python-2.7.15	foss/2018b, intel/2018b
2.0.14		foss/2019a
4.0.1	-Python-3.7.4	foss/2019b
4.0.1	-Python-3.8.2	foss/2020a, intel/2020a
4.2.1		foss/2020b, intel/2020b, intelcuda/2020b
4.3.1		foss/2021a, foss/2021b, intel/2021a
5.0.4		foss/2021a
5.1.1		foss/2022a
5.2.2		gfbf/2022b

at-spi2-atk

AT-SPI 2 toolkit bridge

homepage: https://wiki.gnome.org/Accessibility

version	toolchain
2.26.3	fosscuda/2018b
2.32.0	GCCcore/8.2.0
2.34.1	GCCcore/8.3.0
2.34.2	GCCcore/9.3.0
2.38.0	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

at-spi2-core

Assistive Technology Service Provider Interface.

homepage: https://wiki.gnome.org/Accessibility

version	toolchain
2.26.3	fosscuda/2018b
2.32.0	GCCcore/8.2.0
2.34.0	GCCcore/8.3.0
2.36.0	GCCcore/9.3.0
2.38.0	GCCcore/10.2.0
2.40.2	GCCcore/10.3.0
2.40.3	GCCcore/11.2.0
2.44.1	GCCcore/11.3.0
2.46.0	GCCcore/12.2.0
2.49.91	GCCcore/12.3.0
2.50.0	GCCcore/13.2.0

ATAT

The Alloy-Theoretic Automated Toolkit (ATAT) is a generic name that refers to a collection of alloy theory tools

homepage: https://www.brown.edu/Departments/Engineering/Labs/avdw/atat/

version	toolchain
3.36	GCCcore/9.3.0

ATK

ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications.

homepage: https://developer.gnome.org/atk/

version	toolchain
2.18.0	intel/2016a
2.20.0	foss/2016a, intel/2016a
2.22.0	foss/2016b, intel/2016b
2.26.0	intel/2017a
2.26.1	foss/2018b, intel/2017b
2.27.1	foss/2017b, intel/2017b
2.28.1	foss/2018a, foss/2018b, fosscuda/2018b, intel/2018a
2.32.0	GCCcore/8.2.0
2.34.1	GCCcore/8.3.0
2.36.0	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/9.3.0
2.38.0	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

ATLAS

ATLAS (Automatically Tuned Linear Algebra Software) is the application of the AEOS (Automated Empirical Optimization of Software) paradigm, with the present emphasis on the Basic Linear Algebra Subprograms (BLAS), a widely used, performance-critical, linear algebra kernel library.

homepage: http://math-atlas.sourceforge.net

version	versionsuffix	toolchain
3.10.2	-LAPACK-3.6.1	GCC/5.4.0-2.26

atomate

atomate has implementations of FireWorks workflows for Materials Science.

homepage: https://pythonhosted.org/atomate/

version	versionsuffix	toolchain
0.4.4	-Python-2.7.13	intel/2017a

AtomPAW

AtomPAW is a Projector-Augmented Wave Dataset Generator that can be used both as a standalone program and a library.

homepage: http://users.wfu.edu/natalie/papers/pwpaw/man.html

version	toolchain
4.1.0.5	intel/2018b
4.1.0.6	intel/2018b

atools

Tools to make using job arrays a lot more convenient.

homepage: https://github.com/gjbex/atools

version	versionsuffix	toolchain
1.4.2	-Python-2.7.12	intel/2016b
1.4.6	-Python-2.7.16	GCCcore/8.3.0
1.4.8	-Python-2.7.18	GCCcore/10.3.0, GCCcore/11.2.0
1.5.1		GCCcore/11.2.0, GCCcore/12.3.0, GCCcore/13.2.0

atropos

Atropos is tool for specific, sensitive, and speedy trimming of NGS reads.

homepage: https://atropos.readthedocs.io

version	versionsuffix	toolchain
1.1.21	-Python-3.6.6	intel/2018b

ATSAS

ATSAS is a program suite for small-angle scattering data analysis from biological macromolecules.

homepage: http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html

version	versionsuffix	toolchain
2.5.1-1	.el6.x86_64	system
2.5.1-1	.sl5.x86_64	system
2.7.1-1	.el7.x86_64	system

attr

Commands for Manipulating Filesystem Extended Attributes

homepage: https://savannah.nongnu.org/projects/attr

version	toolchain
2.4.47	GCCcore/8.2.0
2.4.48	GCCcore/9.3.0
2.5.1	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.3.0

attrdict

AttrDict is a Python library that provides mapping objects that allow their elements to be accessed both as keys and as attributes.

homepage: https://github.com/bcj/AttrDict

version	versionsuffix	toolchain
2.0.1	-Python-3.7.4	GCCcore/8.3.0

attrdict3

AttrDict is a Python library that provides mapping objects that allow their elements to be accessed both as keys and as attributes.

homepage: https://github.com/pirofti/AttrDict3

version	toolchain
2.0.2	GCCcore/11.2.0, GCCcore/11.3.0

augur

Pipeline components for real-time phylodynamic analysis

homepage: https://github.com/nextstrain/augur

version	versionsuffix	toolchain
7.0.2	-Python-3.7.4	intel/2019b

AUGUSTUS

AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences

homepage: https://bioinf.uni-greifswald.de/augustus/

version	versionsuffix	toolchain
3.2.3	-Python-2.7.13	intel/2017a
3.3		foss/2018a
3.3.2		intel/2019a
3.3.2	-Python-2.7.13	intel/2017a
3.3.2	-Python-2.7.14	foss/2017b, intel/2017b
3.3.2	-Python-2.7.15	intel/2018b
3.3.3		foss/2019b, intel/2019b
3.4.0		foss/2020a, foss/2020b, foss/2021a, foss/2021b
3.5.0		foss/2022a, foss/2022b

Austin

Austin is a Python frame stack sampler for CPython written in pure C.

homepage: https://github.com/P403n1x87/austin

version	toolchain
3.2.0	GCCcore/11.2.0, system

AUTO-07p

AUTO is a publicly available software for continuation and bifurcation problems in ordinary differential equations originally written in 1980 and widely used in the dynamical systems community.

homepage: https://github.com/auto-07p

version	toolchain
0.9.3	foss/2021a

Autoconf

Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.

homepage: https://www.gnu.org/software/autoconf/

version	toolchain
2.68	foss/2016b
2.69	GCC/4.8.2, GCC/4.8.4, GCC/4.9.2, GCC/4.9.3, GCC/4.9.3-2.25, GCC/5.2.0, GCC/5.4.0-2.26, GCCcore/10.2.0, GCCcore/4.9.2, GCCcore/4.9.3, GCCcore/5.3.0, GCCcore/5.4.0, GCCcore/6.1.0, GCCcore/6.2.0, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.2.0, GCCcore/9.3.0, GNU/4.9.2-2.25, GNU/4.9.3-2.25, GNU/5.1.0-2.25, foss/2016.04, foss/2016a, foss/2016b, gimkl/2.11.5, intel/2016.02-GCC-4.9, intel/2016a, intel/2016b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25, system
2.71	FCC/4.5.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.1.0, GCCcore/13.2.0, system

Autoconf-archive

The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf that have been contributed as free software by friendly supporters of the cause from all over the Internet. Every single one of those macros can be re-used without imposing any restrictions whatsoever on the licensing of the generated configure script. In particular, it is possible to use all those macros in configure scripts that are meant for non-free software. This policy is unusual for a Free Software Foundation project. The FSF firmly believes that software ought to be free, and software licenses like the GPL are specifically designed to ensure that derivative work based on free software must be free as well. In case of Autoconf, however, an exception has been made, because Autoconf is at such a pivotal position in the software development tool chain that the benefits from having this tool available as widely as possible outweigh the disadvantage that some authors may choose to use it, too, for proprietary software.

homepage: https://www.gnu.org/software/autoconf-archive

version	toolchain
2019.01.06	GCC/8.2.0-2.31.1
2021.02.19	GCCcore/10.2.0
2023.02.20	GCCcore/11.3.0

AutoDock

AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

homepage: http://autodock.scripps.edu/

version	toolchain
4.2.5.1	GCC/5.2.0
4.2.6	GCC/10.3.0

AutoDock-GPU

OpenCL and Cuda accelerated version of AutoDock. It leverages its embarrasingly parallelizable LGA by processing ligand-receptor poses in parallel over multiple compute units. AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

homepage: https://github.com/ccsb-scripps/AutoDock-GPU

version	versionsuffix	toolchain
1.5.3	-CUDA-11.3.1	GCC/10.3.0
1.5.3	-CUDA-11.7.0	GCC/11.3.0

AutoDock-Vina

AutoDock Vina is an open-source program for doing molecular docking.

homepage: https://vina.scripps.edu/

version	versionsuffix	toolchain
1.1.2	-linux_x86	system
1.2.3		foss/2021a, foss/2021b

AutoDockSuite

AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

homepage: https://autodock.scripps.edu/

version	toolchain
4.2.6	GCCcore/8.3.0

AutoGeneS

AutoGeneS automatically extracts informative genes and reveals the cellular heterogeneity of bulk RNA samples.

homepage: https://github.com/theislab/AutoGeneS

version	toolchain
1.0.4	foss/2020b

AutoGrid

AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

homepage: http://autodock.scripps.edu/

version	toolchain
4.2.5.1	GCC/5.2.0

Automake

Automake: GNU Standards-compliant Makefile generator

homepage: https://www.gnu.org/software/automake/automake.html

version	toolchain
1.11.3	foss/2016b
1.14	GCC/4.8.2, intel/2016a
1.14.1	GCC/4.8.2
1.15	GCC/4.8.4, GCC/4.9.2, GCC/4.9.3, GCC/4.9.3-2.25, GCC/5.2.0, GCC/5.4.0-2.26, GCCcore/4.9.2, GCCcore/4.9.3, GCCcore/5.3.0, GCCcore/5.4.0, GCCcore/6.1.0, GCCcore/6.2.0, GCCcore/6.3.0, GNU/4.9.2-2.25, GNU/4.9.3-2.25, GNU/5.1.0-2.25, foss/2016.04, foss/2016a, foss/2016b, gimkl/2.11.5, intel/2016.02-GCC-4.9, intel/2016a, intel/2016b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25, system
1.15.1	GCCcore/6.4.0, GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/8.3.0
1.16.1	GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.2.0, GCCcore/9.3.0
1.16.2	GCCcore/10.2.0
1.16.3	FCC/4.5.0, GCCcore/10.3.0
1.16.4	GCCcore/11.2.0
1.16.5	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.1.0, GCCcore/13.2.0, system

AutoMap

Tool to find regions of homozygosity (ROHs) from sequencing data.

homepage: https://github.com/mquinodo/AutoMap

version	versionsuffix	toolchain
1.0	-20200324	foss/2019b

autopep8

A tool that automatically formats Python code to conform to the PEP 8 style guide.

homepage: https://github.com/hhatto/autopep8

version	versionsuffix	toolchain
1.4.4	-Python-3.6.4	intel/2018a
2.0.4		foss/2022a

Autotools

This bundle collect the standard GNU build tools: Autoconf, Automake and libtool

homepage: https://autotools.io

version	toolchain
20150119	GCC/4.9.2
20150215	GCC/4.8.4, GCC/4.9.2, GCC/4.9.3, GCC/4.9.3-2.25, GCC/5.2.0, GCC/5.4.0-2.26, GCCcore/4.9.2, GCCcore/4.9.3, GCCcore/5.3.0, GCCcore/5.4.0, GCCcore/6.1.0, GCCcore/6.2.0, GCCcore/6.3.0, GNU/4.9.2-2.25, GNU/4.9.3-2.25, GNU/5.1.0-2.25, foss/2016.04, foss/2016a, foss/2016b, gimkl/2.11.5, gimkl/2017a, intel/2016.02-GCC-4.9, intel/2016a, intel/2016b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25, system
20170619	GCCcore/6.4.0, GCCcore/7.2.0
20180311	GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.2.0, GCCcore/9.3.0
20200321	GCCcore/10.2.0
20210128	FCC/4.5.0, GCCcore/10.3.0
20210726	GCCcore/11.2.0
20220317	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.1.0, GCCcore/13.2.0, system

Avogadro2

Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.

homepage: https://two.avogadro.cc/index.html

version	versionsuffix	toolchain
1.97.0	-linux-x86_64	system

avro-cpp

C++ implementation of Avro data serialization system.

homepage: https://avro.apache.org

version	toolchain
1.11.1	GCC/11.2.0

awscli

Universal Command Line Environment for AWS

homepage: https://pypi.python.org/pypi/awscli

version	versionsuffix	toolchain
1.11.1	-Python-2.7.12	intel/2016b
1.11.56	-Python-2.7.12	foss/2016b
1.16.290	-Python-3.6.6	foss/2018b
1.17.7	-Python-3.7.4	GCCcore/8.3.0
1.18.89	-Python-3.8.2	GCCcore/9.3.0
2.0.55	-Python-3.8.2	GCCcore/9.3.0
2.11.21		GCCcore/11.3.0
2.15.2		GCCcore/12.2.0

Ax

Ax is an accessible, general-purpose platform for understanding, managing, deploying, and automating adaptive experiments. Adaptive experimentation is the machine-learning guided process of iteratively exploring a (possibly infinite) parameter space in order to identify optimal configurations in a resource-efficient manner. Ax currently supports Bayesian optimization and bandit optimization as exploration strategies. Bayesian optimization in Ax is powered by BoTorch, a modern library for Bayesian optimization research built on PyTorch.

homepage: https://ax.dev/

version	toolchain
0.3.3	foss/2022a

axel

Lightweight CLI download accelerator

homepage: https://github.com/axel-download-accelerator/axel

version	toolchain
2.17.9	GCCcore/8.3.0, GCCcore/9.3.0

B

BA3-SNPS-autotune - BabelStream - babl - Bader - BAGEL - BAli-Phy - bam-readcount - Bambi - bamFilters - BAMM - BAMSurgeon - bamtofastq - BamTools - BamUtil - Bandage - barrnap - basemap - bases2fastq - Bash - bashplotlib - bat - batchgenerators - BatMeth2 - BayesAss - BayesAss3-SNPs - BayeScan - BayeScEnv - BayesPrism - BayesTraits - Bazel - bbcp - bbFTP - BBMap - bc - BCALM - bcbio-gff - BCEL - BCFtools - bcgTree - bcl-convert - bcl2fastq2 - bcolz - bcrypt - BDBag - Beagle - beagle-lib - Beast - BeautifulSoup - BEDOPS - BEDTools - BEEF - behave - bench - BerkeleyGW - BFAST - BFC - BGC-Bayesian-genomic-clines - BgeeCall - BgeeDB - bgen - bgen-reader - BiasAdjustCXX - bibtexparser - BiG-SCAPE - BigDFT - BinSanity - binutils - Bio-DB-HTS - Bio-EUtilities - Bio-SamTools - Bio-SearchIO-hmmer - bioawk - biobakery-workflows - biobambam2 - biogeme - biom-format - biomart-perl - BioPerl - BioPP - Biopython - BioServices - BirdNET - biscuit - Bismark - Bison - bitarray - BLACS - BLASR - blasr_libcpp - BLAST - BLAST+ - BLAT - Blender - BLIS - Blitz++ - BlobTools - Block - Blosc - Blosc2 - BLT - bmtagger - BMTK - bnpy - BOINC - bokeh - BoltzTraP - BoltzTraP2 - Bonito - Bonmin - Bonnie++ - Boost - Boost.MPI - Boost.Python - Boost.Python-NumPy - boost_histogram - BOPTEST - boto3 - Bottleneck - Bowtie - Bowtie2 - Bpipe - bpp - bpytop - Bracken - Braindecode - BRAKER - BreakDancer - breseq - BRiAl - Brotli - Brotli-python - Brunsli - bsddb3 - BSMAPz - Bsoft - BSseeker2 - btllib - BuDDy - BUFRLIB - build - buildenv - buildingspy - Bullet - BUSCO - BUStools - BWA - bwa-mem2 - bwa-meth - bwakit - bwidget - BWISE - bx-python - BXH_XCEDE_TOOLS - byacc - byobu - bzip2

BA3-SNPS-autotune

This program will automatically tune mixing parameters for BA3-SNPs by implementing a binary search algorithm and conducting short exploratory runs of BA3-SNPS.

homepage: https://github.com/stevemussmann/BA3-SNPS-autotune

version	toolchain
2.1.2	GCC/11.3.0

BabelStream

STREAM, for lots of devices written in many programming models

homepage: https://uob-hpc.github.io/BabelStream

version	versionsuffix	toolchain
3.4	-omp	GCC/11.2.0

babl

babl is pixel encoding and color space conversion engine in C

homepage: https://www.gegl.org/babl

version	toolchain
0.1.86	GCCcore/10.3.0

Bader

A fast algorithm for doing Bader's analysis on a charge density grid.

homepage: http://theory.cm.utexas.edu/henkelman/code/bader/

version	toolchain
1.02	intel/2018a
1.03	intel/2018b
1.04	GCC/11.2.0, iccifort/2020.4.304

BAGEL

BAGEL (Brilliantly Advanced General Electronic-structure Library) is a parallel electronic-structure program.

homepage: http://www.nubakery.org

version	toolchain
1.1.1	intel/2016b
1.2.2	foss/2021a, foss/2023a

BAli-Phy

BAli-Phy estimates multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences.

homepage: http://www.bali-phy.org/

version	toolchain
3.6.0	system

bam-readcount

Count DNA sequence reads in BAM files

homepage: https://github.com/genome/bam-readcount

version	toolchain
0.8.0	GCC/11.2.0, GCC/9.3.0, foss/2018b
1.0.1	GCC/12.2.0

Bambi

Bambi is a high-level Bayesian model-building interface written in Python. It works with the probabilistic programming frameworks PyMC3 and is designed to make it extremely easy to fit Bayesian mixed-effects models common in biology, social sciences and other disciplines.

homepage: https://bambinos.github.io/bambi

version	toolchain
0.7.1	foss/2021b, intel/2021b

bamFilters

A utility tool to filter alignments from bam files, using identity percent, low complexity and read coverage.

homepage: https://github.com/institut-de-genomique/bamFilters

version	toolchain
2022-06-30	GCC/11.3.0

BAMM

BAMM is oriented entirely towards detecting and quantifying heterogeneity in evolutionary rates. It uses reversible jump Markov chain Monte Carlo to automatically explore a vast universe of candidate models of lineage diversification and trait evolution.

homepage: http://bamm-project.org/

version	toolchain
2.5.0	foss/2022a

BAMSurgeon

Tools for adding mutations to existing .bam files, used for testing mutation callers

homepage: https://github.com/adamewing/bamsurgeon

version	versionsuffix	toolchain
1.2	-Python-2.7.16	GCC/8.3.0

bamtofastq

Convert 10x BAM files to the original FASTQs compatible with 10x pipelines.

homepage: https://github.com/10XGenomics/bamtofastq

version	toolchain
1.4.0	GCCcore/10.3.0

BamTools

BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.

homepage: https://github.com/pezmaster31/bamtools

version	toolchain
2.4.0	foss/2016b
2.4.1	intel/2017a
2.5.0	foss/2016b, intel/2017b
2.5.1	GCC/10.2.0, GCC/8.2.0-2.31.1, GCC/8.3.0, GCC/9.3.0, foss/2017b, foss/2018a, foss/2018b, iccifort/2019.1.144-GCC-8.2.0-2.31.1, iccifort/2019.5.281, iccifort/2020.4.304, intel/2017b, intel/2018b
2.5.2	GCC/10.3.0, GCC/11.2.0, GCC/11.3.0, GCC/12.2.0, GCC/12.3.0

BamUtil

BamUtil is a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam.

homepage: http://genome.sph.umich.edu/wiki/BamUtil

version	toolchain
1.0.13	intel/2016b
1.0.14	intel/2018a

Bandage

Bandage is a program for visualising de novo assembly graphs

homepage: http://rrwick.github.io/Bandage

version	versionsuffix	toolchain
0.8.1	_Centos	system
0.8.1	_Ubuntu	system
0.9.0		GCCcore/11.2.0, GCCcore/11.3.0

barrnap

Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal RNA genes in genomes.

homepage: https://github.com/tseemann/barrnap

version	toolchain
0.9	GCC/8.2.0-2.31.1, foss/2018b, gompi/2020b, gompi/2021b, gompi/2022a

basemap

The matplotlib basemap toolkit is a library for plotting 2D data on maps in Python

homepage: https://matplotlib.org/basemap/

version	versionsuffix	toolchain
1.0.7	-Python-2.7.13	intel/2017a
1.0.7	-Python-3.6.3	intel/2017b
1.0.7	-Python-3.6.4	intel/2018a
1.2.0	-Python-3.6.6	intel/2018b
1.2.2	-Python-3.8.2	foss/2020a
1.3.6		foss/2022a
1.3.9		foss/2023a

bases2fastq

Bases2Fastq Software demultiplexes sequencing data and converts base calls into FASTQ files for secondary analysis with the FASTQ-compatible software of your choice. The Element AVITI™ System records base calls, which are the main output of a sequencing run, with associated quality scores (Q-scores) in bases files. Bases files must be converted into the FASTQ file format for secondary analysis. To generate QC reports, also load BeautifulSoup and bokeh.

homepage: https://docs.elembio.io/docs/bases2fastq

version	toolchain
1.5.1	system

Bash

Bash is an sh-compatible command language interpreter that executes commands read from the standard input or from a file. Bash also incorporates useful features from the Korn and C shells (ksh and csh).

homepage: http://www.gnu.org/software/bash

version	toolchain
4.3	GCC/4.9.2

bashplotlib

bashplotlib is a python package and command line tool for making basic plots in the terminal. It's a quick way to visualize data when you don't have a GUI.

homepage: https://github.com/glamp/bashplotlib

version	toolchain
0.6.5	GCCcore/10.3.0

bat

The BAT Python package supports the processing and analysis of Bro data with Pandas, scikit-learn, and Spark

homepage: https://pypi.python.org/pypi/bat

version	versionsuffix	toolchain
0.3.3	-Python-3.6.3	intel/2017b

batchgenerators

Data augmentation toolkit developed at the Division of Medical Image Computing at the German Cancer Research Center (DKFZ) to suit all our deep learning data augmentation needs.

homepage: https://github.com/MIC-DKFZ/batchgenerators

version	toolchain
0.25	foss/2021a

BatMeth2

An Integrated Package for Bisulfite DNA Methylation Data Analysis with Indel-sensitive Mapping.

homepage: https://github.com/GuoliangLi-HZAU/BatMeth2

version	toolchain
2.1	foss/2019b

BayesAss

BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes

homepage: http://www.rannala.org/?page_id=245

version	toolchain
3.0.4	foss/2016a

BayesAss3-SNPs

Modification of BayesAss 3.0.4 to allow handling of large SNP datasets generated via methods such as RADseq protocols.

homepage: https://github.com/stevemussmann/BayesAss3-SNPs

version	toolchain
1.1	GCC/11.3.0

BayeScan

BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.

homepage: http://cmpg.unibe.ch/software/BayeScan/

version	toolchain
2.1	foss/2016a, foss/2018a, intel/2018a

BayeScEnv

BayeScEnv is a Fst-based, genome-scan method that uses environmental variables to detect local adaptation.

homepage: https://github.com/devillemereuil/bayescenv

version	toolchain
1.1	GCC/8.3.0, foss/2016a, iccifort/2019.5.281

BayesPrism

Bayesian cell Proportion Reconstruction Inferred using Statistical Marginalization (BayesPrism): A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression

homepage: https://github.com/Danko-Lab/BayesPrism

version	versionsuffix	toolchain
2.0	-R-4.2.1	foss/2022a

BayesTraits

BayesTraits is a computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. This new package incoporates our earlier and separate programes Multistate, Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt a finite number of discrete states, or to the analysis of continuously varying traits. Hypotheses can be tested about models of evolution, about ancestral states and about correlations among pairs of traits.

homepage: https://github.com/AndrewPMeade/BayesTraits-Public

version	versionsuffix	toolchain
1.0-linux32		system
2.0	-Beta-Linux64	system
3.0.2	-Linux	system

Bazel

Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software.

homepage: https://bazel.io/

version	versionsuffix	toolchain
0.4.4		system
0.7.0		GCCcore/6.4.0
0.10.0		GCCcore/6.4.0
0.11.0		GCCcore/6.4.0
0.11.1		GCCcore/6.4.0
0.12.0		GCCcore/6.4.0
0.16.0		GCCcore/6.4.0, GCCcore/7.3.0
0.18.0		GCCcore/7.3.0
0.20.0		GCCcore/7.3.0, GCCcore/8.2.0
0.25.2		GCCcore/8.2.0
0.26.1		GCCcore/8.2.0, GCCcore/8.3.0
0.29.1		GCCcore/8.2.0, GCCcore/8.3.0
0.29.1	-Java-1.8	GCCcore/9.3.0
1.1.0		GCCcore/8.3.0
2.0.0		GCCcore/10.2.0, GCCcore/8.3.0
3.4.1		GCCcore/8.3.0
3.6.0		GCCcore/9.3.0
3.7.1		GCCcore/8.3.0
3.7.2		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/8.3.0
4.2.2		GCCcore/11.2.0
5.1.1		GCCcore/11.3.0
6.3.1		GCCcore/12.2.0, GCCcore/12.3.0

bbcp

BBCP is an alternative to Gridftp when transferring large amounts of data, capable of breaking up your transfer into multiple simultaneous transferring streams, thereby transferring data much faster than single-streaming utilities such as SCP and SFTP. See details at http://pcbunn.cithep.caltech.edu/bbcp/using_bbcp.htm or http://www.nics.tennessee.edu/computing-resources/data-transfer/bbcp

homepage: http://www.slac.stanford.edu/~abh/bbcp/

version	versionsuffix	toolchain
12.01.30.00.0	-amd64_linux26	system

bbFTP

bbFTP is a file transfer software. It implements its own transfer protocol, which is optimized for large files (larger than 2GB) and secure as it does not read the password in a file and encrypts the connection information. bbFTP main features are: * Encoded username and password at connection * SSH and Certificate authentication modules * Multi-stream transfer * Big windows as defined in RFC1323 * On-the-fly data compression * Automatic retry * Customizable time-outs * Transfer simulation * AFS authentication integration * RFIO interface

homepage: https://software.in2p3.fr/bbftp/

version	toolchain
3.2.1	GCCcore/9.3.0, intel/2016a, system

BBMap

BBMap short read aligner, and other bioinformatic tools.

homepage: https://sourceforge.net/projects/bbmap/

version	versionsuffix	toolchain
36.62	-Java-1.8.0_112	intel/2016b
37.93		foss/2018a, intel/2018a
38.26		foss/2018b
38.50b		GCC/8.2.0-2.31.1
38.76		GCC/8.2.0-2.31.1
38.79		GCC/8.3.0
38.87		GCC/8.2.0-2.31.1, iccifort/2020.1.217
38.90		GCC/10.2.0, GCC/9.3.0
38.96		GCC/10.3.0
38.98		GCC/11.2.0
39.01		GCC/11.3.0, GCC/12.2.0

bc

bc is an arbitrary precision numeric processing language.

homepage: https://www.gnu.org/software/bc/

version	toolchain
1.06.95	GCC/4.8.2

BCALM

de Bruijn graph compaction in low memory

homepage: https://github.com/GATB/bcalm

version	toolchain
2.2.0	foss/2018a

bcbio-gff

Read and write Generic Feature Format (GFF) with Biopython integration.

homepage: https://github.com/chapmanb/bcbb/tree/master/gff

version	versionsuffix	toolchain
0.6.6	-Python-3.8.2	foss/2020a
0.6.7		foss/2021a
0.7.0		foss/2020b, foss/2022a, foss/2022b

BCEL

The Byte Code Engineering Library (Apache Commons BCEL™) is intended to give users a convenient way to analyze, create, and manipulate (binary) Java class files (those ending with .class).

homepage: https://commons.apache.org/proper/commons-bcel/

version	versionsuffix	toolchain
5.2	-Java-1.8	system
6.5.0	-Java-1.8	system

BCFtools

Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants

homepage: http://www.htslib.org/

version	toolchain
1.3	foss/2016a, intel/2016a
1.3.1	foss/2016b
1.6	foss/2016b, foss/2017b, intel/2017b
1.8	GCC/6.4.0-2.28
1.9	foss/2018a, foss/2018b, iccifort/2019.1.144-GCC-8.2.0-2.31.1, intel/2018b
1.10.2	GCC/8.3.0, GCC/9.3.0, iccifort/2019.5.281
1.11	GCC/10.2.0
1.12	GCC/10.2.0, GCC/10.3.0, GCC/9.3.0
1.14	GCC/11.2.0
1.15.1	GCC/11.3.0
1.17	GCC/12.2.0
1.18	GCC/12.3.0

bcgTree

Automatized phylogenetic tree building from bacterial core genomes.

homepage: https://github.com/molbiodiv/bcgTree

version	versionsuffix	toolchain
1.0.10	-Perl-5.26.1	intel/2018a
1.1.0	-Perl-5.28.0	intel/2018b

bcl-convert

The Illumina BCL Convert v4.0 is a standalone local software app that converts the Binary Base Call (BCL) files produced by Illumina sequencing systems to FASTQ files.

homepage: https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html

version	versionsuffix	toolchain
4.0.3-2	el7.x86_64	system

bcl2fastq2

bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.

homepage: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html

version	versionsuffix	toolchain
2.19.1	-Python-2.7.12	foss/2016b
2.20.0		GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/11.3.0, GCC/12.2.0, GCC/8.3.0, GCC/9.3.0, foss/2018b, intel/2019a
2.20.0	-Python-2.7.12	foss/2016b
2.20.0	-Python-2.7.14	intel/2017b

bcolz

bcolz provides columnar, chunked data containers that can be compressed either in-memory and on-disk. Column storage allows for efficiently querying tables, as well as for cheap column addition and removal. It is based on NumPy, and uses it as the standard data container to communicate with bcolz objects, but it also comes with support for import/export facilities to/from HDF5/PyTables tables and pandas dataframes.

homepage: https://bcolz.blosc.org/en/latest/

version	versionsuffix	toolchain
1.1.1	-Python-2.7.13	foss/2017a
1.2.1		foss/2020b
1.2.1	-Python-3.8.2	foss/2020a

bcrypt

Acceptable password hashing for your software and your servers (but you should really use argon2id or scrypt)

homepage: https://github.com/pyca/bcrypt/

version	toolchain
4.0.1	GCCcore/12.3.0

BDBag

The bdbag utilities are a collection of software programs for working with BagIt packages that conform to the Bagit and Bagit/RO profiles.

homepage: https://github.com/fair-research/bdbag

version	versionsuffix	toolchain
1.4.1	-Python-2.7.14	intel/2018a
1.4.1	-Python-3.6.4	intel/2018a
1.6.3		intel/2021b

Beagle

Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.

homepage: https://faculty.washington.edu/browning/beagle/beagle.html

version	versionsuffix	toolchain
5.4.22Jul22.46e	-Java-11	system

beagle-lib

beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.

homepage: https://github.com/beagle-dev/beagle-lib

version	versionsuffix	toolchain
2.1.2		foss/2016a, foss/2017a
3.0.1		foss/2018a, intel/2018a
3.0.2		foss/2018b
3.0.2	-CUDA-9.2.88	foss/2018b
3.1.2		GCC/10.2.0, GCC/10.3.0, GCC/8.2.0-2.31.1, GCC/9.3.0, gcccuda/2019b, iccifort/2019.1.144-GCC-8.2.0-2.31.1
4.0.0		GCC/11.3.0

Beast

BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability.

homepage: https://beast2.org

version	toolchain
1.8.4	system
1.10.1	intel/2018a
1.10.4	GCC/10.2.0, GCC/8.2.0-2.31.1
2.4.0	foss/2016a
2.4.7	foss/2017a
2.5.0	foss/2018a
2.5.1	foss/2018b
2.5.2	GCC/8.2.0-2.31.1
2.6.3	gcccuda/2019b
2.6.4	GCC/10.2.0
2.6.7	GCC/10.3.0
2.7.3	GCC/11.3.0

BeautifulSoup

Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping.

homepage: https://www.crummy.com/software/BeautifulSoup

version	versionsuffix	toolchain
4.6.0	-Python-3.6.3	intel/2017b
4.6.3	-Python-3.6.4	intel/2018a
4.7.1	-Python-3.6.6	intel/2018b
4.8.0		GCCcore/8.2.0
4.9.1		GCCcore/8.3.0
4.9.1	-Python-3.8.2	GCCcore/9.3.0
4.9.3		GCCcore/10.2.0
4.10.0		GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0
4.11.1		GCCcore/12.2.0
4.12.2		GCCcore/12.3.0, GCCcore/13.2.0

BEDOPS

BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.

homepage: http://bedops.readthedocs.io/en/latest/index.html

version	toolchain
2.4.1	GCC/4.8.4
2.4.2	GCC/4.8.2
2.4.20	system
2.4.26	system
2.4.30	foss/2016b
2.4.32	foss/2018a, intel/2018a
2.4.35	foss/2018b
2.4.41	foss/2021b

BEDTools

BEDTools: a powerful toolset for genome arithmetic. The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.

homepage: https://bedtools.readthedocs.io/

version	toolchain
2.25.0	foss/2016a
2.26.0	GCCcore/6.4.0, foss/2016a, intel/2016b, intel/2017a, intel/2017b
2.27.1	GCCcore/6.4.0, foss/2016b, foss/2018b, intel/2017a, intel/2018a
2.28.0	GCC/8.2.0-2.31.1, foss/2018b, iccifort/2019.1.144-GCC-8.2.0-2.31.1
2.29.2	GCC/8.3.0, GCC/9.3.0
2.30.0	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/11.3.0, GCC/12.2.0, iccifort/2020.4.304
2.31.0	GCC/12.3.0

BEEF

BEEF is a library-based implementation of the Bayesian Error Estimation Functional, suitable for linking against by Fortran- or C-based DFT codes. A description of BEEF can be found at http://dx.doi.org/10.1103/PhysRevB.85.235149.

homepage: https://confluence.slac.stanford.edu/display/SUNCAT/BEEF+Functional+Software

version	toolchain
0.1.1	iccifort/2019.5.281, iccifort/2020.4.304

behave

behave: Behavior-driven development (or BDD) is an agile software development technique that encourages collaboration between developers, QA and non-technical or business participants in a software project.

homepage: http://pythonhosted.org/behave

version	versionsuffix	toolchain
1.2.5	-Python-2.7.12	foss/2016b
1.2.6	-Python-3.6.4	intel/2018a

bench

Tools to accurately benchmark and analyze execution times for R expressions.

homepage: https://cran.r-project.org/web/packages/bench/index.html

version	versionsuffix	toolchain
1.1.2	-R-4.2.1	foss/2022a

BerkeleyGW

The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules.

homepage: https://www.berkeleygw.org

version	versionsuffix	toolchain
1.0.6		intel/2016.02-GCC-4.9
1.1-beta2		intel/2016.02-GCC-4.9
1.2.0		intel/2017a, intel/2018a
2.0.0		foss/2017b, foss/2018b, intel/2017b, intel/2018a
2.1.0	-Python-3.7.4	foss/2019b, intel/2019b
3.0.1		foss/2020b, foss/2021a
3.1.0		foss/2022a, intel/2022a
4.0		foss/2022a

BFAST

BFAST facilitates the fast and accurate mapping of short reads to reference sequences. Some advantages of BFAST include: 1) Speed: enables billions of short reads to be mapped quickly. 2) Accuracy: A priori probabilities for mapping reads with defined set of variants. 3) An easy way to measurably tune accuracy at the expense of speed.

homepage: http://bfast.sourceforge.net/

version	toolchain
0.7.0a	foss/2016b

BFC

BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes.

homepage: https://github.com/lh3/bfc

version	toolchain
1	foss/2018a

BGC-Bayesian-genomic-clines

Collection of code for Bayesian genomic cline analyses.

homepage: https://github.com/zgompert/BGC-Bayesian-genomic-clines

version	toolchain
1.03	gompi/2021a

BgeeCall

Automatic RNA-Seq present/absent gene expression calls generation

homepage: https://github.com/BgeeDB/BgeeCall

version	versionsuffix	toolchain
1.16.0	-R-%(rver)s	foss/2021a

BgeeDB

Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology.

homepage: https://github.com/BgeeDB/BgeeDB_R

version	versionsuffix	toolchain
2.26.0	-R-%(rver)s	foss/2021a

bgen

A BGEN file format reader. It fully supports the BGEN format specifications 1.2 and 1.3.

homepage: https://github.com/limix/bgen

version	toolchain
3.0.2	GCCcore/7.3.0
3.0.3	GCCcore/9.3.0
4.1.3	GCCcore/10.2.0

bgen-reader

A bgen file format reader. This python package is a wrapper around the bgen library, a low-memory footprint reader that efficiently reads bgen files. It fully supports the bgen format specifications: 1.2 and 1.3; as well as their optional compressed formats.

homepage: https://github.com/limix/bgen-reader-py

version	versionsuffix	toolchain
3.0.2	-Python-3.6.6	foss/2018b

BiasAdjustCXX

BiasAdjustCXX command-line tool for the application of fast and efficient bias corrections in climatic research

homepage: https://biasadjustcxx.readthedocs.io/en/latest/

version	toolchain
1.9.1	gompi/2021b

bibtexparser

Bibtex parser in Python 2.7 and 3.x

homepage: https://github.com/sciunto-org/python-bibtexparser

version	toolchain
1.1.0	GCCcore/8.2.0

BiG-SCAPE

BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.

homepage: https://bigscape-corason.secondarymetabolites.org/index.html

version	versionsuffix	toolchain
1.0.1	-Python-3.7.4	intel/2019b
1.1.5		foss/2022a

BigDFT

BigDFT: electronic structure calculation based on Daubechies wavelets. bigdft-suite is a set of different packages to run bigdft.

homepage: https://gitlab.com/l_sim/bigdft-suite

version	toolchain
1.9.1	foss/2021b

BinSanity

BinSanity contains a suite a scripts designed to cluster contigs generated from metagenomic assembly into putative genomes.

homepage: https://github.com/edgraham/BinSanity/wiki

version	versionsuffix	toolchain
0.3.5	-Python-3.7.4	foss/2019b

binutils

binutils: GNU binary utilities

homepage: https://directory.fsf.org/project/binutils/

version	toolchain
2.25	GCC/4.9.2, GCC/4.9.2-binutils-2.25, GCC/4.9.3, GCC/4.9.3-binutils-2.25, GCC/5.1.0-binutils-2.25, GCCcore/4.9.2, GCCcore/4.9.3, GCCcore/4.9.4, system
2.25.1	system
2.26	GCCcore/5.3.0, GCCcore/5.4.0, GCCcore/5.5.0, GCCcore/6.3.0, system
2.27	GCCcore/6.1.0, GCCcore/6.2.0, GCCcore/6.3.0, system
2.28	GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.1.0, system
2.29	GCCcore/7.2.0, GCCcore/system, system
2.30	GCCcore/7.3.0, GCCcore/8.1.0, system
2.31.1	GCCcore/7.4.0, GCCcore/8.2.0, system
2.32	GCCcore/8.3.0, GCCcore/9.1.0, GCCcore/9.2.0, system
2.34	GCCcore/10.1.0, GCCcore/9.3.0, system
2.35	GCCcore/10.2.0, system
2.36.1	FCC/4.5.0, GCCcore/10.3.0, GCCcore/11.1.0, GCCcore/8.4.0, GCCcore/9.4.0, system
2.37	GCCcore/11.2.0, system
2.38	GCCcore/11.3.0, GCCcore/12.1.0, GCCcore/9.5.0, system
2.39	GCCcore/12.2.0, system
2.40	GCCcore/11.4.0, GCCcore/12.3.0, GCCcore/13.1.0, GCCcore/13.2.0, system

Bio-DB-HTS

Read files using HTSlib including BAM/CRAM, Tabix and BCF database files

homepage: https://metacpan.org/release/Bio-DB-HTS

version	versionsuffix	toolchain
2.11	-Perl-5.26.0	foss/2017b, intel/2017b
2.11	-Perl-5.26.1	intel/2018a
2.11	-Perl-5.28.0	foss/2018b
3.01		GCC/10.2.0, GCC/11.2.0, GCC/11.3.0, GCC/12.2.0
3.01	-Perl-5.28.1	GCC/8.2.0-2.31.1

Bio-EUtilities

BioPerl low-level API for retrieving and storing data from NCBI eUtils

homepage: https://github.com/bioperl/bio-eutilities

version	toolchain
1.76	GCCcore/8.3.0

Bio-SamTools

This is a Perl interface to the SAMtools sequence alignment interface.

homepage: http://search.cpan.org/~lds/Bio-SamTools/

version	versionsuffix	toolchain
1.43	-Perl-5.24.1	intel/2017a

Bio-SearchIO-hmmer

Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible with both version 2 and version 3 of the HMMER package from http://hmmer.org.

homepage: https://metacpan.org/pod/Bio::SearchIO::hmmer3

version	toolchain
1.7.3	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/11.3.0, GCC/12.2.0

bioawk

Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.

homepage: https://github.com/lh3/bioawk

version	toolchain
1.0	GCC/10.3.0, GCC/11.2.0, foss/2018b

biobakery-workflows

bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters. Quality control and statistical summary reports are automatically generated for most data types, which include 16S amplicons, metagenomes, and metatranscriptomes. Workflows are run directly from the command line and tasks can be imported to create your own custom workflows. The workflows and tasks are built with AnADAMA2 which allows for parallel task execution locally and in a grid compute environment.

homepage: http://huttenhower.sph.harvard.edu/biobakery_workflows

version	toolchain
3.1	foss/2022a

biobambam2

Tools for processing BAM files

homepage: https://github.com/gt1/biobambam2

version	toolchain
2.0.87	GCC/11.3.0, intel/2018a
2.0.185	GCC/12.3.0

biogeme

Biogeme is a open source Python package designed for the maximum likelihood estimation of parametric models in general, with a special emphasis on discrete choice models.

homepage: https://pypi.python.org/pypi/biogeme

version	toolchain
3.1.2	foss/2021a
3.2.6	foss/2022a
3.2.8	foss/2021a
3.2.10	foss/2022a

biom-format

The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project.

homepage: https://biom-format.org

version	versionsuffix	toolchain
2.1.10	-Python-3.8.2	foss/2020a
2.1.12		foss/2021b
2.1.14		foss/2022a
2.1.15		foss/2022b

biomart-perl

The BioMart Perl API allows you to go a step further with BioMart and integrate BioMart Perl Code into custom Perl scripts.

homepage: https://useast.ensembl.org/info/data/biomart/biomart_perl_api.html

version	versionsuffix	toolchain
0.7_e6db561	-Perl-5.26.0	GCCcore/6.4.0

BioPerl

Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects.

homepage: https://bioperl.org/

version	versionsuffix	toolchain
1.6.924	-Perl-5.20.3	intel/2016a
1.6.924	-Perl-5.22.1	foss/2016a
1.7.0	-Perl-5.24.0	foss/2016b
1.7.1	-Perl-5.24.0	intel/2016b
1.7.1	-Perl-5.24.1	intel/2017a
1.7.2		GCCcore/8.3.0
1.7.2	-Perl-5.26.0	foss/2017b, intel/2017b
1.7.2	-Perl-5.26.1	intel/2018a
1.7.2	-Perl-5.28.0	foss/2018b, intel/2018b
1.7.2	-Perl-5.28.1	GCCcore/8.2.0
1.7.7		GCCcore/9.3.0
1.7.8		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0

BioPP

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools.

homepage: https://github.com/BioPP/bpp-core

version	toolchain
2.4.1	GCC/8.2.0-2.31.1, GCC/9.3.0

Biopython

Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.

homepage: https://www.biopython.org

version	versionsuffix	toolchain
1.65	-Python-2.7.11	foss/2016a
1.68	-Python-2.7.12	foss/2016b, intel/2016b
1.68	-Python-3.5.2	foss/2016b, intel/2016b
1.70	-Python-2.7.13	foss/2017a
1.70	-Python-2.7.14	foss/2017b, intel/2017b
1.70	-Python-3.6.1	intel/2017a
1.70	-Python-3.6.3	foss/2017b, intel/2017b
1.71	-Python-2.7.14	intel/2018a
1.71	-Python-3.6.4	foss/2018a, intel/2018a
1.72	-Python-2.7.15	foss/2018b, intel/2018b
1.72	-Python-3.6.6	foss/2018b
1.73		foss/2019a, fosscuda/2019a, intel/2019a
1.73	-Python-3.6.6	foss/2018b
1.74		foss/2019a
1.75	-Python-2.7.16	foss/2019b
1.75	-Python-3.7.4	foss/2019b, fosscuda/2019b, intel/2019b
1.76	-Python-2.7.18	foss/2020b, foss/2021b
1.78		foss/2020b, fosscuda/2020b, intel/2020b
1.78	-Python-3.8.2	foss/2020a, intel/2020a
1.79		foss/2021a, foss/2021b, foss/2022a, intel/2021b
1.81		foss/2022b
1.83		foss/2023a

BioServices

Bioservices is a Python package that provides access to many Bioinformatices Web Services (e.g., UniProt) and a framework to easily implement Web Services wrappers (based on WSDL/SOAP or REST protocols).

homepage: https://bioservices.readthedocs.io/

version	versionsuffix	toolchain
1.7.9	-Python-3.8.2	foss/2020a

BirdNET

BirdNET is a research platform that aims at recognizing birds by sound at scale. We support various hardware and operating systems such as Arduino microcontrollers, the Raspberry Pi, smartphones, web browsers, workstation PCs, and even cloud services. BirdNET is a citizen science platform as well as an analysis software for extremely large collections of audio. BirdNET aims to provide innovative tools for conservationists, biologists, and birders alike.

homepage: https://birdnet.cornell.edu/

version	versionsuffix	toolchain
20201214	-Python-3.7.4	fosscuda/2019b

biscuit

Utilities to help analyze bisulfite-treated sequence data

homepage: https://github.com/zwdzwd/biscuit

version	toolchain
0.1.4	foss/2016a

Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

homepage: https://www.bioinformatics.babraham.ac.uk/projects/bismark/

version	toolchain
0.19.0	intel/2017b
0.20.1	foss/2018b, intel/2018b
0.23.1	foss/2021b
0.24.0	GCC/11.3.0
0.24.1	GCC/12.2.0

Bison

Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.

homepage: https://www.gnu.org/software/bison

version	toolchain
2.7	GCC/4.8.1, GCC/4.8.4, GCCcore/6.3.0, GCCcore/6.4.0, system
3.0.2	GCC/4.8.2
3.0.3	GCC/4.9.2
3.0.4	GCC/4.9.2, GCC/4.9.2-binutils-2.25, GCC/4.9.3, GCC/4.9.3-2.25, GCC/4.9.3-binutils-2.25, GCC/5.1.0-binutils-2.25, GCCcore/4.9.2, GCCcore/4.9.3, GCCcore/4.9.4, GCCcore/5.3.0, GCCcore/5.4.0, GCCcore/5.5.0, GCCcore/6.1.0, GCCcore/6.2.0, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.1.0, GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/8.1.0, GCCcore/system, GNU/4.9.3-2.25, foss/2016a, foss/2016b, gimkl/2.11.5, gimkl/2017a, intel/2016.02-GCC-4.9, intel/2016a, intel/2016b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25, system
3.0.5	GCCcore/5.5.0, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/8.1.0, GCCcore/8.2.0, GCCcore/system, system
3.2.2	GCCcore/7.4.0
3.3.2	GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/8.4.0, GCCcore/9.1.0, GCCcore/9.2.0, system
3.5.2	system
3.5.3	GCCcore/10.2.0, GCCcore/9.3.0, system
3.6.1	GCCcore/10.1.0
3.7.1	GCCcore/10.2.0, system
3.7.6	FCC/4.5.0, GCCcore/10.3.0, GCCcore/11.1.0, GCCcore/11.2.0, GCCcore/9.4.0, system
3.8.2	GCCcore/11.3.0, GCCcore/11.4.0, GCCcore/12.1.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.1.0, GCCcore/13.2.0, GCCcore/9.5.0, system

bitarray

bitarray provides an object type which efficiently represents an array of booleans

homepage: https://github.com/ilanschnell/bitarray

version	versionsuffix	toolchain
0.8.3	-Python-2.7.15	intel/2018b
0.8.3	-Python-3.6.6	intel/2018b
1.2.1	-Python-3.7.4	foss/2019b
1.5.3	-Python-2.7.16	GCC/8.3.0

BLACS

The BLACS (Basic Linear Algebra Communication Subprograms) project is an ongoing investigation whose purpose is to create a linear algebra oriented message passing interface that may be implemented efficiently and uniformly across a large range of distributed memory platforms.

homepage: http://www.netlib.org/blacs/

version	toolchain
1.1	gmvapich2/2016a

BLASR

The PacBio® long read aligner

homepage: https://github.com/PacificBiosciences/blasr

version	toolchain
2.2	intel/2016b
5.3.3	gompi/2019a
20170330	intel/2017a

blasr_libcpp

Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for analyzing PacBio sequences

homepage: https://github.com/PacificBiosciences/blasr_libcpp

version	toolchain
20170426	intel/2017a

BLAST

Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.

homepage: http://blast.ncbi.nlm.nih.gov/

version	versionsuffix	toolchain
2.2.26	-Linux_x86_64	system
2.8.1	-Linux_x86_64	system
2.10.0	-Linux_x86_64	system
2.10.1	-Linux_x86_64	system
2.11.0	-Linux_x86_64	system

BLAST+

Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.

homepage: https://blast.ncbi.nlm.nih.gov/

version	versionsuffix	toolchain
2.2.31		system
2.3.0	-Python-2.7.11	foss/2016a
2.6.0	-Python-2.7.12	foss/2016b
2.6.0	-Python-2.7.13	foss/2017a, intel/2017a
2.6.0	-Python-2.7.14	intel/2017b
2.7.1		foss/2018a, foss/2018b, intel/2018a, intel/2018b
2.7.1	-Python-2.7.14	intel/2017b
2.8.1		foss/2018b
2.9.0		gompi/2019a, gompi/2019b, gompi/2021b, iimpi/2019a, iimpi/2019b
2.10.1		gompi/2020a, iimpi/2020a
2.11.0		gompi/2019b, gompi/2020a, gompi/2020b, gompi/2021a
2.12.0		gompi/2021b
2.13.0		gompi/2022a
2.14.0		gompi/2022b
2.14.1		gompi/2023a

BLAT

BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.

homepage: https://genome.ucsc.edu/goldenPath/help/blatSpec.html

version	toolchain
3.5	GCC/8.2.0-2.31.1, GCC/8.3.0, GCC/9.3.0, foss/2016b, foss/2018b, intel/2016b, intel/2017a
3.7	GCC/10.3.0, GCC/11.2.0, GCC/11.3.0

Blender

Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation.

homepage: https://www.blender.org/

version	versionsuffix	toolchain
2.77a	-Python-3.5.2	intel/2016b
2.79	-Python-3.6.1	intel/2017a
2.79b	-Python-3.6.6	intel/2018b
2.79b	-Python-3.6.6-CUDA-9.2.88	foss/2018b
2.81	-Python-3.7.4	foss/2019b, intel/2019b
3.0.0	-linux-x64	system
3.1.2	-linux-x64	system
3.2.2	-linux-x64	system
3.3.1	-linux-x86_64-CUDA-11.7.0	system
3.4.1	-linux-x86_64-CUDA-11.7.0	system
3.5.0	-linux-x86_64-CUDA-11.7.0	system
3.6.5	-linux-x86_64-CUDA-12.1.1	system
4.0.1	-linux-x86_64-CUDA-12.1.1	system

BLIS

AMD's fork of BLIS. BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.

homepage: https://developer.amd.com/amd-cpu-libraries/blas-library/

version	versionsuffix	toolchain
0.3.2		GCC/7.3.0-2.30
0.6.0		GCC/8.3.0-2.32
0.8.0		GCCcore/10.2.0, GCCcore/9.3.0
0.8.1		GCC/10.3.0, GCC/11.2.0, GCCcore/10.3.0
0.9.0		GCC/11.3.0, GCC/12.2.0, GCC/12.3.0, GCC/13.2.0, intel-compilers/2022.1.0
1.2	-amd	GCC/7.3.0-2.30
2.2	-amd	GCCcore/9.3.0
3.0	-amd	GCCcore/10.3.0
3.0.1	-amd	GCC/11.2.0, GCCcore/10.2.0, GCCcore/10.3.0
3.1	-amd	GCCcore/11.2.0

Blitz++

Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in C++ with a speed comparable to Fortran implementations, while preserving an object-oriented interface

homepage: https://github.com/blitzpp/blitz

version	toolchain
0.10	GCCcore/6.4.0, foss/2016a
1.0.2	GCCcore/10.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0, GCCcore/9.3.0

BlobTools

A modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets.

homepage: https://blobtools.readme.io/docs

version	versionsuffix	toolchain
20180528	-Python-2.7.15	foss/2018b

Block

Block implements the density matrix renormalization group (DMRG) algorithm for quantum chemistry.

homepage: https://sanshar.github.io/Block/

version	toolchain
1.5.3-20200525	foss/2022a, foss/2022b

Blosc

Blosc, an extremely fast, multi-threaded, meta-compressor library

homepage: https://www.blosc.org/

version	toolchain
1.11.1	intel/2016b
1.12.1	GCCcore/6.4.0, foss/2016b, foss/2017a, intel/2017a
1.14.2	GCCcore/6.4.0, foss/2016a
1.14.4	GCCcore/7.3.0
1.17.0	GCCcore/8.2.0
1.17.1	GCCcore/8.3.0, GCCcore/9.3.0
1.21.0	GCCcore/10.2.0, GCCcore/10.3.0
1.21.1	GCCcore/11.2.0
1.21.3	GCCcore/11.3.0, GCCcore/12.2.0
1.21.5	GCCcore/12.3.0, GCCcore/13.2.0

Blosc2

Blosc, an extremely fast, multi-threaded, meta-compressor library

homepage: https://www.blosc.org/

version	toolchain
2.0.3	GCCcore/10.2.0
2.0.4	GCCcore/10.3.0
2.4.3	GCCcore/11.2.0, GCCcore/11.3.0
2.6.1	GCCcore/11.3.0
2.8.0	GCCcore/12.2.0, GCCcore/12.3.0
2.13.2	GCCcore/13.2.0

BLT

BLT is an extension to the Tk toolkit, adding new widgets, geometry managers, and miscellaneous commands.

homepage: http://blt.sourceforge.net/

version	toolchain
20181223	GCCcore/11.2.0

bmtagger

Best Match Tagger for removing human reads from metagenomics datasets

homepage: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/

version	toolchain
3.101	foss/2018b, gompi/2019a, gompi/2020b

BMTK

The Brain Modeling Toolkit (BMTK) is a python-based software package for building, simulating and analyzing large-scale neural network models. It supports the building and simulation of models of varying levels-of-resolution; from multi-compartment biophysically detailed networks, to point-neuron models, to filter-based models, and even population-level firing rate models.

homepage: https://alleninstitute.github.io/bmtk/index.html

version	toolchain
1.0.8	foss/2021a

bnpy

Bayesian nonparametric machine learning for python provides code for training popular clustering models on large datasets. The focus is on Bayesian nonparametric models based on the Dirichlet process, but it also provides parametric counterparts.

homepage: https://github.com/bnpy/bnpy

version	versionsuffix	toolchain
0.1.6	-Python-2.7.15	foss/2018b

BOINC

BOINC is a program that lets you donate your idle computer time to science projects like SETI@home, Climateprediction.net, Rosetta@home, World Community Grid, and many others.

homepage: https://boinc.berkeley.edu

version	versionsuffix	toolchain
7.2.42	-client	GCC/4.8.2

bokeh

Statistical and novel interactive HTML plots for Python

homepage: https://github.com/bokeh/bokeh

version	versionsuffix	toolchain
0.12.3	-Python-2.7.12	intel/2016b
0.12.3	-Python-3.5.2	intel/2016b
0.12.15	-Python-3.6.4	intel/2018a
1.0.4	-Python-3.6.6	foss/2018b, intel/2018b
1.3.4	-Python-3.7.2	foss/2019a
1.4.0	-Python-3.7.4	foss/2019b, fosscuda/2019b, intel/2019b
2.0.2	-Python-3.8.2	foss/2020a, intel/2020a
2.2.3		foss/2020b, fosscuda/2020b, intel/2020b, intelcuda/2020b
2.4.1		foss/2021a
2.4.2		foss/2021b
2.4.3		foss/2022a
3.2.1		foss/2022b
3.2.2		foss/2023a

BoltzTraP

Boltzmann Transport Properties (BoltzTraP) is a program for calculating the semi-classic transport coefficients.

homepage: http://www.icams.de/content/departments/cmat/boltztrap/

version	toolchain
1.2.5	intel/2016a

BoltzTraP2

BoltzTraP2 provides a numerically stable and efficient method for obtaining analytic representations of electronic bands based on density-functional-theory results for relatively sparse grids. It achieves this goal by using smoothed Fourier interpolation.

homepage: https://www.boltztrap.org

version	toolchain
22.12.1	foss/2022a

Bonito

Convolution Basecaller for Oxford Nanopore Reads

homepage: https://github.com/nanoporetech/bonito

version	versionsuffix	toolchain
0.1.0	-Python-3.7.4	foss/2019b, fosscuda/2019b
0.1.4	-Python-3.7.4	fosscuda/2019b
0.2.0	-Python-3.7.4	fosscuda/2019b
0.2.2	-Python-3.7.4	fosscuda/2019b
0.3.2	-Python-3.7.4	fosscuda/2019b
0.3.5	-Python-3.7.4	fosscuda/2019b
0.3.8		fosscuda/2020b
0.4.0		fosscuda/2020b

Bonmin

Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a software package for large-scale nonlinear optimization.

homepage: https://coin-or.github.io/Ipopt

version	toolchain
1.8.7	intel/2019a

Bonnie++

Enhanced performance Test of Filesystem I/O

homepage: https://www.coker.com.au/bonnie++

version	toolchain
1.97	foss/2016a
2.00a	GCC/10.3.0

Boost

Boost provides free peer-reviewed portable C++ source libraries.

homepage: https://www.boost.org/

version	versionsuffix	toolchain
1.54.0	-Python-2.7.12	foss/2016b
1.55.0		system
1.55.0	-Python-2.7.11	foss/2016a
1.57.0	-Python-2.7.10	gimkl/2.11.5
1.58.0		intel/2017a
1.58.0	-Python-2.7.11	foss/2016a, intel/2016a
1.58.0	-serial	GCC/4.9.2
1.59.0	-Python-2.7.11	foss/2016a, intel/2016a
1.60.0		foss/2016a, intel/2016a
1.60.0	-Python-2.7.11	foss/2016a, intel/2016a
1.60.0	-Python-3.5.1	foss/2016a
1.61.0		foss/2016a, foss/2016b, intel/2016a, intel/2016b
1.61.0	-Python-2.7.11	foss/2016a, intel/2016a
1.61.0	-Python-2.7.12	foss/2016b, intel/2016b
1.61.0	-Python-3.5.1	foss/2016a
1.62.0	-Python-2.7.12	intel/2016b
1.63.0		foss/2017a
1.63.0	-Python-2.7.12	foss/2016b, intel/2016b
1.63.0	-Python-2.7.13	foss/2017a, intel/2017a
1.63.0	-Python-2.7.14	foss/2018a, intel/2017b
1.63.0	-Python-3.5.2	foss/2016b
1.64.0		gompi/2019a, gompic/2019a, intel/2017a
1.64.0	-Python-2.7.13	intel/2017a
1.65.0	-Python-2.7.13	intel/2017a
1.65.1		foss/2017a, foss/2017b, intel/2017a, intel/2017b
1.65.1	-Python-2.7.13	intel/2017a
1.65.1	-Python-2.7.14	foss/2017b, intel/2017b
1.65.1	-Python-3.6.3	foss/2017b, intel/2017b
1.66.0		foss/2018a, intel/2017b, intel/2018.01, intel/2018a
1.66.0	-Python-2.7.14	foss/2018a, intel/2017b, intel/2018a
1.66.0	-Python-3.6.3	intel/2018.01
1.66.0	-Python-3.6.4	foss/2018a, intel/2018a
1.66.0	-no_mpi	GCCcore/6.4.0
1.67.0		foss/2018b, fosscuda/2018b, intel/2018a, intel/2018b
1.67.0	-Python-2.7.14	foss/2018a
1.68.0	-Python-2.7.15	foss/2018b, intel/2018b
1.68.0	-Python-3.6.6	foss/2018b, intel/2018b
1.69.0		intel/2019.01
1.70.0		gompi/2019a, gompic/2019a, iimpi/2019a, iimpic/2019a
1.71.0		gompi/2019b, gompic/2019b, iimpi/2019b, iimpic/2019b
1.72.0		gompi/2020a, gompic/2020a, iimpi/2020a
1.72.0	-no_mpi	GCCcore/9.3.0
1.74.0		GCC/10.2.0, iccifort/2020.4.304
1.75.0		GCC/11.2.0
1.76.0		GCC/10.3.0, intel-compilers/2021.2.0
1.77.0		GCC/11.2.0, intel-compilers/2021.4.0
1.79.0		GCC/11.2.0, GCC/11.3.0
1.81.0		GCC/12.2.0
1.82.0		GCC/12.3.0
1.83.0		GCC/13.2.0

Boost.MPI

Boost provides free peer-reviewed portable C++ source libraries.

homepage: https://www.boost.org/

version	toolchain
1.76.0	gompi/2021a
1.77.0	gompi/2021b
1.79.0	gompi/2022a, gompi/2022b
1.81.0	gompi/2022b
1.82.0	gompi/2023a

Boost.Python

Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language.

homepage: https://boostorg.github.io/python

version	versionsuffix	toolchain
1.64.0		gompi/2019a, gompic/2019a
1.65.1	-Python-2.7.14	foss/2017b, intel/2017b
1.66.0	-Python-2.7.14	intel/2018a
1.66.0	-Python-3.6.4	foss/2018a, intel/2018a
1.67.0	-Python-2.7.15	foss/2018b, fosscuda/2018b, intel/2018b
1.67.0	-Python-3.6.6	foss/2018b, intel/2018b
1.70.0		gompi/2019a, gompic/2019a, iimpi/2019a, iimpic/2019a
1.71.0		gompi/2019b, gompic/2019b, iimpi/2019b, iimpic/2019b
1.72.0		gompi/2020a, gompic/2020a, iimpi/2020a
1.74.0		GCC/10.2.0
1.76.0		GCC/10.3.0
1.77.0		GCC/11.2.0
1.79.0		GCC/11.3.0
1.83.0		GCC/13.2.0

Boost.Python-NumPy

Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language.

homepage: https://boostorg.github.io/python

version	toolchain
1.79.0	foss/2022a

boost_histogram

Boost-histogram is a Python package providing Python bindings for Boost.Histogram.

homepage: https://boost-histogram.readthedocs.io

version	toolchain
1.2.1	foss/2021a

BOPTEST

This repository contains code for the Building Optimization Performance Test framework (BOPTEST) that is being developed as part of the IBPSA Project 1.

homepage: https://ibpsa.github.io/project1-boptest/

version	toolchain
0.3.0	system

boto3

Boto3 is the Amazon Web Services (AWS) Software Development Kit (SDK) for Python, which allows Python developers to write software that makes use of services like Amazon S3 and Amazon EC2.

homepage: https://github.com/boto/boto3

version	toolchain
1.20.13	GCCcore/10.3.0, GCCcore/11.2.0
1.26.37	GCCcore/11.3.0
1.26.163	GCCcore/12.2.0
1.28.70	GCCcore/12.3.0

Bottleneck

Fast NumPy array functions written in C

homepage: https://kwgoodman.github.io/bottleneck-doc

version	versionsuffix	toolchain
1.2.1	-Python-3.6.4	intel/2018a
1.3.2	-Python-3.8.2	foss/2020a
1.3.6		foss/2022a
1.3.7		foss/2022a

Bowtie

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome.

homepage: http://bowtie-bio.sourceforge.net/index.shtml

version	toolchain
1.1.2	GCCcore/5.4.0, GCCcore/6.3.0, foss/2016a, intel/2016b, intel/2017a, intel/2018a
1.2.1.1	foss/2016b, intel/2017b
1.2.2	foss/2018b, intel/2017b, intel/2018a
1.2.3	GCC/8.2.0-2.31.1, GCC/8.3.0, GCC/9.3.0, foss/2018b, iccifort/2019.1.144-GCC-8.2.0-2.31.1, iccifort/2019.5.281
1.3.0	GCC/10.2.0, GCC/9.3.0
1.3.1	GCC/10.3.0, GCC/11.2.0, GCC/11.3.0

Bowtie2

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

homepage: https://bowtie-bio.sourceforge.net/bowtie2/index.shtml

version	toolchain
2.2.8	foss/2016a
2.2.9	foss/2016a, intel/2016b
2.3.2	foss/2016b, foss/2017a, intel/2017a
2.3.3.1	intel/2017b
2.3.4	intel/2017b
2.3.4.1	foss/2017b, intel/2017b, intel/2018a
2.3.4.2	foss/2018b, intel/2018b
2.3.4.3	foss/2017b
2.3.5.1	GCC/8.2.0-2.31.1, GCC/8.3.0, iccifort/2019.1.144-GCC-8.2.0-2.31.1, iccifort/2019.5.281
2.4.1	GCC/9.3.0
2.4.2	GCC/10.2.0, GCC/9.3.0
2.4.4	GCC/10.3.0, GCC/11.2.0
2.4.5	GCC/11.3.0
2.5.1	GCC/10.3.0, GCC/12.2.0, GCC/12.3.0

Bpipe

Bpipe - a tool for running and managing bioinformatics pipelines

homepage: http://docs.bpipe.org/

version	toolchain
0.9.9.2	intel/2017a

bpp

The aim of this project is to implement a versatile high-performance version of the BPP software.

homepage: https://github.com/bpp/bpp

version	toolchain
4.3.8	GCC/8.3.0
4.4.0	GCC/10.3.0

bpytop

Resource monitor that shows usage and stats for processor, memory, disks, network and processes.

homepage: https://github.com/aristocratos/bpytop/

version	toolchain
1.0.60	GCCcore/10.2.0
1.0.67	GCCcore/10.3.0

Bracken

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Braken uses the taxonomy labels assigned by Kraken, a highly accurate metagenomics classification algorithm, to estimate the number of reads originating from each species present in a sample. Kraken classifies reads to the best matching location in the taxonomic tree, but does not estimate abundances of species. We use the Kraken database itself to derive probabilities that describe how much sequence from each genome is identical to other genomes in the database, and combine this information with the assignments for a particular sample to estimate abundance at the species level, the genus level, or above. Combined with the Kraken classifier, Bracken produces accurate species- and genus-level abundance estimates even when a sample contains two or more near-identical species. NOTE: Bracken is compatible with both Kraken 1 and Kraken 2. However, the default kmer length is different depending on the version of Kraken used. If you use Kraken 1 defaults, specify 31 as the kmer length. If you use Kraken 2 defaults, specify 35 as the kmer length.

homepage: https://ccb.jhu.edu/software/bracken/

version	toolchain
2.6.0	GCCcore/9.3.0
2.6.2	GCCcore/11.2.0
2.7	GCCcore/11.2.0
2.9	GCCcore/10.3.0

Braindecode

Braindecode is an open-source Python toolbox for decoding raw electrophysiological brain data with deep learning models. It includes dataset fetchers, data preprocessing and visualization tools, as well as implementations of several deep learning architectures and data augmentations for analysis of EEG, ECoG and MEG.

homepage: https://braindecode.org/

version	versionsuffix	toolchain
0.7	-PyTorch-1.10.0	foss/2021a
0.7	-PyTorch-1.10.0-CUDA-11.3.1	foss/2021a
0.8.1	-PyTorch-2.1.2	foss/2023a

BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes.

homepage: https://github.com/Gaius-Augustus/BRAKER

version	versionsuffix	toolchain
2.1.2		intel/2019a
2.1.5	-Python-3.7.4	intel/2019b
2.1.6		foss/2021b, foss/2022a

BreakDancer

BreakDancer is a Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads

homepage: http://gmt.genome.wustl.edu/packages/breakdancer

version	toolchain
1.4.5	intel/2017a

breseq

breseq is a computational pipeline for the analysis of short-read re-sequencing data

homepage: https://barricklab.org/breseq

version	versionsuffix	toolchain
0.35.0	-R-3.6.0	intel/2019a
0.35.4	-R-4.0.0	foss/2020a
0.36.1		foss/2021b
0.38.1		foss/2022a

BRiAl

BRiAl is the legacy version of PolyBoRi maintained by sagemath developers.

homepage: https://github.com/BRiAl/BRiAl

version	toolchain
1.2.12	GCC/11.3.0

Brotli

Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate but offers more dense compression. The specification of the Brotli Compressed Data Format is defined in RFC 7932.

homepage: https://github.com/google/brotli

version	toolchain
1.0.9	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/8.3.0
1.1.0	GCCcore/13.2.0

Brotli-python

Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate but offers more dense compression. The specification of the Brotli Compressed Data Format is defined in RFC 7932.

homepage: https://github.com/google/brotli

version	toolchain
1.0.9	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.3.0, GCCcore/12.2.0
1.1.0	GCCcore/13.2.0

Brunsli

Brunsli is a lossless JPEG repacking library.

homepage: https://github.com/google/brunsli/

version	toolchain
0.1	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0

bsddb3

bsddb3 is a nearly complete Python binding of the Oracle/Sleepycat C API for the Database Environment, Database, Cursor, Log Cursor, Sequence and Transaction objects.

homepage: https://pypi.org/project/bsddb3/

version	versionsuffix	toolchain
6.2.6		GCCcore/8.2.0
6.2.6	-Python-2.7.15	fosscuda/2018b
6.2.9		GCCcore/10.2.0, GCCcore/11.3.0

BSMAPz

Updated and optimized fork of BSMAP. BSMAPz is a short reads mapping program for bisulfite sequencing in DNA methylation study.

homepage: https://github.com/zyndagj/BSMAPz

version	versionsuffix	toolchain
1.1.1	-Python-2.7.16	intel/2019b

Bsoft

Bsoft is a collection of programs and a platform for development of software for image and molecular processing in structural biology. Problems in structural biology are approached with a highly modular design, allowing fast development of new algorithms without the burden of issues such as file I/O. It provides an easily accessible interface, a resource that can be and has been used in other packages.

homepage: https://lsbr.niams.nih.gov/bsoft/

version	toolchain
2.0.2	foss/2017b
2.0.7	GCC/9.3.0

BSseeker2

BS-Seeker2 is a seamless and versatile pipeline for accurately and fast mapping the bisulfite-treated reads.

homepage: http://pellegrini-legacy.mcdb.ucla.edu/bs_seeker2

version	versionsuffix	toolchain
2.1.8	-Python-2.7.16	GCC/8.3.0, iccifort/2019.5.281

btllib

Bioinformatics Technology Lab common code library

homepage: https://github.com/bcgsc/btllib

version	toolchain
1.7.0	GCC/12.3.0

BuDDy

A Binary Decision Diagram library, with many highly efficient vectorized BDD operations, dynamic variable reordering, automated garbage collection, a C++ interface with automatic reference counting, and much more.

homepage: http://buddy.sourceforge.net/

version	toolchain
2.4	GCCcore/10.2.0

BUFRLIB

NCEP BUFRLIB software to encode or decode BUFR messages. It is not intended to be a primer on the BUFR code form itself.

homepage: https://www.emc.ncep.noaa.gov/index.php?branch=BUFRLIB

version	toolchain
11.3.0.2	iccifort/2020.1.217

build

A simple, correct Python build frontend.

homepage: https://github.com/pypa/build

version	toolchain
0.10.0	foss/2022a, foss/2022b
1.0.3	foss/2023a, foss/2023b

buildenv

This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that you can use to easily transition between toolchains when building your software. To query the variables being set please use: module show

homepage:

version	versionsuffix	toolchain
default		FCC/4.5.0, Fujitsu/21.05, foss/2017b, foss/2018b, foss/2019b, foss/2020a, foss/2020b, foss/2021a, foss/2021b, foss/2022a, foss/2022b, foss/2023a, foss/2023b, fosscuda/2019b, fosscuda/2020a, fosscuda/2020b, intel/2016b, intel/2017a, intel/2019b, intel/2020a, intel/2020b, intel/2021a, intel/2021b, intel/2022a, intel/2022b, intel/2023a, intel/2023b, intelcuda/2019b, intelcuda/2020a, intelcuda/2020b, nvompi/2022.07
default	-CUDA-11.3.1	foss/2021a
default	-CUDA-11.4.1	foss/2021b
default	-CUDA-11.7.0	foss/2022a
default	-CUDA-12.0.0	foss/2022b
default	-CUDA-12.1.1	foss/2023a

buildingspy

Python modules for automating Modelica simulations and for running unit test for the Buildings library

homepage: https://simulationresearch.lbl.gov/modelica/buildingspy

version	toolchain
4.0.0	foss/2022a

Bullet

Bullet professional 3D Game Multiphysics Library provides state of the art collision detection, soft body and rigid body dynamics.

homepage: http://bulletphysics.org/

version	toolchain
2.83.7	foss/2016a, intel/2016a

BUSCO

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

homepage: https://busco.ezlab.org/

version	versionsuffix	toolchain
1.22	-Python-2.7.13	intel/2017a
2.0.1	-Python-2.7.13	intel/2017a
3.0.2	-Python-2.7.15	intel/2018b
4.0.5	-Python-3.7.4	foss/2019b
4.0.6		foss/2020b
5.0.0		foss/2020b
5.1.2		foss/2020b
5.4.2		foss/2021a
5.4.3		foss/2021b
5.4.5		foss/2022a
5.4.7		foss/2022b

BUStools

bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. It can be used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks. See the kallisto | bustools website for examples and instructions on how to use bustools as part of a single-cell RNA-seq workflow.

homepage: https://github.com/BUStools/bustools

version	toolchain
0.40.0	GCCcore/9.3.0, foss/2018b
0.43.1	GCCcore/11.3.0

BWA

Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.

homepage: http://bio-bwa.sourceforge.net/

version	toolchain
0.7.12	foss/2016b
0.7.13	foss/2016a, intel/2016a
0.7.15	GCCcore/5.4.0, GCCcore/6.4.0, foss/2016a, foss/2016b, intel/2016b, intel/2017a
0.7.16a	foss/2016b, intel/2017a
0.7.17	GCC/10.2.0, GCC/10.3.0, GCC/8.2.0-2.31.1, GCC/8.3.0, GCC/9.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, foss/2017b, foss/2018a, foss/2018b, iccifort/2019.1.144-GCC-8.2.0-2.31.1, iccifort/2019.5.281, iccifort/2020.4.304, intel/2017b, intel/2018a, intel/2018b
0.7.17-20220923	GCCcore/12.3.0

bwa-mem2

The tool bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine.

homepage: https://github.com/bwa-mem2/bwa-mem2

version	toolchain
2.2.1	intel-compilers/2023.1.0

bwa-meth

Fast and accurante alignment of BS-Seq reads.

homepage: https://github.com/brentp/bwa-meth

version	toolchain
0.2.2	iccifort/2019.1.144-GCC-8.2.0-2.31.1, iccifort/2019.5.281
0.2.6	GCC/11.3.0

bwakit

Bwakit is a self-consistent installation-free package of scripts and precompiled binaries, providing an end-to-end solution to read mapping.

homepage: https://github.com/lh3/bwa/tree/master/bwakit

version	versionsuffix	toolchain
0.7.15	_x64-linux	system

bwidget

The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl/Tk 8.x namespaces.

homepage: https://core.tcl-lang.org/bwidget/home

version	toolchain
1.9.13	GCCcore/8.2.0
1.9.14	GCCcore/10.2.0, GCCcore/8.3.0, GCCcore/9.3.0
1.9.15	GCCcore/11.2.0, GCCcore/11.3.0

BWISE

de Bruijn Workflow using Integral information of Short pair End reads

homepage: https://github.com/Malfoy/BWISE

version	versionsuffix	toolchain
20180820	-Python-3.6.4	foss/2018a

bx-python

The bx-python project is a Python library and associated set of scripts to allow for rapid implementation of genome scale analyses.

homepage: https://github.com/bxlab/bx-python

version	versionsuffix	toolchain
0.7.4	-Python-2.7.12	foss/2016b
0.7.4	-Python-2.7.13	intel/2017a
0.8.1	-Python-2.7.14	intel/2018a
0.8.2	-Python-3.6.6	foss/2018b
0.8.4		foss/2019a
0.8.8	-Python-3.7.4	foss/2019b
0.8.9	-Python-3.8.2	foss/2020a
0.8.11		foss/2021a
0.8.13		foss/2021b
0.9.0		foss/2022a
0.10.0		foss/2023a

BXH_XCEDE_TOOLS

A collection of data processing and image analysis tools for data in BXH or XCEDE format. This includes data format encapsulation/conversion, event-related analysis, QA tools, and more. These tools form the basis of the fBIRN QA procedures and are also distributed as part of the fBIRN Data Upload Scripts.

homepage: http://www.nitrc.org/projects/bxh_xcede_tools/

version	toolchain
1.11.1	system

byacc

Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. In contrast to bison, it is written to avoid dependencies upon a particular compiler.

homepage: http://invisible-island.net/byacc/byacc.html

version	toolchain
20160324	intel/2016a
20160606	foss/2016b, intel/2016b
20170709	GCCcore/6.4.0

byobu

Byobu is an elegant enhancement of the otherwise functional, plain, practical GNU Screen. Byobu includes an enhanced profile, configuration utilities, and system status notifications for the GNU screen window manager as well as the Tmux terminal multiplexer

homepage: https://byobu.org

version	toolchain
5.133	GCC/8.3.0

bzip2

bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.

homepage: https://sourceware.org/bzip2

version	toolchain
1.0.6	GCC/4.8.1, GCC/4.8.2, GCC/4.8.4, GCC/4.9.2, GCC/4.9.3-2.25, GCC/5.4.0-2.26, GCCcore/4.9.3, GCCcore/5.4.0, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/8.2.0, GNU/4.9.3-2.25, foss/2016.04, foss/2016a, foss/2016b, gimkl/2.11.5, gimkl/2017a, intel/2016.02-GCC-4.9, intel/2016a, intel/2016b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25, system
1.0.8	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.1.0, GCCcore/13.2.0, GCCcore/8.3.0, GCCcore/9.3.0, system

C

c-ares - C3D - cadaver - CaDiCaL - CAFE5 - Caffe - cairo - cairomm - Calcam - CalculiX-CrunchiX - Calendrical - Calib - CAMPARI - Cantera - canu - Canvas - CAP3 - CapnProto - captum - Cargo - Carma - carputils - Cartopy - CASA - casacore - Casanovo - CaSpER - CASPR - CASTEP - castor - CastXML - CAT-BAT - CatBoost - Catch2 - category_encoders - CatLearn - CatMAP - causallift - causalml - CaVEMan - CAVIAR - Cbc - CBLAS - ccache - CCfits - CCL - cclib - cctbx-base - cctools - CD-HIT - CDAT - cdbfasta - CDBtools - cddlib - CDFlib - cDNA_Cupcake - CDO - cdo-bindings - cdsapi - cell2location - CellBender - CellChat - CellMix - CellOracle - Cellpose - CellRanger - CellRanger-ARC - CellRanger-ATAC - CellRank - CellTypist - CENSO - centerline - Centrifuge - Cereal - CESM-deps - CFDEMcoupling - cffi - CFITSIO - cftime - CGAL - cget - Cgl - CGmapTools - CGNS - CharLS - CHASE - Check - CheckM - CheckM-Database - Cheetah - Chemaxon-Marvin - chemprop - CheMPS2 - CHERAB - chewBBACA - chi2comb - Chimera - ChimPipe - ChIPseeker - Chromaprint - cicero - CIF2Cell - cimfomfa - CIRCexplorer - CIRCexplorer2 - Circlator - Circos - Circuitscape - CIRI - CIRI-long - CIRIquant - cisTEM - CITE-seq-Count - Clair3 - Clang - Clang-AOMP - Clang-Python-bindings - CLAPACK - Clarabel.rs - CLEAR - CLEASE - CLHEP - CliMetLab - CLIP - cliquer - CLISP - ClonalFrameML - CLooG - CloudCompare - Clp - Clustal-Omega - ClustalW2 - Cluster-Buster - ClusterShell - CMake - CMAverse - CmdStanR - cmocean - CMSeq - CNT-ILP - CNVkit - CNVnator - Co-phylog - COBRApy - CoCoALib - CodAn - code-cli - code-server - CODEX2 - CodingQuarry - Cogent - Coin - CoinUtils - ColabFold - colossalai - Commet - CompareM - Compress-Raw-Zlib - COMSOL - Con3F - conan - CONCOCT - Concorde - ConcurrentVersionsSystem - configparser - configurable-http-proxy - CONN - connected-components-3d - ConnectomeWorkbench - contextily - Control-FREEC - cooler - CoordgenLibs - Coot - CopyKAT - core-counter - Coreutils - corner - CoSymLib - coverage - cowsay - CP2K - CPB - CPC2 - cpio - CPLEX - CPMD - CPPE - CppHeaderParser - CppUnit - cppy - cppyy - cppzmq - cpu_features - cram - cramtools - CrayCCE - CrayGNU - CrayIntel - CrayPGI - crb-blast - CREST - CRF++ - CRISPR-DAV - CRISPResso2 - cromwell - crossguid - CrossMap - CrossTalkZ - CRPropa - Crumble - cryoCARE - cryoDRGN - cryptography - CryptoMiniSat - CrystFEL - CSB - CSBDeep - CSBLAST - cscope - csvkit - ctags - ctffind - CTPL - Cube - CubeGUI - CubeLib - CubeWriter - CuCLARK - CUDA - CUDA-Samples - CUDAcompat - CUDAcore - CUDD - cuDNN - Cufflinks - CUnit - CuPy - cURL - cuSPARSELt - custodian - cutadapt - cuTENSOR - cuteSV - CUTLASS - CVglasso - CVXOPT - CVXPY - CWIPI - cwltool - cxxopts - cysignals - Cython - cython-blis - cytoolz - Cytoscape - cytosim - cyvcf2

c-ares

c-ares is a C library for asynchronous DNS requests (including name resolves)

homepage: https://c-ares.org/

version	toolchain
1.17.2	GCCcore/10.2.0, GCCcore/10.3.0
1.18.1	GCCcore/11.2.0, GCCcore/11.3.0
1.19.1	GCCcore/12.3.0
1.27.0	GCCcore/13.2.0

C3D

Convert3D Medical Image Processing Tool

homepage: https://sourceforge.net/projects/c3d/

version	toolchain
1.0.0	system

cadaver

cadaver is a command-line WebDAV client for Unix.

homepage: http://www.webdav.org/cadaver/

version	toolchain
0.23.3	intel/2017a

CaDiCaL

CaDiCaL is a simplified satisfiability solver. The original goal of the development of CaDiCaL was to obtain a CDCL solver, which is easy to understand and change, while at the same time not being much slower than other state-of-the-art CDCL solvers.

homepage: https://github.com/arminbiere/cadical

version	toolchain
1.3.0	GCC/9.3.0

CAFE5

Software for Computational Analysis of gene Family Evolution The purpose of CAFE is to analyze changes in gene family size in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences. The program uses a birth and death process to model gene gain and loss across a user-specified phylogenetic tree. The distribution of family sizes generated under this model can provide a basis for assessing the significance of the observed family size differences among taxa.

homepage: https://github.com/hahnlab/CAFE5

version	toolchain
5.0.0	GCC/10.2.0

Caffe

Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (BVLC) and community contributors.

homepage: https://github.com/BVLC/caffe

version	versionsuffix	toolchain
1.0	-CUDA-9.1.85-Python-2.7.14	intel/2017b
1.0	-Python-2.7.13	intel/2017a
1.0	-Python-2.7.14	intel/2017b
rc3	-CUDA-7.5.18-Python-2.7.11	foss/2016a

cairo

Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB

homepage: https://cairographics.org

version	versionsuffix	toolchain
1.14.6		foss/2016a, foss/2016b, intel/2016a, intel/2016b
1.14.6	-GLib-2.48.0	foss/2016a, intel/2016a
1.14.8		intel/2017a
1.14.10		GCCcore/6.3.0, GCCcore/6.4.0, intel/2017b
1.14.12		GCCcore/6.4.0, GCCcore/7.3.0
1.16.0		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
1.17.4		GCCcore/11.3.0, GCCcore/12.2.0
1.17.8		GCCcore/12.3.0
1.18.0		GCCcore/13.2.0

cairomm

The Cairomm package provides a C++ interface to Cairo.

homepage: http://cairographics.org

version	toolchain
1.12.2	GCCcore/6.4.0, GCCcore/7.3.0
1.16.2	GCC/11.3.0

Calcam

Calcam is a Python package providing tools for spatial calibration of cameras, i.e. determining the mapping between pixel coordinates in an image and real-world 3D sight lines & coordinates.

homepage: https://euratom-software.github.io/calcam

version	versionsuffix	toolchain
2.1.0	-Python-2.7.14	intel/2018a
2.1.0	-Python-3.6.4	intel/2018a

CalculiX-CrunchiX

A Free Software Three-Dimensional Structural Finite Element Program

homepage: http://www.calculix.de

version	toolchain
2.20	foss/2021a, foss/2022b, foss/2023a

Calendrical

Calendrical module is for calendrical calculations.

homepage: https://www.funaba.org/code#calendrical

version	versionsuffix	toolchain
2.0.1	-Python-3.6.3	intel/2017b
2.0.2a	-Python-3.6.4	intel/2018a
2.0.2a	-Python-3.6.6	intel/2018b

Calib

Calib clusters paired-end reads using their barcodes and sequences. Calib is suitable for amplicon sequencing where a molecule is tagged, then PCR amplified with high depth, also known as Unique Molecule Identifier (UMI) sequencing.

homepage: https://github.com/vpc-ccg/calib

version	toolchain
0.3.4	GCC/9.3.0

CAMPARI

CAMPARI is a joint package for performing and analyzing molecular simulations, in particular of systems of biological relevance. It focuses on a wide availability of algorithms for (advanced) sampling and is capable of combining Monte Carlo and molecular dynamics in seamless fashion.

homepage: http://campari.sourceforge.net/V4/index.html

version	toolchain
4.0	intel/2020b

Cantera

Chemical kinetics, thermodynamics, and transport tool suite

homepage: https://github.com/Cantera/cantera

version	versionsuffix	toolchain
2.2.1	-Python-2.7.12	intel/2016b
2.3.0	-Python-2.7.12	foss/2016b, intel/2016b
2.3.0	-Python-2.7.13	intel/2017a
2.3.0	-Python-2.7.14	foss/2017b, intel/2017b, intel/2018a
2.4.0	-Python-2.7.14	intel/2018a
2.6.0		foss/2022a
3.0.0		foss/2023a

canu

Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing

homepage: https://canu.readthedocs.io

version	versionsuffix	toolchain
1.4		foss/2016b
1.7		intel/2018a
1.8	-Perl-5.26.0	foss/2017b, intel/2017b
1.8	-Perl-5.28.0	foss/2018b
1.8	-Perl-5.28.1	GCCcore/8.2.0
1.9	-Java-11	GCCcore/8.3.0
2.1.1		GCCcore/10.2.0
2.1.1	-Java-11	GCCcore/9.3.0
2.2		GCC/12.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0
2.2	-Java-11	GCCcore/10.3.0

Canvas

Copy number variant (CNV) calling from DNA sequencing data

homepage: https://github.com/Illumina/canvas

version	toolchain
1.39.0.1598	system

CAP3

CAP3 assembly program

homepage: http://seq.cs.iastate.edu/

version	toolchain
20071221-intel-x86	system
20071221-intel-x86_64	system
20071221-opteron	system

CapnProto

Cap’n Proto is an insanely fast data interchange format and capability-based RPC system.

homepage: https://capnproto.org

version	toolchain
0.6.1	GCCcore/6.4.0
0.7.0	GCCcore/7.3.0
0.8.0	GCCcore/9.3.0
0.9.1	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0
0.10.2	GCCcore/11.3.0
0.10.3	GCCcore/12.2.0
1.0.1	GCCcore/12.3.0
1.0.1.1	GCCcore/13.2.0

captum

Captum is a model interpretability and understanding library for PyTorch. Captum means comprehension in Latin and contains general purpose implementations of integrated gradients, saliency maps, smoothgrad, vargrad and others for PyTorch models. It has quick integration for models built with domain-specific libraries such as torchvision, torchtext, and others.

homepage: https://captum.ai/

version	versionsuffix	toolchain
0.5.0		foss/2022a
0.5.0	-CUDA-11.7.0	foss/2022a

Cargo

The Rust package manager

homepage: https://crates.io/

version	toolchain
0.13.0	foss/2016b

Carma

Carma - A molecular dynamics analysis program

homepage: http://utopia.duth.gr/~glykos/Carma.html

version	toolchain
2.01	foss/2019b

carputils

carputils is a Python framework for generating and running openCARP examples.

homepage: https://git.opencarp.org/openCARP/carputils

version	versionsuffix	toolchain
20200915	-Python-3.8.2	foss/2020a
20210513		foss/2020b

Cartopy

Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy.

homepage: https://scitools.org.uk/cartopy/docs/latest/

version	versionsuffix	toolchain
0.18.0	-Python-3.7.4	foss/2019b
0.18.0	-Python-3.8.2	foss/2020a
0.19.0.post1		foss/2020b, intel/2020b
0.20.0		foss/2021a
0.20.3		foss/2021b, foss/2022a
0.22.0		foss/2023a

CASA

CASA, the Common Astronomy Software Applications package, is the primary data processing software for the Atacama Large Millimeter/submillimeter Array (ALMA) and NSF's Karl G. Jansky Very Large Array (VLA), and is frequently used also for other radio telescopes. The CASA software can process data from both single-dish and aperture-synthesis telescopes, and one of its core functionalities is to support the data reduction and imaging pipelines for ALMA, VLA and the VLA Sky Survey (VLASS).

homepage: https://casa.nrao.edu/

version	versionsuffix	toolchain
6.5.5-21	-py3.8	system

casacore

A suite of C++ libraries for radio astronomy data processing. The ephemerides data needs to be in DATA_DIR and the location must be specified at runtime. Thus user's can update them.

homepage: https://github.com/casacore/casacore

version	toolchain
3.4.0	foss/2021b
3.5.0	foss/2022a, foss/2023b

Casanovo

De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model

homepage: https://casanovo.readthedocs.io

version	versionsuffix	toolchain
3.3.0		foss/2022a
3.3.0	-CUDA-11.7.0	foss/2022a

CaSpER

CaSpER is a signal processing approach for identification, visualization, and integrative analysis of focal and large-scale CNV events in multiscale resolution using either bulk or single-cell RNA sequencing data.

homepage: https://github.com/akdess/CaSpER

version	toolchain
2.0	foss/2019b

CASPR

Running CASPR is extremely easy and convenient to analyze CRIPR-Cas9 screens using pgRNAs.

homepage: https://judithbergada.github.io/CASPR

version	toolchain
20200730	foss/2022a

CASTEP

CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more.

homepage: http://www.castep.org

version	toolchain
21.1.1	CrayCCE/19.06, CrayGNU/19.06, foss/2019b, intel/2019b, iomkl/2019b
22.11	foss/2022a
23.1	foss/2023a

castor

Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format.

homepage: https://CRAN.R-project.org/package=castor

version	toolchain
1.7.11	foss/2022a

CastXML

CastXML is a C-family abstract syntax tree XML output tool.

homepage: https://github.com/CastXML/CastXML

version	toolchain
0.4.3	GCCcore/8.3.0
20160617	foss/2016a
20180806	foss/2018a

CAT-BAT

Tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs).

homepage: https://github.com/dutilh/CAT

version	toolchain
5.2.3	GCC/10.3.0

CatBoost

CatBoost is a high-performance open source library for gradient boosting on decision trees

homepage: https://catboost.ai

version	toolchain
1.2	gfbf/2023a

Catch2

A modern, C++-native, header-only, test framework for unit-tests, TDD and BDD - using C++11, C++14, C++17 and later (or C++03 on the Catch1.x branch)

homepage: https://github.com/catchorg/Catch2

version	toolchain
2.9.1	system
2.11.0	system
2.13.4	system
2.13.9	GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0, system

category_encoders

A set of scikit-learn-style transformers for encoding categorical variables into numeric by means of different techniques.

homepage: https://github.com/scikit-learn-contrib/category_encoders

version	toolchain
2.4.1	foss/2021b

CatLearn

An environment for atomistic machine learning in Python for applications in catalysis

homepage: https://catlearn.readthedocs.io

version	toolchain
0.6.2	intel/2022a

CatMAP

Catalyst Micro-kinetic Analysis Package for automated creation of micro-kinetic models used in catalyst screening.

homepage: https://catmap.readthedocs.io

version	versionsuffix	toolchain
20170927	-Python-2.7.14	intel/2017b
20220519		foss/2022a

causallift

CausalLift: Python package for Uplift Modeling in real-world business; applicable for both A/B testing and observational data

homepage: https://github.com/Minyus/causallift

version	versionsuffix	toolchain
1.0.6	-Python-3.8.2	foss/2020a

causalml

Causal ML: A Python Package for Uplift Modeling and Causal Inference with ML

homepage: https://github.com/uber/causalml

version	versionsuffix	toolchain
0.3.0-20180610	-Python-3.7.2	foss/2019a
0.8.0-20200909	-Python-3.8.2	foss/2020a

CaVEMan

SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib

homepage: http://cancerit.github.io/CaVEMan/

version	toolchain
1.13.2	foss/2018a

CAVIAR

CAusal Variants Identication in Associated Regions. A statistical framework that quantifies the probability of each variant to be causal while allowing an arbitrary number of causal variants.

homepage: https://github.com/fhormoz/caviar

version	toolchain
2.2-20190419	foss/2019b

Cbc

Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming solver written in C++. It can be used as a callable library or using a stand-alone executable.

homepage: https://github.com/coin-or/Cbc

version	toolchain
2.10.3	foss/2018b
2.10.5	foss/2020b, foss/2021a, foss/2022b
2.10.11	foss/2023a

CBLAS

C interface to the BLAS

homepage: https://www.netlib.org/blas/

version	toolchain
20110120	foss/2016b, intel/2019b, intel/2020a

ccache

Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by caching previous compilations and detecting when the same compilation is being done again

homepage: https://ccache.dev/

version	versionsuffix	toolchain
3.2.5		system
3.3.1		system
3.3.3		system
3.3.4	-f90	system
3.7.11		system
4.2.1		system
4.6.1		GCCcore/11.2.0
4.6.3		GCCcore/11.3.0, system
4.7.5		system
4.8.3		system
4.9		GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

CCfits

CCfits is an object oriented interface to the cfitsio library. It is designed to make the capabilities of cfitsio available to programmers working in C++.

homepage: https://heasarc.gsfc.nasa.gov/fitsio/CCfits/

version	toolchain
2.5	GCCcore/9.3.0

CCL

Clozure CL (often called CCL for short) is a free Common Lisp implementation with a long history. Some distinguishing features of the implementation include fast compilation speed, native threads, a precise, generational, compacting garbage collector, and a convenient foreign-function interface.

homepage: https://ccl.clozure.com/

version	toolchain
1.11.5	system
1.12	GCCcore/9.3.0
1.12.1	GCCcore/10.3.0
1.12.2	GCCcore/11.3.0, GCCcore/12.3.0, GCCcore/13.2.0

cclib

cclib is a Python library that provides parsers for computational chemistry log files. It also provides a platform to implement algorithms in a package-independent manner.

homepage: https://cclib.github.io/

version	versionsuffix	toolchain
1.5	-Python-3.5.2	foss/2016b
1.6.3	-Python-3.8.2	foss/2020a, intel/2020a
1.7.2		foss/2021b
1.8		foss/2023a

cctbx-base

The Computational Crystallography Toolbox (cctbx) is being developed as the open source component of the Phenix project. The goal of the Phenix project is to advance automation of macromolecular structure determination. Phenix depends on the cctbx, but not vice versa. This hierarchical approach enforces a clean design as a reusable library. The cctbx is therefore also useful for small-molecule crystallography and even general scientific applications.

homepage: https://github.com/cctbx/cctbx_project

version	toolchain
2020.8	foss/2020b, fosscuda/2020b

cctools

The Cooperating Computing Tools (CCTools) help you to design and deploy scalable applications that run on hundreds or thousands of machines at once.

homepage: https://ccl.cse.nd.edu/

version	toolchain
7.0.22	GCCcore/8.3.0

CD-HIT

CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.

homepage: https://github.com/weizhongli/cdhit

version	versionsuffix	toolchain
4.6.4	-2015-0603	GNU/4.9.3-2.25
4.6.6		foss/2016b
4.6.8		foss/2018b, intel/2017a, intel/2018a
4.8.1		GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/11.3.0, GCC/12.2.0, GCC/8.3.0, GCC/9.3.0, foss/2018b, iccifort/2019.5.281

CDAT

CDAT is a powerful and complete front-end to a rich set of visual-data exploration and analysis capabilities well suited for data analysis problems.

homepage: https://github.com/CDAT/cdat

version	versionsuffix	toolchain
8.2.1	-Python-3.8.2	foss/2020a

cdbfasta

Fasta file indexing and retrival tool

homepage: https://sourceforge.net/projects/cdbfasta

version	toolchain
0.99	GCC/8.3.0, iccifort/2019.1.144-GCC-8.2.0-2.31.1, iccifort/2019.5.281

CDBtools

CDB (Constant DataBase) indexing and retrieval tools for FASTA files

homepage: http://compbio.dfci.harvard.edu/tgi

version	toolchain
0.99	GCC/10.2.0, GCC/11.3.0

cddlib

An efficient implementation of the Double Description Method

homepage: https://github.com/cddlib/cddlib

version	toolchain
0.94i	GCCcore/8.2.0
0.94j	GCCcore/8.3.0
0.94m	GCCcore/11.3.0

CDFlib

cdflib is a python module to read/write CDF (Common Data Format .cdf) files without needing to install the CDF NASA library.

homepage: https://github.com/MAVENSDC/cdflib

version	toolchain
0.4.9	foss/2022a

cDNA_Cupcake

cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data.

homepage: https://github.com/Magdoll/cDNA_Cupcake

version	versionsuffix	toolchain
5.8	-Python-2.7.14	intel/2018a
24.2.0	-Python-3.8.2	foss/2020a
26.0.0		foss/2021a

CDO

CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.

homepage: https://code.zmaw.de/projects/cdo

version	toolchain
1.7.2	intel/2016b
1.8.1	intel/2017a
1.9.1	intel/2017b
1.9.2	intel/2017b
1.9.5	intel/2018a, intel/2018b, iomkl/2018b
1.9.8	intel/2019b
1.9.10	gompi/2019b, gompi/2020b, gompi/2021a, iimpi/2021b
2.0.5	gompi/2021b
2.0.6	gompi/2022a
2.1.1	gompi/2021a
2.2.2	gompi/2023a, gompi/2023b

cdo-bindings

Python interface to CDO.

homepage: https://github.com/Try2Code/cdo-bindings

version	toolchain
1.5.7	foss/2021b
1.6.0	foss/2022a

cdsapi

Climate Data Store API

homepage: https://pypi.org/project/cdsapi

version	versionsuffix	toolchain
0.1.4		foss/2019a
0.1.4	-Python-3.6.6	foss/2018b
0.3.0		GCCcore/9.3.0
0.5.1		GCCcore/11.3.0

cell2location

Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)

homepage: https://github.com/BayraktarLab/cell2location/

version	toolchain
0.05-alpha	fosscuda/2020b

CellBender

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

homepage: http://github.com/broadinstitute/CellBender

version	versionsuffix	toolchain
0.2.1	-CUDA-11.3.1	foss/2021a
0.2.2		foss/2022a
0.3.1		foss/2022a
0.3.1	-CUDA-11.7.0	foss/2022a

CellChat

" R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

homepage: https://github.com/sqjin/CellChat

version	toolchain
1.5.0	foss/2022a

CellMix

A Comprehensive Toolbox for Gene Expression Deconvolution

homepage: http://web.cbio.uct.ac.za/~renaud/CRAN/web/CellMix

version	versionsuffix	toolchain
1.6.2	-R-3.5.1	foss/2018b

CellOracle

CellOracle is a Python library for in silico gene perturbation analyses using single-cell omics data and Gene Regulatory Network models.

homepage: https://github.com/morris-lab/CellOracle

version	toolchain
0.12.0	foss/2022a

Cellpose

a generalist algorithm for cellular segmentation

homepage: https://www.cellpose.org

version	versionsuffix	toolchain
0.6.5		foss/2020b, fosscuda/2020b
2.2.2		foss/2022a
2.2.2	-CUDA-11.7.0	foss/2022a

CellRanger

Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.

homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger

version	toolchain
3.0.0	system
3.0.2	system
3.1.0	system
4.0.0	system
5.0.0	system
5.0.1	system
6.0.0	system
6.0.1	system
6.0.2	system
6.1.2	system
7.0.0	system
7.1.0	system
7.2.0	system

CellRanger-ARC

Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a variety of analyses pertaining to gene expression, chromatin accessibility and their linkage. Furthermore, since the ATAC and gene expression measurements are on the very same cell, we are able to perform analyses that link chromatin accessibility and gene expression.

homepage: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc

version	toolchain
1.0.1	system
2.0.0	system
2.0.1	system

CellRanger-ATAC

Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data.

homepage: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac

version	toolchain
1.2.0	system
2.0.0	system
2.1.0	system

CellRank

CellRank is a toolkit to uncover cellular dynamics based on Markov state modeling of single-cell data. It contains two main modules: kernels compute cell-cell transition probabilities and estimators generate hypothesis based on these.

homepage: https://cellrank.readthedocs.io/en/stable/

version	toolchain
1.4.0	foss/2021a

CellTypist

A tool for semi-automatic cell type annotation

homepage: https://www.celltypist.org/

version	toolchain
1.0.0	foss/2021b
1.6.2	foss/2023a

CENSO

Commandline Energetic SOrting (CENSO) is a sorting algorithm for efficient evaluation of Structure Ensembles (SE). The input ensemble (or single structure) originating from a CREST[SQM/FF] run can be ranked by free energy at DFT level and/or geometries can be optimized using DFT.

homepage: https://xtb-docs.readthedocs.io/en/latest/CENSO_docs/censo.html

version	toolchain
1.2.0	GCCcore/12.3.0, intel/2022a

centerline

Roads, rivers and similar linear structures are often represented by long and complex polygons. Since one of the most important attributes of a linear structure is its length, extracting that attribute from a polygon can prove to be more or less difficult. This library tries to solve this problem by creating the the polygon's centerline using the Voronoi diagram. For more info on how to use this package, see the official documentation.

homepage: https://github.com/fitodic/centerline

version	toolchain
1.0.1	foss/2022a

Centrifuge

Classifier for metagenomic sequences

homepage: https://ccb.jhu.edu/software/centrifuge

version	toolchain
1.0.3	foss/2018b
1.0.4	gompi/2020b, gompi/2021a
1.0.4-beta	foss/2018b, gompi/2020a

Cereal

cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone.

homepage: https://uscilab.github.io/cereal/

version	toolchain
1.3.0	system
1.3.2	GCCcore/12.2.0, system

CESM-deps

CESM is a fully-coupled, community, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states.

homepage: https://www.cesm.ucar.edu/models/cesm2/

version	toolchain
2	foss/2018b, foss/2021b, foss/2022a, intel/2018b, iomkl/2018b

CFDEMcoupling

CFDEMcoupling is an open source CFD-DEM engine. It provides the possibility to couple the DEM engine LIGGGHTS to a CFD framework.

homepage: https://www.cfdem.com/cfdemrcoupling-open-source-cfd-dem-framework

version	toolchain
3.8.0	foss/2018a, foss/2019b

cffi

C Foreign Function Interface for Python. Interact with almost any C code from Python, based on C-like declarations that you can often copy-paste from header files or documentation.

homepage: https://cffi.readthedocs.io/en/latest/

version	toolchain
1.15.1	GCCcore/11.3.0, GCCcore/12.3.0, GCCcore/13.2.0

CFITSIO

CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.

homepage: https://heasarc.gsfc.nasa.gov/fitsio/

version	toolchain
3.38	foss/2016a, intel/2016a
3.41	GCCcore/5.4.0, GCCcore/6.3.0, intel/2016b
3.42	GCCcore/6.4.0, intel/2017b
3.45	GCCcore/7.3.0, intel/2018b
3.47	GCCcore/8.2.0, GCCcore/8.3.0
3.48	GCCcore/9.3.0
3.49	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0
4.2.0	GCCcore/11.3.0, GCCcore/12.2.0
4.3.0	GCCcore/12.3.0
4.3.1	GCCcore/13.2.0

cftime

Time-handling functionality from netcdf4-python

homepage: https://github.com/Unidata/cftime

version	versionsuffix	toolchain
1.0.0	-Python-3.6.4	intel/2018a
1.0.0b1	-Python-3.6.2	foss/2017b
1.0.1	-Python-2.7.15	intel/2018b
1.0.1	-Python-3.6.6	foss/2018b, intel/2018b

CGAL

The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library.

homepage: https://www.cgal.org/

version	versionsuffix	toolchain
4.8	-Python-2.7.11	foss/2016a, intel/2016a
4.8.1		foss/2016b, intel/2016b
4.8.1	-Python-2.7.12	foss/2016b, intel/2016b
4.9	-Python-2.7.12	intel/2016b
4.9	-Python-2.7.13	intel/2017a
4.11	-Python-2.7.13	intel/2017a
4.11	-Python-2.7.14	foss/2017b, intel/2017b
4.11	-Python-3.6.3	foss/2017b, intel/2017b
4.11.1	-Python-2.7.14	foss/2018a, intel/2018a
4.11.1	-Python-2.7.15	foss/2018b
4.11.1	-Python-3.6.4	foss/2018a
4.11.1	-Python-3.6.6	foss/2018b
4.14	-Python-3.7.2	foss/2019a, intel/2019a
4.14.1	-Python-2.7.16	foss/2019b
4.14.1	-Python-3.7.4	foss/2019b, intel/2019b
4.14.3		gompi/2021a, gompi/2021b, gompi/2022a, iimpi/2021a
4.14.3	-Python-3.8.2	gompi/2020a, iimpi/2020a
5.2		gompi/2020b
5.5.2		GCCcore/12.2.0
5.6		GCCcore/12.3.0

cget

Cmake package retrieval. This can be used to download and install cmake packages

homepage: https://cget.readthedocs.io/en/latest/index.html

version	versionsuffix	toolchain
0.1.6	-Python-3.6.4	foss/2018a

Cgl

The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that can be used with other COIN-OR packages that make use of cuts, such as, among others, the linear solver Clp or the mixed integer linear programming solvers Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or communicate with a solver. It does not directly call a solver.

homepage: https://github.com/coin-or/Cgl

version	toolchain
0.60.2	foss/2018b
0.60.3	foss/2020b, foss/2021a
0.60.7	foss/2022b
0.60.8	foss/2023a

CGmapTools

Command-line Toolset for Bisulfite Sequencing Data Analysis

homepage: https://cgmaptools.github.io/

version	toolchain
0.1.2	intel/2019b

CGNS

The CGNS system is designed to facilitate the exchange of data between sites and applications, and to help stabilize the archiving of aerodynamic data.

homepage: https://cgns.github.io/

version	toolchain
3.3.1	foss/2016b
4.1.0	intelcuda/2019b

CharLS

CharLS is a C++ implementation of the JPEG-LS standard for lossless and near-lossless image compression and decompression. JPEG-LS is a low-complexity image compression standard that matches JPEG 2000 compression ratios.

homepage: https://github.com/team-charls/charls

version	toolchain
2.0.0	GCCcore/6.4.0, GCCcore/7.3.0
2.1.0	GCCcore/8.2.0, GCCcore/8.3.0
2.2.0	GCCcore/10.2.0
2.3.4	GCCcore/10.3.0
2.4.1	GCCcore/11.3.0
2.4.2	GCCcore/12.2.0

CHASE

Case-control HAplotype Sharing analyses. Haplotype sharing analyses for genome-wide association studies.

homepage: http://people.duke.edu/~asallen/Software.html

version	toolchain
20130626	system

Check

Check is a unit testing framework for C. It features a simple interface for defining unit tests, putting little in the way of the developer. Tests are run in a separate address space, so both assertion failures and code errors that cause segmentation faults or other signals can be caught. Test results are reportable in the following: Subunit, TAP, XML, and a generic logging format.

homepage: https://libcheck.github.io/check/

version	toolchain
0.12.0	GCCcore/6.4.0
0.15.2	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/13.2.0, GCCcore/9.3.0

CheckM

CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.

homepage: https://github.com/Ecogenomics/CheckM

version	versionsuffix	toolchain
1.0.13	-Python-2.7.14	foss/2017b, intel/2017b
1.0.13	-Python-2.7.15	foss/2018b
1.0.13	-Python-3.6.3	foss/2017b, intel/2017b
1.0.18	-Python-2.7.15	foss/2019a
1.0.18	-Python-2.7.18	foss/2020b
1.1.2	-Python-3.7.4	foss/2019b, intel/2019b
1.1.3		foss/2021a, foss/2021b
1.1.3	-Python-3.8.2	intel/2020a
1.2.2		foss/2022a

CheckM-Database

CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. This is the corresponding database.

homepage: https://github.com/Ecogenomics/CheckM

version	toolchain
2015_01_16	system

Cheetah

Cheetah is an open source template engine and code generation tool.

homepage: https://cheetahtemplate.org

version	versionsuffix	toolchain
2.4.4	-Python-2.7.15	intel/2018b

Chemaxon-Marvin

Marvin suite is a chemically intelligent desktop toolkit built to help you draw, edit, publish, render, import and export your chemical structures and as well as allowing you to convert between various chemical and graphical file formats. It is free for individual, academic and non-commercial use.

homepage: https://chemaxon.com/marvin

version	toolchain
21.14	system
23.9	system

chemprop

Message Passing Neural Networks for Molecule Property Prediction

homepage: https://github.com/chemprop/chemprop

version	versionsuffix	toolchain
1.5.2		foss/2022a
1.5.2	-CUDA-11.7.0	foss/2022a

CheMPS2

CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry.

homepage: https://github.com/SebWouters/CheMPS2

version	toolchain
1.6	intel/2016a
1.7-rc2	intel/2016a
1.7.1	intel/2016a
1.7.2	intel/2016a
1.8	intel/2016b
1.8.8	intel/2018b
1.8.9	foss/2018b, foss/2019a, intel/2018b, intel/2019a, intel/2019b
1.8.11	foss/2021b
1.8.12	foss/2022a, foss/2022b

CHERAB

CHERAB is a python library for forward modelling diagnostics based on spectroscopic plasma emission.

homepage: https://cherab.github.io/documentation/index.html

version	versionsuffix	toolchain
1.2.0	-Python-3.6.6	intel/2018b
1.3.0		foss/2020b, intel/2020b
1.4.0		foss/2020b, intel/2020b

chewBBACA

chewBBACA stands for "BSR-Based Allele Calling Algorithm". chewBBACA is a comprehensive pipeline including a set of functions for the creation and validation of whole genome and core genome MultiLocus Sequence Typing (wg/cgMLST) schemas, providing an allele calling algorithm based on Blast Score Ratio that can be run in multiprocessor settings and a set of functions to visualize and validate allele variation in the loci.

homepage: https://github.com/B-UMMI/chewBBACA

version	versionsuffix	toolchain
2.5.5	-Python-3.8.2	intel/2020a

chi2comb

Cumulative density function of linear combinations of independent chi-square random variables and a standard Normal distribution. As of now, this is basically a repackaging of the davies function implemented in the CompQuadForm library for R.

homepage: https://github.com/limix/chi2comb

version	toolchain
0.0.3	GCCcore/7.3.0

Chimera

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.

homepage: https://www.cgl.ucsf.edu/chimera/

version	versionsuffix	toolchain
1.10	-linux_x86_64	system
1.16	-linux_x86_64	system

ChimPipe

ChimPipe is a computational method for the detection of novel transcription-induced chimeric transcripts and fusion genes from Illumina Paired-End RNA-seq data. It combines junction spanning and paired-end read information to accurately detect chimeric splice junctions at base-pair resolution.

homepage: https://chimpipe.readthedocs.org/

version	versionsuffix	toolchain
0.9.5		foss/2018b
0.9.5	-Python-2.7.12	foss/2016b

ChIPseeker

This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database.

homepage: https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html

version	versionsuffix	toolchain
1.32.1	-R-4.2.1	foss/2022a

Chromaprint

Chromaprint is the core component of the AcoustID project. It's a client-side library that implements a custom algorithm for extracting fingerprints from any audio source.

homepage: https://acoustid.org/chromaprint

version	toolchain
1.4.3	GCCcore/8.2.0

cicero

Cicero is an R package that provides tools for analyzing single-cell chromatin accessibility experiments.

homepage: https://cole-trapnell-lab.github.io/cicero-release

version	versionsuffix	toolchain
1.3.4.11	-R-4.0.3-Monocle3	foss/2020b
1.3.8	-R-4.2.1-Monocle3	foss/2022a

CIF2Cell

CIF2Cell is a tool to generate the geometrical setup for various electronic structure codes from a CIF (Crystallographic Information Framework) file. The program currently supports output for a number of popular electronic structure programs, including ABINIT, ASE, CASTEP, CP2K, CPMD, CRYSTAL09, Elk, EMTO, Exciting, Fleur, FHI-aims, Hutsepot, MOPAC, Quantum Espresso, RSPt, Siesta, SPR-KKR, VASP. Also exports some related formats like .coo, .cfg and .xyz-files.

homepage: https://sourceforge.net/projects/cif2cell

version	versionsuffix	toolchain
1.2.10	-Python-2.7.16	GCCcore/8.3.0

cimfomfa

This library supports both MCL, a cluster algorithm for graphs, and zoem, a macro/DSL language. It supplies abstractions for memory management, I/O, associative arrays, strings, heaps, and a few other things. The string library has had heavy testing as part of zoem. Both understandably and regrettably I chose long ago to make it C-string-compatible, hence nul bytes may not be part of a string. At some point I hope to rectify this, perhaps unrealistically.

homepage: https://github.com/micans/cimfomfa

version	toolchain
22.273	GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.3.0

CIRCexplorer

CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset.

homepage: https://circexplorer2.readthedocs.io/

version	versionsuffix	toolchain
1.1.10	-Python-2.7.14	intel/2017b

CIRCexplorer2

CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset.

homepage: http://circexplorer2.readthedocs.io/

version	versionsuffix	toolchain
2.3.2	-Python-2.7.14	intel/2017b
2.3.3	-Python-2.7.14	intel/2018a
2.3.8	-Python-2.7.18	foss/2020b, foss/2021b

Circlator

A tool to circularize genome assemblies.s

homepage: https://github.com/sanger-pathogens/circlator/

version	toolchain
1.5.5	foss/2023a

Circos

Circos is a software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions.

homepage: http://www.circos.ca/

version	versionsuffix	toolchain
0.69-5	-Perl-5.24.0	foss/2016b
0.69-6	-Perl-5.26.1	GCCcore/6.4.0
0.69-6	-Perl-5.28.0	GCCcore/7.3.0
0.69-9		GCCcore/11.3.0, GCCcore/9.3.0

Circuitscape

Algorithms from circuit theory to predict connectivity in heterogeneous landscapes

homepage: https://github.com/Circuitscape/Circuitscape.jl

version	versionsuffix	toolchain
5.12.3	-Julia-1.7.2	system
5.12.3	-Julia-1.9.2	system

CIRI

CircRNA Identifier. A de novo circular RNA identification tool

homepage: https://sourceforge.net/projects/ciri/

version	versionsuffix	toolchain
2.0.6	-Perl-5.26.0	intel/2017b

CIRI-long

Circular RNA Identification for Long-Reads Nanopore Sequencing Data

homepage: https://github.com/bioinfo-biols/CIRI-long/

version	toolchain
1.0.2	foss/2020b

CIRIquant

CIRIquant is a comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data

homepage: https://github.com/bioinfo-biols/CIRIquant

version	versionsuffix	toolchain
1.1.2-20221201	-Python-2.7.18	foss/2021b

cisTEM

cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.

homepage: https://cistem.org/

version	toolchain
1.0.0-beta	foss/2018a

CITE-seq-Count

A python package that allows to count antibody TAGS from a CITE-seq and/or cell hashing experiment.

homepage: https://github.com/Hoohm/CITE-seq-Count

version	versionsuffix	toolchain
1.4.3	-Python-3.6.6	foss/2018b
1.4.3	-Python-3.7.4	foss/2019b

Clair3

Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.

homepage: https://github.com/HKU-BAL/Clair3

version	toolchain
1.0.4	foss/2022a

Clang

C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.

homepage: https://clang.llvm.org/

version	versionsuffix	toolchain
3.3		GCC/4.8.1
3.4		GCC/4.8.2
3.4.1		GCC/4.8.2
3.4.2		GCC/4.8.2
3.6.0		GCC/4.9.2
3.6.1		GCC/4.9.2
3.7.0		GNU/4.9.3-2.25
3.7.1		GCC/4.9.3-2.25, foss/2016a
3.8.0		GCC/4.9.3-2.25
3.8.1		GCC/5.4.0-2.26, foss/2016b
5.0.0		GCC/6.4.0-2.28
5.0.1		GCC/6.4.0-2.28
6.0.1		GCC/6.4.0-2.28, GCC/7.3.0-2.30
7.0.0		GCC/6.4.0-2.28
7.0.1		GCC/7.3.0-2.30
8.0.0		GCCcore/8.2.0
8.0.0	-CUDA-10.1.105	GCCcore/8.2.0
8.0.1	-CUDA-10.1.105	GCC/8.2.0-2.31.1
8.0.1	-CUDA-10.1.243	GCC/8.3.0
9.0.1		GCCcore/8.3.0, GCCcore/9.3.0
9.0.1	-CUDA-10.1.243	GCC/8.3.0
10.0.0		GCCcore/8.3.0, GCCcore/9.3.0
10.0.1		GCCcore/9.3.0
11.0.0		GCCcore/9.3.0
11.0.1		GCCcore/10.2.0, gcccuda/2020b
12.0.1		GCCcore/10.3.0, GCCcore/11.2.0
12.0.1	-CUDA-11.3.1	GCCcore/10.3.0
13.0.1		GCCcore/11.2.0, GCCcore/11.3.0
13.0.1	-CUDA-11.4.1	GCCcore/11.2.0
13.0.1	-CUDA-11.7.0	GCCcore/11.3.0
15.0.5		GCCcore/11.3.0
16.0.4		GCCcore/12.2.0
16.0.6		GCCcore/12.3.0
16.0.6	-CUDA-12.1.1	GCCcore/12.3.0

Clang-AOMP

AOMP is an open source Clang/LLVM based compiler with added support for the OpenMP® API on Radeon™ GPUs.

homepage: https://github.com/RadeonOpenCompute/llvm-project

version	toolchain
4.5.0	GCCcore/11.2.0

Clang-Python-bindings

Python bindings for libclang

homepage: https://clang.llvm.org

version	versionsuffix	toolchain
8.0.0	-Python-2.7.15	GCCcore/8.2.0
10.0.1	-Python-3.8.2	GCCcore/9.3.0
13.0.1		GCCcore/11.2.0, GCCcore/11.3.0
16.0.6		GCCcore/12.3.0

CLAPACK

C version of LAPACK

homepage: http://www.netlib.org/clapack

version	toolchain
3.2.1	GCC/6.4.0-2.28, iccifort/2017.4.196-GCC-6.4.0-2.28, intel/2017a

Clarabel.rs

Interior-point solver for convex conic optimisation problems in Rust.

homepage: https://github.com/oxfordcontrol/Clarabel.rs

version	toolchain
0.7.1	gfbf/2023a

CLEAR

Direct comparison of circular and linear RNA expression

homepage: https://github.com/YangLab/CLEAR

version	versionsuffix	toolchain
20210117	-Python-2.7.18	foss/2021b

CLEASE

CLuster Expansion in Atomic Simulation Environment (CLEASE) is a package that automates the cumbersome setup and construction procedure of cluster expansion (CE). It provides a comprehensive list of tools for specifying parameters for CE, generating training structures, fitting effective cluster interaction (ECI) values and running Monte Carlo simulations.

homepage: https://gitlab.com/computationalmaterials/clease

version	toolchain
0.10.6	intel/2021a

CLHEP

The CLHEP project is intended to be a set of HEP-specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra. CLHEP is structured in a set of packages independent of any external package.

homepage: https://proj-clhep.web.cern.ch/proj-clhep/

version	toolchain
2.1.1.0	intel/2016a
2.1.3.1	intel/2016a
2.2.0.8	intel/2016a
2.3.1.1	intel/2016a
2.3.4.3	foss/2017b, intel/2017b
2.4.0.0	intel/2017b
2.4.1.0	foss/2017b, foss/2018b, intel/2017b, intel/2018b
2.4.1.3	foss/2019b, foss/2020a
2.4.4.0	GCC/10.2.0, GCC/11.2.0
2.4.5.1	GCC/11.2.0
2.4.5.3	GCC/11.3.0
2.4.6.2	GCC/11.3.0
2.4.6.4	GCC/12.2.0

CliMetLab

CliMetLab is a Python package aiming at simplifying access to climate and meteorological datasets, allowing users to focus on science instead of technical issues such as data access and data formats. It is mostly intended to be used in Jupyter notebooks, and be interoperable with all popular data analytic packages, such as Numpy, Pandas, Xarray, SciPy, Matplotlib, etc. as well as machine learning frameworks, such as Tensorflow, Keras or PyTorch.

homepage: https://climetlab.readthedocs.io/

version	toolchain
0.12.6	foss/2022a

CLIP

CLIP (Contrastive Language-Image Pre-Training) is a neural network trained on a variety of (image, text) pairs. It can be instructed in natural language to predict the most relevant text snippet, given an image, without directly optimizing for the task, similarly to the zero-shot capabilities of GPT-2 and 3.

homepage: https://github.com/openai/CLIP

version	versionsuffix	toolchain
20230220	-CUDA-11.7.0	foss/2022a

cliquer

Cliquer is a set of C routines for finding cliques in an arbitrary weighted graph. It uses an exact branch-and-bound algorithm developed by Patric Ostergard. It is designed with the aim of being efficient while still being flexible and easy to use.

homepage: https://users.aalto.fi/~pat/cliquer.html

version	toolchain
1.21	GCCcore/11.3.0

CLISP

Common Lisp is a high-level, general-purpose, object-oriented, dynamic, functional programming language.

homepage: https://clisp.sourceforge.io/

version	toolchain
2.49	GCCcore/6.4.0, GCCcore/9.3.0

ClonalFrameML

Efficient Inference of Recombination in Whole Bacterial Genomes

homepage: https://github.com/xavierdidelot/ClonalFrameML

version	toolchain
1.11	foss/2016b

CLooG

CLooG is a free software and library to generate code for scanning Z-polyhedra. That is, it finds a code (e.g. in C, FORTRAN...) that reaches each integral point of one or more parameterized polyhedra. CLooG has been originally written to solve the code generation problem for optimizing compilers based on the polytope model. Nevertheless it is used now in various area e.g. to build control automata for high-level synthesis or to find the best polynomial approximation of a function. CLooG may help in any situation where scanning polyhedra matters. While the user has full control on generated code quality, CLooG is designed to avoid control overhead and to produce a very effective code.

homepage: http://www.bastoul.net/cloog/index.php

version	toolchain
0.18.1	GCC/4.8.2

CloudCompare

3D point cloud and mesh processing software

homepage: https://www.cloudcompare.org/

version	toolchain
2.12.4	foss/2021b

Clp

Clp (Coin-or linear programming) is an open-source linear programming solver. It is primarily meant to be used as a callable library, but a basic, stand-alone executable version is also available.

homepage: https://github.com/coin-or/Clp

version	toolchain
1.17.3	foss/2018b
1.17.6	foss/2020b, foss/2021a
1.17.7	foss/2021b
1.17.8	foss/2022b
1.17.9	foss/2023a

Clustal-Omega

Clustal Omega is a multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms

homepage: http://www.clustal.org/omega/

version	toolchain
1.2.0	foss/2016b
1.2.4	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/8.3.0, foss/2018b, intel-compilers/2021.2.0, intel/2018a, intel/2018b

ClustalW2

ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.

homepage: https://www.ebi.ac.uk/Tools/msa/clustalw2/

version	toolchain
2.1	GCC/10.3.0, GCC/11.2.0, GCC/12.3.0, foss/2016b, foss/2018b, foss/2021a, iccifort/2019.1.144-GCC-8.2.0-2.31.1, intel/2017b, intel/2018b, intel/2020a

Cluster-Buster

Cluster-Buster is a program for finding interesting functional regions, such as transcriptional enhancers, in DNA sequences.

homepage: https://github.com/weng-lab/cluster-buster

version	toolchain
20160106	intel/2016a
20200507	GCC/12.2.0

ClusterShell

ClusterShell is an event-driven open source Python library, designed to run local or distant commands in parallel on server farms or on large Linux clusters.

homepage: https://cea-hpc.github.io/clustershell/

version	toolchain
1.7.3	system

CMake

CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.

homepage: https://www.cmake.org

version	toolchain
2.8.11	GCC/4.8.1
2.8.12	GCC/4.8.1, GCC/4.8.2
3.0.0	GCC/4.8.3
3.1.0	GCC/4.9.2
3.1.3	GCC/4.9.2, system
3.2.1	GCC/4.9.2, GNU/4.9.3-2.25
3.3.1	system
3.3.2	GNU/4.9.3-2.25, gimkl/2.11.5
3.4.1	GCC/4.9.2, GCCcore/4.9.3, foss/2016a, intel/2016.02-GCC-4.9, intel/2016a, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25
3.4.3	foss/2016a, foss/2016b, gimkl/2.11.5, intel/2016a
3.5.1	intel/2016a
3.5.2	GCC/4.9.3-2.25, foss/2016a, foss/2016b, intel/2016a, intel/2016b, system
3.6.1	GCC/5.4.0-2.26, GCCcore/4.9.3, foss/2016b, intel/2016b, system
3.6.2	GCCcore/5.4.0, foss/2016b, intel/2016b
3.7.1	GCCcore/5.4.0, GCCcore/6.2.0, foss/2016b, intel/2016b
3.7.2	GCCcore/6.3.0, foss/2016b, intel/2016b
3.8.0	GCCcore/6.3.0
3.8.1	GCCcore/6.3.0
3.8.2	GCCcore/6.3.0
3.9.1	GCCcore/6.3.0, GCCcore/6.4.0, system
3.9.4	GCCcore/6.4.0
3.9.5	GCCcore/6.4.0
3.9.6	system
3.10.0	GCCcore/6.4.0
3.10.1	GCCcore/6.4.0
3.10.2	GCCcore/6.4.0, GCCcore/7.2.0
3.10.3	GCCcore/6.4.0, GCCcore/7.2.0
3.11.1	GCCcore/6.4.0
3.11.4	GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.3.0
3.12.1	GCCcore/6.4.0, GCCcore/7.2.0, GCCcore/7.3.0, system
3.13.3	GCCcore/8.2.0
3.15.1	system
3.15.3	GCCcore/8.3.0
3.16.4	GCCcore/9.3.0
3.18.4	GCCcore/10.2.0, system
3.20.1	GCCcore/10.2.0, GCCcore/10.3.0
3.21.1	GCCcore/11.2.0
3.22.1	GCCcore/11.2.0
3.23.1	GCCcore/11.3.0
3.24.3	GCCcore/11.3.0, GCCcore/12.2.0
3.26.3	GCCcore/12.3.0, GCCcore/13.1.0
3.27.6	GCCcore/13.2.0

CMAverse

The R package CMAverse provides a suite of functions for reproducible causal mediation analysis including cmdag for DAG visualization, cmest for statistical modeling and cmsens for sensitivity analysis.

homepage: https://bs1125.github.io/CMAverse/

version	toolchain
20220112	foss/2021b

CmdStanR

CmdStanR is a lightweight interface to Stan for R users

homepage: https://mc-stan.org/cmdstanr

version	versionsuffix	toolchain
0.5.0	-R-4.1.2	foss/2021b
0.5.2	-R-4.2.1	foss/2022a
0.7.1	-R-4.3.2	foss/2023a

cmocean

This package contains colormaps for commonly-used oceanographic variables. Most of the colormaps started from matplotlib colormaps, but have now been adjusted using the viscm tool to be perceptually uniform.

homepage: https://github.com/matplotlib/cmocean

version	toolchain
2.0	foss/2022a

CMSeq

CMSeq is a set of commands to provide an interface to .bam files for coverage and sequence consensus.

homepage: https://github.com/SegataLab/cmseq/

version	versionsuffix	toolchain
1.0.3	-Python-3.8.2	foss/2020a
1.0.4		foss/2022a

CNT-ILP

Integer Linear Program for the Copy-Number Tree Problem

homepage: https://compbio.cs.brown.edu/projects/cnt-ilp/

version	toolchain
20171031	GCC/8.2.0-2.31.1

CNVkit

A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing.

homepage: https://github.com/etal/cnvkit

version	versionsuffix	toolchain
0.9.2	-Python-2.7.14	intel/2017b
0.9.3	-Python-3.6.4	intel/2018a
0.9.6	-Python-3.7.2-R-3.6.0	foss/2019a
0.9.8	-R-4.0.3	foss/2020b
0.9.10	-R-4.2.2	foss/2022b

CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads

homepage: https://github.com/abyzovlab/CNVnator

version	toolchain
0.3.3	foss/2016b

Co-phylog

Co-phylog: an assembly-free phylogenomic approach for closely related organisms H Yi, L Jin Nucleic acids research 41 (7), e75-e75

homepage: https://github.com/yhg926/co-phylog

version	toolchain
20201012	GCC/7.3.0-2.30

COBRApy

COBRApy is a package for constraint-based modeling of metabolic networks.

homepage: https://opencobra.github.io/cobrapy/

version	toolchain
0.26.0	foss/2021a
0.29.0	foss/2023b

CoCoALib

CoCoALib is a free GPL3 C++ library for doing Computations in Commutative Algebra.

homepage: https://cocoa.dima.unige.it/cocoa/cocoalib/

version	toolchain
0.99601	GCC/8.2.0-2.31.1
0.99700	GCC/8.3.0
0.99818	GCC/11.3.0

CodAn

CodAn (Coding sequence Annotator) is a computational tool designed to characterize the CDS and UTR regions on transcripts from any Eukaryote species.

homepage: https://github.com/pedronachtigall/CodAn

version	toolchain
1.2	foss/2021b

code-cli

Visual Studio Code is a lightweight but powerful source code editor which runs on your desktop and is available for Windows, macOS and Linux. It comes with built-in support for JavaScript, TypeScript and Node.js and has a rich ecosystem of extensions for other languages and runtimes (such as C++, C#, Java, Python, PHP, Go, .NET). Begin your journey with VS Code with these introductory videos.

homepage: https://code.visualstudio.com/

version	versionsuffix	toolchain
1.85.1	-x64	system

code-server

Run VS Code on any machine anywhere and access it in the browser.

homepage: https://github.com/cdr/code-server

version	toolchain
3.7.3	system
4.9.1	system
4.16.1	system
4.21.1	system
4.22.1	system

CODEX2

Full-spectrum copy number variation detection by high-throughput DNA sequencing

homepage: https://github.com/yuchaojiang/CODEX2

version	versionsuffix	toolchain
20180227	-R-3.4.3	intel/2017b

CodingQuarry

Highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts

homepage: https://sourceforge.net/p/codingquarry

version	toolchain
2.0	foss/2021b

Cogent

Cogent is a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences. It is designed to be used on Iso-Seq data and in cases where there is no reference genome or the ref genome is highly incomplete.

homepage: https://github.com/Magdoll/Cogent

version	toolchain
8.0.0	foss/2021a

Coin

Coin is an OpenGL-based, 3D graphics library that has its roots in the Open Inventor 2.1 API, which Coin still is compatible with.

homepage: https://coin3d.github.io

version	toolchain
4.0.0	GCC/10.3.0, GCC/11.2.0

CoinUtils

CoinUtils (Coin-OR Utilities) is an open-source collection of classes and functions that are generally useful to more than one COIN-OR project.

homepage: https://github.com/coin-or/CoinUtils

version	toolchain
2.11.3	GCCcore/7.3.0, foss/2018b
2.11.4	GCC/10.3.0, GCCcore/10.2.0
2.11.6	GCC/11.2.0
2.11.9	GCC/12.2.0
2.11.10	GCC/12.3.0

ColabFold

Making protein folding accessible to all. Predict proteins structures both in google colab and on your machine.

homepage: https://github.com/sokrypton/ColabFold

version	versionsuffix	toolchain
1.5.2		foss/2022a
1.5.2	-CUDA-11.7.0	foss/2022a

colossalai

Colossal-AI: A Unified Deep Learning System for Big Model Era

homepage: https://colossalai.org/

version	versionsuffix	toolchain
0.1.8	-CUDA-11.3.1	foss/2021a

Commet

COMMET ("COmpare Multiple METagenomes") provides a global similarity overview between all datasets of a large metagenomic project.

homepage: https://colibread.inria.fr/software/commet/

version	versionsuffix	toolchain
20150415	-Python-2.7.11	foss/2016a

CompareM

A toolbox for comparative genomics.

homepage: https://github.com/dparks1134/CompareM

version	versionsuffix	toolchain
0.0.23	-Python-2.7.15	foss/2018b
0.1.2		foss/2021b

Compress-Raw-Zlib

Low-Level Interface to zlib or zlib-ng compression library

homepage: https://metacpan.org/pod/Compress::Raw::Zlib

version	toolchain
2.202	GCCcore/11.3.0, GCCcore/12.2.0

COMSOL

COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems.

homepage: https://www.comsol.se/

version	toolchain
5.4.0.225	system
6.2.0.290	system

Con3F

Con3F is a Python package to read, manipulate and convert force field files

homepage: https://github.ugent.be/CMM/con3f

version	versionsuffix	toolchain
1.0-20190329	-Python-3.7.2	intel/2019a

conan

Decentralized, open-source (MIT), C/C++ package manager.

homepage: https://conan.io

version	toolchain
1.58.0	GCCcore/11.3.0
1.60.2	GCCcore/12.3.0

CONCOCT

Clustering cONtigs with COverage and ComposiTion (CONCOCT) is a program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.

homepage: https://concoct.readthedocs.io

version	versionsuffix	toolchain
1.0.0	-Python-2.7.14	foss/2017b
1.0.0	-Python-2.7.15	foss/2018b
1.0.0	-Python-3.6.3	foss/2017b
1.1.0	-Python-2.7.15	foss/2019a
1.1.0	-Python-2.7.18	foss/2020b

Concorde

Concorde is a computer code for the symmetric traveling salesman problem (TSP) and some related network optimization problems

homepage: https://www.math.uwaterloo.ca/tsp/concorde.html

version	toolchain
20031219	GCC/12.3.0

ConcurrentVersionsSystem

CVS is a version control system, an important component of Source Configuration Management (SCM).

homepage: https://savannah.nongnu.org/projects/cvs

version	toolchain
1.11.23	GCC/4.8.2, GCCcore/11.2.0, GCCcore/4.9.3, GCCcore/6.4.0

configparser

configparser is a Python library that brings the updated configparser from Python 3.5 to Python 2.6-3.5

homepage: https://docs.python.org/3/library/configparser.html

version	versionsuffix	toolchain
3.5.0	-Python-2.7.11	foss/2016a
3.5.0	-Python-2.7.12	foss/2016b, intel/2016b
3.5.0	-Python-3.5.2	intel/2016b
3.5.0	-Python-3.6.3	intel/2017b

configurable-http-proxy

HTTP proxy for node.js including a REST API for updating the routing table. Developed as a part of the Jupyter Hub multi-user server.

homepage: https://github.com/jupyterhub/configurable-http-proxy

version	versionsuffix	toolchain
1.3.0	-nodejs-4.4.7	foss/2016a
3.1.1	-nodejs-8.9.4	foss/2017a
4.2.1		GCCcore/10.2.0
4.4.0		GCCcore/10.3.0
4.5.3		GCCcore/11.3.0
4.5.5		GCCcore/12.2.0
4.5.6		GCCcore/12.3.0

CONN

CONN is an open-source Matlab/SPM-based cross-platform software for the computation, display, and analysis of functional connectivity Magnetic Resonance Imaging (fcMRI). CONN is used to analyze resting state data (rsfMRI) as well as task-related designs.

homepage: https://web.conn-toolbox.org/home

version	versionsuffix	toolchain
21a	-MATLAB-2021a	system

connected-components-3d

cc3d is an implementation of connected components in three dimensions using a 26, 18, or 6-connected neighborhood in 3D or 4 and 8-connected in 2D.

homepage: https://github.com/seung-lab/connected-components-3d/

version	toolchain
3.12.1	foss/2022b

ConnectomeWorkbench

Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project.

homepage: https://www.humanconnectome.org/software/connectome-workbench

version	versionsuffix	toolchain
1.2.2		system
1.3.2		GCCcore/8.2.0, foss/2017b, intel/2017b
1.4.2	-rh_linux64	system
1.5.0		GCCcore/10.3.0

contextily

contextily is a small Python 3 package to retrieve tile maps from the internet. It can add those tiles as basemap to matplotlib figures or write tile maps to disk into geospatial raster files. Bounding boxes can be passed in both WGS84 (EPSG:4326) and Spheric Mercator (EPSG:3857).

homepage: https://contextily.readthedocs.io/

version	toolchain
1.5.0	foss/2023a

Control-FREEC

Copy number and genotype annotation from whole genome and whole exome sequencing data.

homepage: https://github.com/BoevaLab/FREEC

version	toolchain
11.5	GCC/7.3.0-2.30, GCC/8.2.0-2.31.1
11.6	GCC/10.2.0

cooler

Cooler is a support library for a storage format, also called cooler, used to store genomic interaction data of any size, such as Hi-C contact matrices.

homepage: https://open2c.github.io/cooler

version	toolchain
0.9.1	foss/2022a

CoordgenLibs

Schrodinger-developed 2D Coordinate Generation

homepage: https://github.com/schrodinger/coordgenlibs

version	toolchain
1.3.2	gompi/2019a, iimpi/2019a
3.0.1	gompi/2019b, gompi/2021a, gompi/2022a, iimpi/2020a
3.0.2	gompi/2023a

Coot

Coot is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data.

homepage: http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot

version	versionsuffix	toolchain
0.8.1	-binary-Linux-x86_64-rhel-6-python-gtk2	system
0.9.8.92	-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2	system

CopyKAT

CopyKAT: Inference of genomic copy number and subclonal structure of human tumors from high-throughput single cell RNAseq data

homepage: https://github.com/navinlabcode/copykat

version	versionsuffix	toolchain
1.1.0	-R-4.2.1	foss/2022a
1.1.0	-R-4.2.2	foss/2022b

core-counter

Tool to check available cores and OMP threads

homepage: https://github.com/gjbex/core-counter

version	toolchain
1.1.1	system

Coreutils

The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system.

homepage: https://www.gnu.org/software/coreutils/

version	toolchain
8.23	GCC/4.9.2
8.27	GCCcore/5.4.0
8.29	GCCcore/6.4.0
8.32	GCCcore/8.3.0, GCCcore/9.3.0
9.0	GCCcore/11.2.0
9.1	GCCcore/11.3.0, GCCcore/12.2.0

corner

Make some beautiful corner plots.

homepage: https://corner.readthedocs.io/en/latest/

version	versionsuffix	toolchain
2.0.1	-Python-2.7.15	foss/2019a
2.0.1	-Python-3.7.2	foss/2019a
2.2.2		foss/2021b

CoSymLib

Cosymlib is a python library for computing continuous symmetry & shape measures (CSMs & CShMs). Although its main aim is to provide simple and ready-to-use tools for the analysis of the symmetry & shape of molecules, many of the procedures contained in cosymlib can be easily applied to any finite geometrical object defined by a set of vertices or a by mass distribution function.

homepage: https://cosymlib.readthedocs.io

version	toolchain
0.10.9	foss/2022a

coverage

Coverage.py is a tool for measuring code coverage of Python programs. It monitors your program, noting which parts of the code have been executed, then analyzes the source to identify code that could have been executed but was not.

homepage: https://coverage.readthedocs.io

version	versionsuffix	toolchain
4.5.1	-Python-2.7.14	intel/2017b
5.5		GCCcore/10.2.0, GCCcore/10.3.0
7.2.3		GCCcore/12.2.0, GCCcore/12.3.0
7.2.7		GCCcore/11.3.0

cowsay

Configurable talking characters in ASCII art

homepage: https://github.com/tnalpgge/rank-amateur-cowsay

version	toolchain
3.04	system

CP2K

CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.

homepage: https://www.cp2k.org/

version	versionsuffix	toolchain
3.0		intel/2016a, intel/2016b, intel/2017b, intel/2018a
3.0	-psmp	intel/2016b
4.1		intel/2016b
4.1	-psmp	foss/2016b
5.1		foss/2018a, foss/2020a, foss/2020b, intel/2017b, intel/2018a, intel/2020a
6.1		foss/2019a, intel/2018a, intel/2020a
7.1		foss/2020a, foss/2020b, intel/2020a, intel/2020b
7.1	-psmp	foss/2020b
8.1		foss/2020b
8.2		foss/2021a, intel/2021a
9.1		foss/2022a
2022.1		foss/2022a
2023.1		foss/2022b, foss/2023a

CPB

CPB is a novel two-step Pearson correlation based biclustering approach to mine genes that are co-regulated with a given reference gene in order to discover genes that function in a common biological process. In the first step, the algorithm identifies subsets of genes with high correlation, reducing false negatives with a nonparametric filtering scheme. In the second step, biclusters from multiple datasets are used to extract and rank gene correlation information.

homepage: http://tda.gatech.edu/software/cpb/index.html

version	versionsuffix	toolchain
11-4-2011	-Python-2.7.13	foss/2017a

CPC2

a fast and accurate coding potential calculator based on sequence intrinsic features

homepage: http://cpc2.gao-lab.org/

version	toolchain
1.0.1	foss/2022a

cpio

The cpio package contains tools for archiving.

homepage: https://savannah.gnu.org/projects/cpio/

version	toolchain
2.14	GCCcore/11.3.0

CPLEX

IBM ILOG CPLEX Optimizer's mathematical programming technology enables analytical decision support for improving efficiency, reducing costs, and increasing profitability.

homepage: https://www.ibm.com/analytics/cplex-optimizer

version	versionsuffix	toolchain
12.9		GCCcore/8.2.0
12.10	-Python-3.7.4	GCCcore/8.3.0
22.1.1		GCCcore/11.2.0, system

CPMD

The CPMD code is a parallelized plane wave / pseudopotential implementation of DFT, particularly designed for ab-initio molecular dynamics.

homepage: https://github.com/CPMD-code

version	toolchain
4.3	foss/2022a

CPPE

CPPE is an open-source, light-weight C++ and Python library for Polarizable Embedding (PE)1,2 calculations. It provides an easy-to-use API to implement PE for ground-state self-consistent field (SCF) calculations and post-SCF methods. A convenient Python interface is also available.

homepage: https://github.com/maxscheurer/cppe

version	toolchain
0.3.1	GCC/11.3.0, GCC/12.2.0

CppHeaderParser

CppHeaderParser is a pure python module that will parse C++ header files and generate a data structure representing the class.

homepage: https://senexcanis.com/open-source/cppheaderparser

version	toolchain
2.7.4	GCCcore/11.3.0

CppUnit

CppUnit is the C++ port of the famous JUnit framework for unit testing.

homepage: https://freedesktop.org/wiki/Software/cppunit/

version	toolchain
1.12.1	GCCcore/6.4.0, GCCcore/7.3.0, foss/2016a
1.15.1	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.3.0, GCCcore/12.3.0, GCCcore/8.3.0, GCCcore/9.3.0

cppy

A small C++ header library which makes it easier to write Python extension modules. The primary feature is a PyObject smart pointer which automatically handles reference counting and provides convenience methods for performing common object operations.

homepage: https://github.com/nucleic/cppy

version	toolchain
1.1.0	GCCcore/10.3.0, GCCcore/11.2.0
1.2.1	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

cppyy

cppyy is an automatic, run-time, Python-C++ bindings generator, for calling C++ from Python and Python from C++.

homepage: https://cppyy.readthedocs.io

version	toolchain
3.0.0	GCCcore/11.3.0

cppzmq

cppzmq is a C++ binding for libzmq.

homepage: https://github.com/zeromq/cppzmq

version	toolchain
4.9.0	system

cpu_features

A cross-platform C library to retrieve CPU features (such as available instructions) at runtime.

homepage: https://github.com/google/cpu_features

version	toolchain
0.6.0	GCCcore/10.2.0

cram

Cram is a functional testing framework for command line applications.

homepage: https://bitheap.org/cram

version	toolchain
0.7	GCCcore/8.2.0

cramtools

CRAMTools is a set of Java tools and APIs for efficient compression of sequence read data. Although this is intended as a stable version the code is released as early access. Parts of the CRAMTools are experimental and may not be supported in the future.

homepage: https://github.com/enasequence/cramtools/

version	versionsuffix	toolchain
2.0	-Java-1.7.0_80	system
3.0	-Java-1.7.0_80	system

CrayCCE

Toolchain using Cray compiler wrapper, using PrgEnv-cray (PE release: June 2019).

homepage: https://pubs.cray.com/discover

version	toolchain
19.06	system

CrayGNU

Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: June 2019).

homepage: https://pubs.cray.com/discover

version	toolchain
19.06	system

CrayIntel

Toolchain using Cray compiler wrapper, using PrgEnv-intel (PE release: June 2019).

homepage: https://pubs.cray.com/discover

version	toolchain
19.06	system

CrayPGI

Toolchain using Cray compiler wrapper, PrgEnv-pgi compiler (PE release: June 2019).

homepage: https://pubs.cray.com/discover

version	toolchain
19.06	system

crb-blast

Conditional Reciprocal Best BLAST - high confidence ortholog assignment. CRB-BLAST is a novel method for finding orthologs between one set of sequences and another. This is particularly useful in genome and transcriptome annotation.

homepage: https://github.com/cboursnell/crb-blast

version	versionsuffix	toolchain
0.6.9		gompi/2021a, gompi/2021b, intel/2017a
0.6.9	-Ruby-2.6.1	foss/2018b

CREST

CREST is an utility/driver program for the xtb program. Originally it was designed as conformer sampling program, hence the abbreviation Conformer–Rotamer Ensemble Sampling Tool, but now offers also some utility functions for calculations with the GFNn–xTB methods. Generally the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb program) and tool for the creation and analysation of structure ensembles.

homepage: https://xtb-docs.readthedocs.io/en/latest/crest.html

version	toolchain
2.11	intel/2021a
2.11.2	intel/2021a
2.12	gfbf/2023a, intel/2022a

CRF++

CRF++ is a simple, customizable, and open source implementation of Conditional Random Fields (CRFs) for segmenting/labeling sequential data. CRF++ is designed for generic purpose and will be applied to a variety of NLP tasks, such as Named Entity Recognition, Information Extraction and Text Chunking.

homepage: https://taku910.github.io/crfpp/

version	toolchain
0.58	iccifort/2019.1.144-GCC-8.2.0-2.31.1, intel/2018b

CRISPR-DAV

CRISPR-DAV is a pipeline to analyze amplicon-based NGS data of CRISPR clones in a high throughput manner.

homepage: https://github.com/pinetree1/crispr-dav/

version	toolchain
2.3.4	foss/2020b

CRISPResso2

CRISPResso2 is a software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments.

homepage: https://github.com/pinellolab/CRISPResso2/

version	versionsuffix	toolchain
2.0.44	-Python-2.7.16	foss/2019b
2.1.2	-Python-2.7.18	foss/2020b
2.2.1		foss/2020b

cromwell

Cromwell is a Workflow Management System geared towards scientific workflows.

homepage: http://cromwell.readthedocs.io/

version	versionsuffix	toolchain
56	-Java-11	system

crossguid

CrossGuid is a minimal, cross platform, C++ GUID library. It uses the best native GUID/UUID generator on the given platform and has a generic class for parsing, stringifying, and comparing IDs. The guid generation technique is determined by your platform:

homepage: https://github.com/graeme-hill/crossguid

version	toolchain
20190529	GCCcore/11.2.0, GCCcore/11.3.0

CrossMap

CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF and VCF.

homepage: http://crossmap.sourceforge.net

version	versionsuffix	toolchain
0.3.9	-Python-3.7.2	foss/2019a

CrossTalkZ

CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment between pairs of gene or protein groups in large biological networks.

homepage: http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/

version	toolchain
1.4	foss/2016a

CRPropa

CRPropa is a publicly available code to study the propagation of ultra high energy nuclei up to iron on their voyage through an extra galactic environment.

homepage: https://crpropa.desy.de

version	versionsuffix	toolchain
3.1.5	-Python-3.7.2	foss/2019a
3.1.6	-Python-3.8.2	foss/2020a

Crumble

Exploration of controlled loss of quality values for compressing CRAM files

homepage: https://github.com/jkbonfield/crumble

version	toolchain
0.8.3	GCC/11.2.0

cryoCARE

This package is a memory efficient implementation of cryoCARE. This setup trains a denoising U-Net for tomographic reconstruction according to the Noise2Noise training paradigm. Therefore the user has to provide two tomograms of the same sample. The simplest way to achieve this is with direct- detector movie-frames. You can use Warp to generate two reconstructed tomograms based on the even/odd frames. Alternatively, the movie-frames can be split in two halves (e.g. with MotionCor2 -SplitSum 1 or with IMOD alignframes -debug 10000) from which two identical, up to random noise, tomograms can be reconstructed. These two (even and odd) tomograms can be used as input to this cryoCARE implementation.

homepage: https://github.com/juglab/cryoCARE_pip

version	versionsuffix	toolchain
0.2.1	-CUDA-11.3.1	foss/2021a
0.3.0	-CUDA-11.7.0	foss/2022a

cryoDRGN

cryoDRGN: Deep Reconstructing Generative Networks for cryo-EM heterogeneous reconstruction. CryoDRGN is a neural network based algorithm for heterogeneous cryo-EM reconstruction. In particular, the method models a continuous distribution over 3D structures by using a neural network based representation for the volume.

homepage: https://cb.csail.mit.edu/cb/cryodrgn/

version	versionsuffix	toolchain
0.3.2		fosscuda/2020b
0.3.5	-CUDA-11.3.1	foss/2021a
1.0.0-beta	-CUDA-11.3.1	foss/2021a

cryptography

cryptography is a package designed to expose cryptographic primitives and recipes to Python developers.

homepage: https://github.com/pyca/cryptography

version	toolchain
41.0.1	GCCcore/12.3.0
41.0.5	GCCcore/13.2.0

CryptoMiniSat

CryptoMiniSat is an advanced SAT solver

homepage: https://github.com/msoos/cryptominisat

version	versionsuffix	toolchain
5.0.1	-Python-2.7.12	intel/2016b

CrystFEL

CrystFEL is a suite of programs for processing diffraction data acquired "serially" in a "snapshot" manner, such as when using the technique of Serial Femtosecond Crystallography (SFX) with a free-electron laser source.

homepage: http://www.desy.de/~twhite/crystfel/

version	toolchain
0.8.0	foss/2019a, intel/2019a

CSB

Computational Structural Biology Toolbox CSB is a python library and application framework, which can be used to solve problems in the field of structural bioinformatics. If you are a bioinformatician, software engineer or a researcher working in this field, chances are you may find something useful here. Our package consists of a few major components: 1. Core class library - object-oriented, granular, with an emphasis on design and clean interfaces. 2. Application framework - console applications ("protocols"), which consume objects from the core library in order to build something executable (and hopefully useful). 3. Test framework - ensures that the library actually works.

homepage: https://github.com/csb-toolbox

version	toolchain
1.2.5	foss/2020b

CSBDeep

CSBDeep is a toolbox for Content-aware Image Restoration (CARE).

homepage: https://csbdeep.bioimagecomputing.com/

version	versionsuffix	toolchain
0.4.1	-Python-3.7.2	foss/2019a, fosscuda/2019a
0.7.4		foss/2022a
0.7.4	-CUDA-11.7.0	foss/2022a

CSBLAST

Context-specific extension of BLAST that significantly improves sensitivity and alignment quality.

homepage: https://github.com/soedinglab/csblast/

version	toolchain
2.2.3	GCCcore/8.3.0
2.2.4	GCCcore/11.3.0

cscope

Cscope is a developer's tool for browsing source code.

homepage: http://cscope.sourceforge.net/

version	toolchain
15.9	system

csvkit

csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats.

homepage: https://github.com/wireservice/csvkit

version	versionsuffix	toolchain
1.0.4		GCCcore/8.2.0
1.0.5	-Python-3.7.4	GCCcore/8.3.0
1.1.0		GCCcore/11.3.0

ctags

Ctags generates an index (or tag) file of language objects found in source files that allows these items to be quickly and easily located by a text editor or other utility.

homepage: http://ctags.sourceforge.net/

version	toolchain
5.8	system

ctffind

Program for finding CTFs of electron micrographs.

homepage: https://grigoriefflab.umassmed.edu/ctffind4

version	versionsuffix	toolchain
4.1.13		foss/2019a, fosscuda/2019a, fosscuda/2019b
4.1.14		foss/2019b, foss/2021b, foss/2022a, foss/2022b, foss/2023a, fosscuda/2019b, fosscuda/2020b
4.1.14	-CUDA-11.3.1	foss/2021a

CTPL

Modern and efficient C++ Thread Pool Library

homepage: https://github.com/vit-vit/CTPL.git

version	toolchain
0.0.2	GCC/11.3.0

Cube

Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity.

homepage: http://www.scalasca.org/software/cube-4.x/download.html

version	toolchain
4.3.4	foss/2016a

CubeGUI

Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube graphical report explorer.

homepage: https://www.scalasca.org/software/cube-4.x/download.html

version	toolchain
4.4.4	GCCcore/8.2.0, GCCcore/9.3.0
4.6	GCCcore/10.2.0, GCCcore/10.3.0
4.8	GCCcore/11.3.0

CubeLib

Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube general purpose C++ library component and command-line tools.

homepage: https://www.scalasca.org/software/cube-4.x/download.html

version	toolchain
4.4.4	GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
4.6	GCCcore/10.2.0, GCCcore/10.3.0
4.8	GCCcore/11.2.0, GCCcore/11.3.0
4.8.1	GCCcore/12.2.0, GCCcore/12.3.0
4.8.2	GCCcore/12.2.0, GCCcore/13.2.0

CubeWriter

Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube high-performance C writer library component.

homepage: https://www.scalasca.org/software/cube-4.x/download.html

version	toolchain
4.4.3	GCCcore/10.2.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
4.6	GCCcore/10.2.0, GCCcore/10.3.0
4.8	GCCcore/11.2.0, GCCcore/11.3.0
4.8.1	GCCcore/12.2.0, GCCcore/12.3.0
4.8.2	GCCcore/12.2.0, GCCcore/13.2.0

CuCLARK

Metagenomic classifier for CUDA-enabled GPUs

homepage: https://github.com/Funatiq/cuclark

version	toolchain
1.1	fosscuda/2019b

CUDA

CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.

homepage: https://developer.nvidia.com/cuda-toolkit

version	toolchain
5.5.22	GCC/4.8.2, system
6.0.37	system
6.5.14	system
7.0.28	system
7.5.18	GCC/4.9.4-2.25, iccifort/2016.3.210-GCC-4.9.3-2.25, system
8.0.44	GCC/5.4.0-2.26, iccifort/2016.3.210-GCC-5.4.0-2.26, system
8.0.61	system
8.0.61_375.26	GCC/5.4.0-2.26
9.0.176	GCC/6.4.0-2.28, iccifort/2017.4.196-GCC-6.4.0-2.28, system
9.1.85	GCC/6.4.0-2.28, system
9.2.88	GCC/6.4.0-2.28, GCC/7.3.0-2.30, system
9.2.148.1	system
10.0.130	system
10.1.105	GCC/8.2.0-2.31.1, iccifort/2019.1.144-GCC-8.2.0-2.31.1, system
10.1.168	system
10.1.243	GCC/8.3.0, iccifort/2019.5.281, system
10.2.89	GCC/8.3.0
11.0.2	GCC/9.3.0, iccifort/2020.1.217
11.1.1	GCC/10.2.0, iccifort/2020.4.304
11.3.1	system
11.4.1	system
11.4.2	system
11.5.0	system
11.5.1	system
11.5.2	system
11.6.0	system
11.7.0	system
11.8.0	system
12.0.0	system
12.1.0	system
12.1.1	system
12.2.0	system
12.2.2	system
12.3.0	system
12.3.2	system
12.4.0	system

CUDA-Samples

Samples for CUDA Developers which demonstrates features in CUDA Toolkit

homepage: https://github.com/NVIDIA/cuda-samples

version	versionsuffix	toolchain
11.3	-CUDA-11.3.1	GCC/10.3.0
11.6	-CUDA-11.7.0	GCC/11.3.0
12.1	-CUDA-12.1.1	GCC/12.3.0

CUDAcompat

Using the CUDA Forward Compatibility package, system administrators can run applications built using a newer toolkit even when an older driver that does not satisfy the minimum required driver version is installed on the system. This forward compatibility allows the CUDA deployments in data centers and enterprises to benefit from the faster release cadence and the latest features and performance of CUDA Toolkit.

homepage: https://docs.nvidia.com/deploy/cuda-compatibility/index.html

version	versionsuffix	toolchain
11		system
11.6		system
11.6	-510.85.02	system
11.7		system
11.7	-515.65.01	system

CUDAcore

CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.

homepage: https://developer.nvidia.com/cuda-toolkit

version	toolchain
11.0.2	system
11.1.1	system
11.2.1	system
11.2.2	system
11.3.0	system
11.4.0	system
11.5.1	system

CUDD

The CUDD package is a package written in C for the manipulation of decision diagrams. It supports binary decision diagrams (BDDs), algebraic decision diagrams (ADDs), and Zero-Suppressed BDDs (ZDDs).

homepage: https://github.com/ivmai/cudd

version	toolchain
3.0.0	GCC/11.3.0

cuDNN

The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.

homepage: https://developer.nvidia.com/cudnn

version	versionsuffix	toolchain
4.0		system
5.0	-CUDA-7.5.18	system
5.0-rc		system
5.1	-CUDA-8.0.44	system
6.0	-CUDA-8.0.61	system
6.0.21	-CUDA-7.5.18	system
6.0.21	-CUDA-8.0.44	system
7.0.2	-CUDA-9.0.176	system
7.0.5	-CUDA-8.0.44	system
7.0.5	-CUDA-9.0.176	system
7.0.5	-CUDA-9.1.85	system
7.0.5.15		fosscuda/2017b, fosscuda/2018a, intelcuda/2017b
7.1.4.18		fosscuda/2018b
7.4.2.24		gcccuda/2019a
7.4.2.24	-CUDA-10.0.130	system
7.5.0.56	-CUDA-10.0.130	system
7.6.2.24	-CUDA-10.1.243	system
7.6.4.38		gcccuda/2019a, gcccuda/2019b
7.6.4.38	-CUDA-10.0.130	system
8.0.4.30	-CUDA-11.0.2	system
8.0.4.30	-CUDA-11.1.1	system
8.0.5.39	-CUDA-11.1.1	system
8.1.0.77	-CUDA-11.2.1	system
8.1.1.33	-CUDA-11.2.1	system
8.2.1.32	-CUDA-11.3.1	system
8.2.2.26	-CUDA-11.4.0	system
8.2.2.26	-CUDA-11.4.1	system
8.4.0.27	-CUDA-11.6.0	system
8.4.1.50	-CUDA-11.5.2	system
8.4.1.50	-CUDA-11.6.0	system
8.4.1.50	-CUDA-11.7.0	system
8.6.0.163	-CUDA-11.8.0	system
8.7.0.84	-CUDA-11.8.0	system
8.8.0.121	-CUDA-12.0.0	system
8.9.2.26	-CUDA-12.1.1	system
8.9.2.26	-CUDA-12.2.0	system
8.9.7.29	-CUDA-12.3.0	system

Cufflinks

Transcript assembly, differential expression, and differential regulation for RNA-Seq

homepage: http://cole-trapnell-lab.github.io/cufflinks/

version	toolchain
2.2.1	foss/2016a, foss/2016b, foss/2018b, gompi/2019b, intel/2017b, intel/2018a
20190706	GCC/10.2.0, GCC/11.2.0, gompi/2019a

CUnit

Automated testing framework for C.

homepage: https://sourceforge.net/projects/cunit/

version	toolchain
2.1-3	GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/6.4.0

CuPy

CuPy is an open-source array library accelerated with NVIDIA CUDA.

homepage: https://cupy.dev

version	versionsuffix	toolchain
8.2.0	-Python-3.7.4	fosscuda/2019b
8.5.0		fosscuda/2020b
11.4.0	-CUDA-11.4.1	foss/2021b
12.1.0	-CUDA-12.0.0	foss/2022b
13.0.0	-CUDA-12.1.1	foss/2023a

cURL

libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more.

homepage: https://curl.haxx.se

version	toolchain
7.33.0	GCC/4.8.2
7.34.0	GCC/4.8.2
7.40.0	GCC/4.9.2
7.46.0	iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25
7.47.0	foss/2016a, intel/2016.02-GCC-4.9, intel/2016a
7.49.1	GCCcore/5.4.0, foss/2016a, foss/2016b, intel/2016a, intel/2016b
7.52.1	gimkl/2017a, intel/2016b
7.53.1	GCCcore/6.3.0
7.54.0	GCCcore/6.3.0
7.55.1	GCCcore/6.4.0
7.56.0	GCCcore/6.4.0
7.56.1	GCCcore/6.4.0
7.58.0	GCCcore/6.4.0
7.59.0	GCCcore/6.4.0
7.60.0	GCCcore/7.2.0, GCCcore/7.3.0
7.63.0	GCCcore/8.2.0
7.66.0	GCCcore/8.3.0
7.69.1	GCCcore/9.3.0
7.72.0	GCCcore/10.2.0
7.76.0	GCCcore/10.3.0
7.78.0	GCCcore/11.2.0
7.83.0	GCCcore/11.3.0
7.84.0	GCCcore/12.1.0
7.86.0	GCCcore/12.2.0
8.0.1	GCCcore/12.3.0, GCCcore/13.1.0
8.3.0	GCCcore/13.2.0

cuSPARSELt

NVIDIA cuSPARSELt is a high-performance CUDA library dedicated to general matrix-matrix operations in which at least one operand is a sparse matrix

homepage: https://docs.nvidia.com/cuda/cusparselt/index.html

version	versionsuffix	toolchain
0.3.0.3	-CUDA-11.4.1	system
0.6.0.6	-CUDA-12.1.1	system

custodian

A simple JIT job management framework in Python.

homepage: https://pypi.python.org/pypi/custodian

version	versionsuffix	toolchain
1.1.0	-Python-2.7.13	intel/2017a

cutadapt

Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

homepage: https://opensource.scilifelab.se/projects/cutadapt/

version	versionsuffix	toolchain
1.9.1	-Python-2.7.11	foss/2016a
1.9.1	-Python-2.7.12	foss/2016b
1.14	-Python-2.7.13	foss/2017a, intel/2017a
1.15	-Python-3.5.2	foss/2016b
1.16	-Python-2.7.14	foss/2017b, intel/2017b, intel/2018a
1.16	-Python-3.6.3	foss/2017b, intel/2017b
1.16	-Python-3.6.4	foss/2018a, intel/2018a
1.18		GCCcore/8.2.0, GCCcore/8.3.0
1.18	-Python-2.7.15	foss/2018b
1.18	-Python-2.7.18	GCC/10.2.0
1.18	-Python-3.6.6	foss/2018b, intel/2018b
2.1	-Python-3.6.6	foss/2018b
2.7	-Python-3.7.4	GCCcore/8.3.0
2.8	-Python-3.7.4	GCCcore/8.3.0
2.10		GCCcore/10.2.0
2.10	-Python-3.7.4	GCCcore/8.3.0
2.10	-Python-3.8.2	GCCcore/9.3.0
3.4		GCCcore/10.2.0, GCCcore/10.3.0
3.5		GCCcore/11.2.0
4.2		GCCcore/11.3.0
4.4		GCCcore/12.2.0

cuTENSOR

The cuTENSOR Library is a GPU-accelerated tensor linear algebra library providing tensor contraction, reduction and elementwise operations.

homepage: https://developer.nvidia.com/cutensor

version	versionsuffix	toolchain
1.2.2.5		gcccuda/2019b
1.2.2.5	-CUDA-11.1.1	system
1.6.0.3	-CUDA-11.3.1	system
1.6.1.5	-CUDA-11.4.1	system
1.6.1.5	-CUDA-11.7.0	system
1.7.0.1	-CUDA-12.0.0	system
2.0.1.2	-CUDA-12.1.1	system
2.0.1.2	-CUDA-12.2.2	system

cuteSV

cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection.

homepage: https://github.com/tjiangHIT/cuteSV

version	toolchain
2.0.3	foss/2022a

CUTLASS

CUTLASS is a collection of CUDA C++ template abstractions for implementing high-performance matrix-matrix multiplication (GEMM) and related computations at all levels and scales within CUDA. It incorporates strategies for hierarchical decomposition and data movement similar to those used to implement cuBLAS and cuDNN. CUTLASS decomposes these "moving parts" into reusable, modular software components abstracted by C++ template classes. Primitives for different levels of a conceptual parallelization hierarchy can be specialized and tuned via custom tiling sizes, data types, and other algorithmic policy. The resulting flexibility simplifies their use as building blocks within custom kernels and applications.

homepage: https://github.com/NVIDIA/cutlass

version	versionsuffix	toolchain
2.11.0	-CUDA-11.7.0	foss/2022a

CVglasso

CVglasso is an R package that estimates a lasso-penalized precision matrix via block-wise coordinate descent – also known as the graphical lasso (glasso) algorithm.

homepage: https://github.com/MGallow/CVglasso

version	versionsuffix	toolchain
1.0	-R-4.2.1	foss/2022a

CVXOPT

CVXOPT is a free software package for convex optimization based on the Python programming language. Its main purpose is to make the development of software for convex optimization applications straightforward by building on Python's extensive standard library and on the strengths of Python as a high-level programming language.

homepage: https://cvxopt.org

version	versionsuffix	toolchain
1.1.9	-Python-2.7.13	intel/2017a
1.2.1	-Python-3.6.4	intel/2018a
1.2.3		foss/2019a
1.2.3	-Python-3.6.6	intel/2018b
1.2.4	-Python-3.7.4	intel/2019b
1.2.6		foss/2020b, foss/2021a
1.3.1		foss/2022a

CVXPY

CVXPY is a Python-embedded modeling language for convex optimization problems. It allows you to express your problem in a natural way that follows the math, rather than in the restrictive standard form required by solvers.

homepage: https://www.cvxpy.org/

version	versionsuffix	toolchain
1.0.24		foss/2019a
1.0.28	-Python-3.7.4	foss/2019b
1.3.0		foss/2022a
1.4.2		foss/2023a

CWIPI

CWIPI (Coupling With Interpolation Parallel Interface) library helps in chaining and coupling codes. Provides exchanges of interpolated fields through a non-compliant geometric interface and allows control of the coupling algorithm using control parameters. CWIPI takes advantage of the distribution of the definition of the coupling algorithm in the different codes.

homepage: https://w3.onera.fr/cwipi/

version	toolchain
0.12.0	gompi/2021a, gompi/2022a

cwltool

Common workflow language (CWL) reference implementation.

homepage: https://github.com/common-workflow-language/cwltool

version	toolchain
3.1.20221008225030	foss/2021a
3.1.20221018083734	foss/2021a

cxxopts

cxxopts is a lightweight C++ command line option parser

homepage: https://github.com/jarro2783/cxxopts

version	toolchain
3.0.0	system

cysignals

The cysignals package provides mechanisms to handle interrupts (and other signals and errors) in Cython code.

homepage: https://pypi.org/project/cysignals/

version	versionsuffix	toolchain
1.10.2	-Python-2.7.14	foss/2017b, intel/2017b
1.10.2	-Python-3.6.3	foss/2017b, intel/2017b
1.11.2		GCCcore/11.3.0

Cython

Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex).

homepage: https://cython.org/

version	versionsuffix	toolchain
0.23.4	-Python-2.7.10	gimkl/2.11.5
0.24.1	-Python-2.7.11	foss/2016a
0.25.2	-Python-2.7.12	foss/2016b
0.25.2	-Python-3.6.4	intel/2018a
0.27.3	-Python-2.7.15	GCCcore/8.2.0
0.29.10	-Python-2.7.14	foss/2017b, intel/2017b
0.29.10	-Python-3.6.3	foss/2017b, intel/2017b
0.29.22		GCCcore/10.2.0
0.29.33		GCCcore/11.3.0
3.0.7		GCCcore/12.3.0
3.0.8		GCCcore/11.3.0, GCCcore/12.2.0
3.0a5		GCCcore/10.2.0

cython-blis

Fast BLAS-like operations from Python and Cython, without the tears. Provides the Blis linear algebra routines as a self-contained Python C-extension.

homepage: https://github.com/explosion/cython-blis

version	toolchain
0.9.1	foss/2022a

cytoolz

Cython implementation of the toolz package, which provides high performance utility functions for iterables, functions, and dictionaries.

homepage: https://github.com/pytoolz/cytoolz

version	versionsuffix	toolchain
0.10.1	-Python-3.6.6	foss/2018b
0.10.1	-Python-3.7.2	GCCcore/8.2.0

Cytoscape

Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of Apps are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.

homepage: https://cytoscape.org/

version	versionsuffix	toolchain
3.9.1	-Java-11	system

cytosim

Cytosim is a cytoskeleton simulation engine written in C++ working on Mac OS, GNU/Linux and Windows (with Cygwin).

homepage: https://github.com/nedelec/cytosim

version	versionsuffix	toolchain
20190117	-mkl	gomkl/2019a

cyvcf2

cython + htslib == fast VCF and BCF processing

homepage: https://github.com/brentp/cyvcf2

version	versionsuffix	toolchain
0.10.10	-Python-3.6.6	foss/2018b
0.11.5		foss/2019a, intel/2019a

D

dadi - dagitty - Dakota - DALI - DaliLite - Dalton - damageproto - dammit - DANPOS2 - DAS_Tool - dask - dask-labextension - datalad - datamash - davix - DB - DB_File - DBCSR - DBD-mysql - DBG2OLC - DBus - dbus-glib - dclone - dcm2niix - DCMTK - dd - deal.II - deap - decona - deconf - DeconICA - deepdiff - DeepLabCut - DeepLoc - deepmedic - DeepMod2 - DeepSurv - deepTools - DEICODE - Delft3D - Delly - DeltaLake - DeMixT - Demystify - DendroPy - denseweight - DensPart - Deprecated - desktop-file-utils - destiny - Detectron2 - DETONATE - devbio-napari - Devito - DFA - DFT-D3 - DFT-D4 - DFTB+ - dftd3-lib - dftd4 - DGL - DIA-NN - DIAL - dialog - DIALOGUE - DIAMOND - Dice - DiCE-ML - dicom2nifti - DicomBrowser - DiffBind - Diffutils - dijitso - dill - DIRAC - distributed - DistributedStream - DjVuLibre - DL_POLY_4 - DL_POLY_Classic - dlb - dlib - DLPack - dm-haiku - dm-reverb - dm-tree - DMCfun - DMLC-Core - DMTCP - DOLFIN - dominate - dorado - Doris - DosageConvertor - dotNET-Core-Runtime - dotNET-SDK - double-conversion - DoubletFinder - Doxygen - DP3 - DRAGMAP - Drake - dRep - drmaa-python - DROP - dropEst - DSA - dSFMT - DSRC - Dsuite - dtcmp - dtcwt - DualSPHysics - DUBStepR - dune-core - dune-fem - duplex-tools - dx-toolkit - dxpy - DyMat - dynesty

dadi

∂a∂i implements methods for demographic history and selection inference from genetic data, based on diffusion approximations to the allele frequency spectrum.

homepage: https://bitbucket.org/gutenkunstlab/dadi

version	versionsuffix	toolchain
1.7.0	-Python-2.7.12	intel/2016b

dagitty

A port of the web-based software 'DAGitty', available at http://dagitty.net, for analyzing structural causal models (also known as directed acyclic graphs or DAGs). This package computes covariate adjustment sets for estimating causal effects, enumerates instrumental variables, derives testable implications (d-separation and vanishing tetrads), generates equivalent models, and includes a simple facility for data simulation.

homepage: https://cran.r-project.org/web/packages/dagitty/

version	versionsuffix	toolchain
0.2-2	-R-3.5.1	foss/2018b

Dakota

The Dakota project delivers both state-of-the-art research and robust, usable software for optimization and UQ. Broadly, the Dakota software's advanced parametric analyses enable design exploration, model calibration, risk analysis, and quantification of margins and uncertainty with computational models.

homepage: https://dakota.sandia.gov/

version	toolchain
6.16.0	foss/2021b

DALI

R-package for the analysis of single-cell TCR/BCR data in the Seurat ecosystem

homepage: https://github.com/vibscc/DALI

version	versionsuffix	toolchain
2.1.2	-R-4.2.2	foss/2022b

DaliLite

DaliLite is a light version of the software run by the Dali server. The web server has search and data visualization options which are not included in this package. DaliLite supports data import (import.pl) to convert PDB entries to Dali's internal data format and pairwise comparison (dali.pl) to structurally align a list of query structures to a list of target structures.

homepage: http://ekhidna2.biocenter.helsinki.fi/dali/

version	toolchain
4.1	gompi/2021a

Dalton

The Dalton code is a powerful tool for a wide range of molecular properties at different levels of theory. Any published work arising from use of one of the Dalton2016 programs must acknowledge that by a proper reference, https://www.daltonprogram.org/www/citation.html.

homepage: https://daltonprogram.org/

version	versionsuffix	toolchain
2016	-i8	intel/2017b
2020.0		foss/2021a
2020.1		foss/2022b

damageproto

X protocol and ancillary headers for xinerama

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.2.1	foss/2016a, intel/2016a

dammit

dammit is a simple de novo transcriptome annotator. It was born out of the observations that annotation is mundane and annoying, all the individual pieces of the process exist already, and the existing solutions are overly complicated or rely on crappy non-free software.

homepage: http://www.camillescott.org/dammit/

version	versionsuffix	toolchain
0.3.2	-Python-2.7.13	intel/2017a

DANPOS2

A toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing, version 2

homepage: https://sites.google.com/site/danposdoc

version	versionsuffix	toolchain
2.2.2	-Python-2.7.12	foss/2016b

DAS_Tool

DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.

homepage: https://github.com/cmks/DAS_Tool

version	versionsuffix	toolchain
1.1.1	-R-3.5.1-Python-2.7.15	foss/2018b
1.1.1	-R-4.1.2	foss/2021b
1.1.3	-R-4.1.0	foss/2021a

dask

Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love.

homepage: https://dask.org/

version	versionsuffix	toolchain
0.8.2	-Python-2.7.11	intel/2016a
0.8.2	-Python-3.5.1	intel/2016a
0.11.0	-Python-2.7.11	foss/2016a
0.11.0	-Python-2.7.12	intel/2016b
0.11.0	-Python-3.5.2	intel/2016b
0.12.0	-Python-2.7.12	intel/2016b
0.12.0	-Python-3.5.2	foss/2016b, intel/2016b
0.16.0	-Python-2.7.14	foss/2017b, intel/2017b
0.16.0	-Python-3.6.3	foss/2017b, intel/2017b
0.17.0	-Python-2.7.13	foss/2017a, intel/2017a
0.17.0	-Python-3.6.1	intel/2017a
0.17.2	-Python-3.6.4	foss/2018a, intel/2018a
0.19.4	-Python-3.6.6	foss/2018b, fosscuda/2018b, intel/2018b
1.0.0	-Python-3.6.6	foss/2018b, intel/2018b
1.1.4	-Python-2.7.15	fosscuda/2018b
2.3.0	-Python-3.7.2	foss/2019a
2.8.0	-Python-3.7.4	foss/2019b, fosscuda/2019b, intel/2019b
2.18.1	-Python-3.8.2	foss/2020a, intel/2020a
2021.2.0		foss/2020b, fosscuda/2020b, intel/2020b, intelcuda/2020b
2021.9.1		foss/2021a
2022.1.0		foss/2021b
2022.10.0		foss/2022a
2023.7.1		foss/2022b
2023.9.2		foss/2023a
2023.12.1		foss/2023a

dask-labextension

This package provides a JupyterLab extension to manage Dask clusters, as well as embed Dask's dashboard plots directly into JupyterLab panes.

homepage: https://github.com/dask/dask-labextension

version	toolchain
6.0.0	foss/2022a

datalad

DataLad is a free and open source distributed data management system that keeps track of your data, creates structure, ensures reproducibility, supports collaboration, and integrates with widely used data infrastructure.

homepage: https://www.datalad.org/

version	toolchain
0.18.4	GCCcore/12.2.0
0.19.5	GCCcore/12.3.0

datamash

GNU datamash performs basic numeric, textual and statistical operations on input data files

homepage: https://www.gnu.org/software/datamash/

version	toolchain
1.3	foss/2018a
1.5	GCCcore/10.2.0, GCCcore/7.3.0, GCCcore/8.3.0
1.8	GCCcore/11.3.0

davix

The davix project aims to make file management over HTTP-based protocols simple. The focus is on high-performance remote I/O and data management of large collections of files. Currently, there is support for the WebDav (link is external), Amazon S3 (link is external), Microsoft Azure (link is external), and HTTP (link is external) protocols.

homepage: https://dmc.web.cern.ch/projects/davix/home

version	toolchain
0.6.6	intel/2017a
0.7.5	GCCcore/8.3.0

DB

Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.

homepage: http://www.oracle.com/technetwork/products/berkeleydb

version	toolchain
4.8.30	intel/2016a
6.2.23	foss/2016a
6.2.32	GCCcore/6.4.0, intel/2017a
18.1.25	GCCcore/7.3.0
18.1.32	GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
18.1.40	FCC/4.5.0, GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.1.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/8.2.0, GCCcore/8.3.0

DB_File

Perl5 access to Berkeley DB version 1.x.

homepage: https://perldoc.perl.org/DB_File.html

version	versionsuffix	toolchain
1.835		GCCcore/9.3.0
1.835	-Perl-5.20.3	intel/2016a
1.835	-Perl-5.22.1	foss/2016a
1.855		GCCcore/10.2.0
1.856		GCCcore/10.3.0
1.857		GCCcore/11.2.0
1.858		GCCcore/11.3.0
1.859		GCCcore/12.3.0

DBCSR

DBCSR stands for Distributed Blocked Compressed Sparse Row. DBCSR is a library designed to efficiently perform sparse matrix-matrix multiplication, among other operations.

homepage: https://cp2k.github.io/dbcsr/develop/

version	toolchain
2.5.0	foss/2021b

DBD-mysql

Perl binding for MySQL

homepage: https://metacpan.org/pod/distribution/DBD-mysql/lib/DBD/mysql.pm

version	versionsuffix	toolchain
4.032	-Perl-5.22.2	intel/2016a
4.033	-Perl-5.24.0	intel/2016b
4.042	-Perl-5.24.1	intel/2017a
4.046	-Perl-5.26.0	foss/2017b, intel/2017b
4.046	-Perl-5.26.1	intel/2018a
4.048	-Perl-5.28.0	foss/2018b
4.050		GCC/10.2.0, GCC/11.2.0, GCC/11.3.0, GCC/12.2.0
4.050	-Perl-5.28.1	foss/2019a

DBG2OLC

DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies

homepage: https://github.com/yechengxi/DBG2OLC

version	toolchain
20170208	intel/2016b, intel/2017a
20180221	GCC/6.4.0-2.28, iccifort/2017.4.196-GCC-6.4.0-2.28
20200724	GCC/11.3.0

DBus

D-Bus is a message bus system, a simple way for applications to talk to one another. In addition to interprocess communication, D-Bus helps coordinate process lifecycle; it makes it simple and reliable to code a "single instance" application or daemon, and to launch applications and daemons on demand when their services are needed.

homepage: https://dbus.freedesktop.org/

version	toolchain
1.10.8	foss/2016a, intel/2016a
1.10.12	intel/2016b
1.10.20	GCCcore/6.4.0
1.11.20	intel/2017a
1.13.0	intel/2017b
1.13.6	GCCcore/6.4.0, GCCcore/7.3.0
1.13.8	GCCcore/8.2.0
1.13.12	GCCcore/8.3.0, GCCcore/9.3.0
1.13.18	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0
1.14.0	GCCcore/11.3.0
1.15.2	GCCcore/12.2.0
1.15.4	GCCcore/12.3.0
1.15.8	GCCcore/13.2.0

dbus-glib

D-Bus is a message bus system, a simple way for applications to talk to one another.

homepage: https://dbus.freedesktop.org/doc/dbus-glib

version	toolchain
0.106	foss/2016a, intel/2016a
0.108	intel/2016b, intel/2017a
0.110	GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, intel/2017b
0.112	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0

dclone

Low level functions for implementing maximum likelihood estimating procedures for complex models using data cloning and Bayesian Markov chain Monte Carlo methods

homepage: https://cran.r-project.org/web/packages/dclone

version	versionsuffix	toolchain
2.3-0	-R-4.2.1	foss/2022a

dcm2niix

dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format.

homepage: https://github.com/rordenlab/dcm2niix

version	toolchain
1.0.20180622	GCCcore/6.4.0, GCCcore/7.3.0
1.0.20190902	GCCcore/7.3.0, GCCcore/8.2.0
1.0.20200331	GCCcore/8.3.0
1.0.20201102	GCCcore/8.3.0
1.0.20211006	GCCcore/10.3.0
1.0.20220720	GCCcore/11.3.0
1.0.20230411	GCCcore/12.2.0

DCMTK

DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. It includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over a network connection, as well as demonstrative image storage and worklist servers.

homepage: https://dicom.offis.de/dcmtk

version	toolchain
3.6.3	GCCcore/7.3.0
3.6.5	GCCcore/8.2.0, GCCcore/8.3.0
3.6.6	GCCcore/10.3.0, GCCcore/11.2.0
3.6.7	GCCcore/11.3.0

dd

dd is a package for working with binary decision diagrams that includes both a pure Python implementation and Cython bindings to C libraries (CUDD, Sylvan, BuDDy). The Python and Cython modules implement the same API, so the same user code runs with both. All the standard operations on BDDs are available, including dynamic variable reordering using sifting, garbage collection, dump/load from files, plotting, and a parser of quantified Boolean expressions. This module includes bindings for: CUDD v3.0.0, Sylvan v1.0.0

homepage: https://github.com/tulip-control/dd

version	versionsuffix	toolchain
0.5.6	-Python-3.8.2	foss/2020a

deal.II

deal.II is a C++ program library targeted at the computational solution of partial differential equations using adaptive finite elements.

homepage: https://www.dealii.org

version	toolchain
9.1.1	foss/2019a, intel/2019a
9.3.3	foss/2021a

deap

DEAP is a novel evolutionary computation framework for rapid prototyping and testing of ideas. It seeks to make algorithms explicit and data structures transparent.

homepage: http://deap.readthedocs.org/en/master/

version	versionsuffix	toolchain
0.9.2	-Python-2.7.12	intel/2016b

decona

fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads

homepage: https://github.com/Saskia-Oosterbroek/decona

version	versionsuffix	toolchain
0.1.2	-Python-3.7.4	foss/2019b

deconf

decomposition (deconfounding) of OMICS datasets in heterogeneous tissues

homepage: http://web.cbio.uct.ac.za/~renaud/CRAN/

version	versionsuffix	toolchain
1.0.1	-R-3.5.1	foss/2018b

DeconICA

Deconvolution of transcriptome through Immune Component Analysis (DeconICA) is an R package for identifying immune-related signals in transcriptome through deconvolution or unsupervised source separation methods.

homepage: https://urszulaczerwinska.github.io/DeconICA

version	versionsuffix	toolchain
0.1.0	-R-3.5.1	foss/2018b

deepdiff

DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively.

homepage: https://zepworks.com/deepdiff/current/

version	versionsuffix	toolchain
3.3.0	-Python-2.7.15	intel/2018b
3.3.0	-Python-3.6.6	foss/2018b, intel/2018b
4.0.6	-Python-3.7.2	GCCcore/8.2.0
5.0.2	-Python-3.7.4	GCCcore/8.3.0
5.7.0		GCCcore/11.2.0
5.8.1		GCCcore/11.3.0
6.7.1		GCCcore/12.2.0, GCCcore/12.3.0

DeepLabCut

Markerless tracking of user-defined features with deep learning

homepage: http://www.mousemotorlab.org/deeplabcut

version	versionsuffix	toolchain
2.2.0.6		foss/2021a
2.2.0.6	-CUDA-11.3.1	foss/2021a
2.3.6	-CUDA-11.7.0	foss/2022a

DeepLoc

DeepLoc 2.0 predicts the subcellular localization(s) of eukaryotic proteins

homepage: https://services.healthtech.dtu.dk/services/DeepLoc-2.0

version	toolchain
2.0	foss/2022b

deepmedic

Efficient Multi-Scale 3D Convolutional Neural Network for Segmentation of 3D Medical Scans.

homepage: https://biomedia.doc.ic.ac.uk/software/deepmedic/

version	versionsuffix	toolchain
0.8.2		foss/2021a
0.8.2	-CUDA-11.3.1	foss/2021a

DeepMod2

DeepMod2 is a computational tool for detecting DNA methylation and modifications from Oxford Nanopore reads.

homepage: https://github.com/WGLab/DeepMod2

version	toolchain
0.0.1	foss/2021a

DeepSurv

DeepSurv is a deep learning approach to survival analysis.

homepage: https://github.com/jaredleekatzman/DeepSurv

version	versionsuffix	toolchain
2.0.0-20180922	-Python-3.6.6	fosscuda/2018b

deepTools

deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.

homepage: https://deeptools.readthedocs.io/

version	versionsuffix	toolchain
2.5.4	-Python-3.6.3	intel/2017b
3.3.1	-Python-3.6.6	foss/2018b
3.3.1	-Python-3.7.4	intel/2019b
3.3.1	-Python-3.8.2	foss/2020a
3.5.0		foss/2021a
3.5.1		foss/2021b
3.5.2		foss/2022a

DEICODE

DEICODE is a form of Aitchison Distance that is robust to high levels of sparsity. DEICODE utilizes a natural solution to the zero problem formulated in recommendation systems called matrix completion. A simple way to interpret the method is, as a robust compositional PCA (via SVD) where zero values do not influence the resulting ordination.

homepage: https://library.qiime2.org/plugins/deicode/19/

version	toolchain
0.2.4	foss/2022a

Delft3D

Simulation of multi-dimensional hydrodynamic flows and transport phenomena, including sediments. Delft3D-FLOW is part of Delft3D 4.

homepage: https://oss.deltares.nl/web/delft3d

version	versionsuffix	toolchain
4.04.01	-FLOW	foss/2022a

Delly

Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.

homepage: https://github.com/dellytools/delly/

version	versionsuffix	toolchain
0.7.8	-linux_x86_64	system
0.8.7		gompi/2020b
1.1.5		GCC/11.3.0
1.1.6		GCC/12.2.0

DeltaLake

Native Delta Lake Python binding based on delta-rs with Pandas integration. The Delta Lake project aims to unlock the power of the Deltalake for as many users and projects as possible by providing native low-level APIs aimed at developers and integrators, as well as a high-level operations API that lets you query, inspect, and operate your Delta Lake with ease.

homepage: https://delta-io.github.io/delta-rs/

version	toolchain
0.15.1	gfbf/2023a

DeMixT

Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms.

homepage: https://bioinformatics.mdanderson.org/main/DeMixT

version	versionsuffix	toolchain
0.2.1	-R-3.5.1	foss/2018b

Demystify

Demystify is a tool which allows puzzles to be expressed in a high-level constraint programming language and uses MUSes to automatically produce descriptions of steps in the puzzle solving.

homepage: https://github.com/stacs-cp/demystify

version	toolchain
0.0.17	foss/2020b

DendroPy

A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.

homepage: https://dendropy.org/

version	versionsuffix	toolchain
4.4.0		GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0, intel/2019a
4.4.0	-Python-2.7.15	intel/2018b
4.5.2		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0
4.5.2	-Python-2.7.18	GCCcore/10.2.0
4.6.1		GCCcore/12.3.0

denseweight

This package implements the method for imbalanced regression DenseWeight. The corresponding paper "Density-based weighting for imbalanced regression". The goal of DenseWeight is to allow training machine learning models for regression tasks that emphasize performance for data points with rare target values in comparison to data points with more common target values.

homepage: https://github.com/steimi/denseweight

version	toolchain
0.1.2	foss/2022a, foss/2023a

DensPart

Atoms-in-molecules density partitioning schemes based on stockholder recipe

homepage: https://github.com/theochem/denspart

version	toolchain
20220603	intel/2022a

Deprecated

If you need to mark a function or a method as deprecated, you can use the @deprecated decorator.

homepage: https://github.com/tantale/deprecated

version	toolchain
1.2.13	foss/2021a, foss/2022a
1.2.14	foss/2023a

desktop-file-utils

desktop-file-utils contains a few command line utilities for working with desktop entries: * desktop-file-validate: validates a desktop file and prints warnings/errors about desktop entry specification violations. * desktop-file-install: installs a desktop file to the applications directory, optionally munging it a bit in transit. * update-desktop-database: updates the database containing a cache of MIME types handled by desktop files. It requires GLib to compile, because the implementation requires Unicode utilities and such.

homepage: https://www.freedesktop.org/wiki/Software/desktop-file-utils/

version	toolchain
0.27	GCCcore/12.3.0

destiny

R packages to create and plot diffusion maps.

homepage: https://bioconductor.org/packages/destiny

version	versionsuffix	toolchain
2.5.6	-R-3.4.0	intel/2017a

Detectron2

Detectron2 is Facebook AI Research's next generation library that provides state-of-the-art detection and segmentation algorithms. It is the successor of Detectron and maskrcnn-benchmark. It supports a number of computer vision research projects and production applications in Facebook.

homepage: https://github.com/facebookresearch/detectron2

version	versionsuffix	toolchain
0.6		foss/2021a
0.6	-CUDA-11.3.1	foss/2021a

DETONATE

DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation) consists of two component packages, RSEM-EVAL and REF-EVAL. Both packages are mainly intended to be used to evaluate de novo transcriptome assemblies, although REF-EVAL can be used to compare sets of any kinds of genomic sequences.

homepage: http://deweylab.biostat.wisc.edu/detonate/

version	toolchain
1.11	GCC/12.3.0, intel/2017b

devbio-napari

A bundle of napari plugins useful for 3D+t image processing and analysis for studying developmental biology.

homepage: https://github.com/haesleinhuepf/devbio-napari

version	versionsuffix	toolchain
0.10.1		foss/2022a
0.10.1	-CUDA-11.7.0	foss/2022a

Devito

Devito is a domain-specific Language (DSL) and code generation framework for performing optimised Finite Difference (FD) computation from high-level symbolic problem definitions. Devito performs automated code generation and Just-In-time (JIT) compilation based on symbolic equations defined in SymPy to create and execute highly optimised Finite Difference stencil kernels on multiple computer platforms.

homepage: https://www.devitoproject.org

version	versionsuffix	toolchain
4.6.1	-Python-3.8.2	foss/2020a

DFA

Python library for modeling DFAs, Moore Machines, and Transition Systems.

homepage: https://github.com/mvcisback/dfa

version	versionsuffix	toolchain
0.3.4	-Python-3.8.2	GCCcore/9.3.0
2.1.2		GCCcore/10.2.0

DFT-D3

DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods.

homepage: https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3

version	toolchain
3.2.0	GCC/8.3.0, iccifort/2020.4.304, intel-compilers/2021.2.0, intel-compilers/2021.4.0, intel-compilers/2022.2.1, intel/2019a

DFT-D4

Generally Applicable Atomic-Charge Dependent London Dispersion Correction.

homepage: https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dftd4

version	versionsuffix	toolchain
3.2.0	-Python-3.7.4	intel/2019b
3.6.0		intel/2022a

DFTB+

DFTB+ is a fast and efficient versatile quantum mechanical simulation package. It is based on the Density Functional Tight Binding (DFTB) method, containing almost all of the useful extensions which have been developed for the DFTB framework so far. Using DFTB+ you can carry out quantum mechanical simulations like with ab-initio density functional theory based packages, but in an approximate way gaining typically around two order of magnitude in speed.

homepage: https://www.dftb-plus.info

version	versionsuffix	toolchain
1.3.1		intel/2017a
17.1	-Python-2.7.14	intel/2017b
19.1	-Python-2.7.16	foss/2019b
19.1	-Python-2.7.16-mpi	foss/2019b
21.1		intel/2021a

dftd3-lib

This is a repackaged version of the DFTD3 program by S. Grimme and his coworkers. The original program (V3.1 Rev 1) was downloaded at 2016-04-03. It has been converted to free format and encapsulated into modules.

homepage: https://github.com/dftbplus/dftd3-lib

version	toolchain
0.9	GCC/8.3.0, intel-compilers/2021.2.0

dftd4

Generally Applicable Atomic-Charge Dependent London Dispersion Correction.

homepage: https://github.com/dftd4/dftd4

version	toolchain
3.4.0	gfbf/2022b, iimkl/2022b

DGL

DGL is an easy-to-use, high performance and scalable Python package for deep learning on graphs. DGL is framework agnostic, meaning if a deep graph model is a component of an end-to-end application, the rest of the logics can be implemented in any major frameworks, such as PyTorch, Apache MXNet or TensorFlow.

homepage: https://www.dgl.ai

version	versionsuffix	toolchain
0.6.1	-Python-3.7.4-PyTorch-1.8.1	fosscuda/2019b
0.9.1	-CUDA-11.3.1	foss/2021a

DIA-NN

DIA-NN is a universal software for data-independent acquisition (DIA) proteomics data processing.

homepage: https://github.com/vdemichev/DiaNN

version	toolchain
1.8.1	system

DIAL

DIAL (De novo Identification of Alleles) is a collection of programs to automate the discovery of alleles for a species where we lack a reference sequence. The SNPs/alleles are specifically selected for a low error rate in genotyping assays.

homepage: http://www.bx.psu.edu/miller_lab/

version	toolchain
2011.06.06	foss/2016a

dialog

A utility for creating TTY dialog boxes

homepage: https://invisible-island.net/

version	toolchain
1.3-20231002	GCCcore/10.3.0

DIALOGUE

DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map the cell transcriptome as a function of its environment.

homepage: https://github.com/livnatje/DIALOGUE

version	versionsuffix	toolchain
1.0-20230228	-R-4.2.0	foss/2021b

DIAMOND

Accelerated BLAST compatible local sequence aligner

homepage: https://github.com/bbuchfink/diamond

version	toolchain
0.9.22	foss/2018a, foss/2018b, intel/2018a, intel/2018b
0.9.24	iccifort/2019.1.144-GCC-8.2.0-2.31.1
0.9.30	GCC/8.3.0, iccifort/2019.5.281
0.9.36	GCC/9.3.0
2.0.4	GCC/9.3.0
2.0.6	GCC/7.3.0-2.30
2.0.7	GCC/10.2.0
2.0.11	GCC/10.3.0
2.0.13	GCC/10.3.0, GCC/11.2.0
2.1.0	GCC/11.3.0
2.1.8	GCC/10.3.0, GCC/12.2.0, GCC/12.3.0
2.1.9	GCC/13.2.0

Dice

Dice contains code for performing SHCI, VMC, GFMC, DMC, FCIQMC, stochastic MRCI and SC-NEVPT2, and AFQMC calculations with a focus on ab initio systems.

homepage: https://github.com/sanshar/Dice

version	toolchain
20221025	foss/2022a
20240101	foss/2022b

DiCE-ML

Diverse Counterfactual Explanations (DiCE) for ML

homepage: https://interpret.ml/DiCE

version	toolchain
0.9	foss/2022a

dicom2nifti

Python library for converting dicom files to nifti

homepage: https://github.com/icometrix/dicom2nifti

version	versionsuffix	toolchain
2.2.12	-Python-3.8.2	foss/2020a
2.3.0		foss/2020b, fosscuda/2020b

DicomBrowser

DicomBrowser is an application for inspecting and modifying DICOM metadata in many files at once.

homepage: http://nrg.wustl.edu/software/dicom-browser/

version	versionsuffix	toolchain
1.7.0b5	-Java-1.7.0_80	system

DiffBind

Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.

homepage: https://bioconductor.org/packages/release/bioc/html/DiffBind.html

version	versionsuffix	toolchain
3.6.5	-R-4.2.1	foss/2022a

Diffutils

Diffutils: GNU diff utilities - find the differences between files

homepage: http://www.gnu.org/software/diffutils/diffutils.html

version	toolchain
3.3	GCC/4.8.2

dijitso

dijitso is a Python module for distributed just-in-time shared library building.

homepage: https://bitbucket.org/fenics-project/dijitso

version	versionsuffix	toolchain
2019.1.0	-Python-3.7.4	foss/2019b

dill

dill extends python's pickle module for serializing and de-serializing python objects to the majority of the built-in python types. Serialization is the process of converting an object to a byte stream, and the inverse of which is converting a byte stream back to on python object hierarchy.

homepage: https://pypi.org/project/dill/

version	toolchain
0.3.0	GCCcore/8.2.0
0.3.3	GCCcore/10.2.0, GCCcore/8.3.0
0.3.4	GCCcore/10.3.0, GCCcore/11.2.0
0.3.6	GCCcore/11.3.0
0.3.7	GCCcore/12.2.0, GCCcore/12.3.0

DIRAC

DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations

homepage: http://www.diracprogram.org

version	versionsuffix	toolchain
19.0	-Python-2.7.18-int64	intel/2020a
19.0	-Python-2.7.18-mpi-int64	intel/2020a
22.0		foss/2021a, intel/2021a
22.0	-int64	intel/2021a
23.0		foss/2022a, foss/2022b, foss/2023a, intel/2022a, intel/2022b, intel/2023a
23.0	-int64	intel/2022b, intel/2023a

distributed

Dask.distributed is a lightweight library for distributed computing in Python. It extends both the concurrent.futures and dask APIs to moderate sized clusters.

homepage: https://distributed.readthedocs.io/

version	versionsuffix	toolchain
1.14.3	-Python-2.7.12	intel/2016b
1.14.3	-Python-3.5.2	intel/2016b
1.21.6	-Python-3.6.4	intel/2018a

DistributedStream

A MPI distributed stream benchmark, useful to identifying nodes with poor memory performance and characterising memory bandwidth variation over systems.

homepage: https://github.com/adrianjhpc/DistributedStream

version	toolchain
1.0	gompi/2021a

DjVuLibre

DjVuLibre is an open source (GPL'ed) implementation of DjVu, including viewers, browser plugins, decoders, simple encoders, and utilities.

homepage: http://djvu.sourceforge.net/

version	toolchain
3.5.28	GCCcore/12.3.0

DL_POLY_4

DL_POLY is a general purpose classical molecular dynamics (MD) simulation software

homepage: https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx

version	toolchain
5.0.0	foss/2020b, intel/2020b
5.1.0	foss/2022b, intel/2022b

DL_POLY_Classic

DL_POLY Classic is a freely available molecular dynamics program developed from the DL_POLY_2 package. This version does not install the java gui.

homepage: http://ccpforge.cse.rl.ac.uk/gf/project/dl_poly_classic/

version	versionsuffix	toolchain
1.9		intel/2016b
1.9	-PLUMED-2.2.3	intel/2016b
1.10		foss/2019b, intel/2019b

dlb

DLB is a dynamic library designed to speed up HPC hybrid applications (i.e., two levels of parallelism) by improving the load balance of the outer level of parallelism (e.g., MPI) by dynamically redistributing the computational resources at the inner level of parallelism (e.g., OpenMP). at run time.

homepage: https://pm.bsc.es/dlb/

version	toolchain
3.2	gompi/2022a, iimpi/2022a
3.3.1	gompi/2022a, iimpi/2022a
3.4	gompi/2023b, iimpi/2023b

dlib

Dlib is a modern C++ toolkit containing machine learning algorithms and tools for creating complex software in C++ to solve real world problems. It is used in both industry and academia in a wide range of domains including robotics, embedded devices, mobile phones, and large high performance computing environments.

homepage: https://github.com/davisking/dlib

version	versionsuffix	toolchain
19.22		foss/2021a
19.22	-CUDA-11.3.1	foss/2021a

DLPack

DLPack is a stable in-memory data structure for an ndarray system to interact with a variety of frameworks.

homepage: https://dmlc.github.io/dlpack/latest/

version	toolchain
0.3	GCC/10.3.0
0.8	GCC/11.3.0

dm-haiku

Haiku is a simple neural network library for JAX developed by some of the authors of Sonnet, a neural network library for TensorFlow.

homepage: https://github.com/deepmind/dm-haiku

version	versionsuffix	toolchain
0.0.9		foss/2022a
0.0.9	-CUDA-11.3.1	foss/2021a

dm-reverb

Reverb is an efficient and easy-to-use data storage and transport system designed for machine learning research. Reverb is primarily used as an experience replay system for distributed reinforcement learning algorithms but the system also supports multiple data structure representations such as FIFO, LIFO, and priority queues.

homepage: https://github.com/deepmind/reverb

version	toolchain
0.2.0	foss/2020b
0.7.0	foss/2021b

dm-tree

dm-tree provides tree, a library for working with nested data structures. In a way, tree generalizes the builtin map function which only supports flat sequences, and allows to apply a function to each "leaf" preserving the overall structure.

homepage: https://github.com/deepmind/tree

version	toolchain
0.1.1	GCCcore/8.3.0
0.1.5	GCCcore/10.2.0
0.1.6	GCCcore/10.3.0, GCCcore/11.2.0
0.1.8	GCCcore/11.3.0, GCCcore/12.3.0

DMCfun

Diffusion Model of Conflict (DMC) in Reaction Time Tasks

homepage: https://cran.r-project.org/web/packages/DMCfun

version	versionsuffix	toolchain
1.3.0	-R-3.6.2	foss/2019b

DMLC-Core

DMLC-Core is the backbone library to support all DMLC projects, offers the bricks to build efficient and scalable distributed machine learning libraries.

homepage: https://dmlc-core.readthedocs.io/en/latest

version	toolchain
0.5	GCC/10.3.0, GCC/11.3.0

DMTCP

DMTCP is a tool to transparently checkpoint the state of multiple simultaneous applications, including multi-threaded and distributed applications. It operates directly on the user binary executable, without any Linux kernel modules or other kernel modifications.

homepage: http://dmtcp.sourceforge.net/index.html

version	toolchain
2.4.5	system
2.5.0	foss/2016a
2.5.1	system
2.5.2	GCCcore/8.3.0, foss/2016b, foss/2018b
2.6.0	GCCcore/8.2.0, GCCcore/9.3.0
3.0.0	GCCcore/11.3.0

DOLFIN

DOLFIN is the C++/Python interface of FEniCS, providing a consistent PSE (Problem Solving Environment) for ordinary and partial differential equations.

homepage: https://bitbucket.org/fenics-project/dolfin

version	versionsuffix	toolchain
2018.1.0.post1	-Python-3.6.4	foss/2018a
2019.1.0.post0	-Python-3.7.4	foss/2019b

dominate

Dominate is a Python library for creating and manipulating HTML documents using an elegant DOM API. It allows you to write HTML pages in pure Python very concisely, which eliminates the need to learn another template language, and lets you take advantage of the more powerful features of Python.

homepage: https://github.com/Knio/dominate/

version	toolchain
2.8.0	GCCcore/11.3.0

dorado

Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.

homepage: https://github.com/nanoporetech/dorado

version	versionsuffix	toolchain
0.1.1	-CUDA-11.7.0	foss/2022a
0.3.0	-CUDA-11.7.0	foss/2022a
0.3.1	-CUDA-11.7.0	foss/2022a
0.5.1	-CUDA-11.7.0	foss/2022a

Doris

Delft object-oriented radar interferometric software

homepage: http://doris.tudelft.nl/

version	toolchain
4.02	intel/2017a
4.04beta4	foss/2018a, intel/2017a
4.06beta2	intel/2017a

DosageConvertor

DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3/4 to other formats such as MaCH or PLINK. Please note that this tool CANNOT handle missing values in the input files and may NOT work for non-Minimac3/4 VCF files.

homepage: http://genome.sph.umich.edu/wiki/DosageConvertor

version	toolchain
1.0.4	GCC/10.2.0

dotNET-Core-Runtime

.NET is a free, cross-platform, open source developer platform for building many different types of applications.

homepage: https://www.microsoft.com/net/

version	toolchain
2.0.7	GCCcore/6.4.0
5.0.17	GCCcore/10.3.0
6.0.1	GCCcore/11.2.0

dotNET-SDK

.NET is a free, cross-platform, open source developer platform for building many different types of applications.

homepage: https://www.microsoft.com/net/

version	versionsuffix	toolchain
3.1.300	-linux-x64	system
6.0.101	-linux-x64	system

double-conversion

Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles.

homepage: https://github.com/google/double-conversion

version	toolchain
3.0.3	foss/2018a
3.1.4	GCCcore/8.2.0, GCCcore/8.3.0
3.1.5	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/9.3.0
3.2.0	GCCcore/11.3.0
3.2.1	GCCcore/12.2.0
3.3.0	GCCcore/12.3.0, GCCcore/13.2.0

DoubletFinder

R package for detecting doublets in single-cell RNA sequencing data

homepage: https://github.com/chris-mcginnis-ucsf/DoubletFinder

version	versionsuffix	toolchain
2.0.3	-R-4.0.0	foss/2020a
2.0.3-20230131	-R-4.2.1	foss/2022a
2.0.3-20230819	-R-4.2.2	foss/2022b

Doxygen

Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.

homepage: https://www.doxygen.org

version	toolchain
1.8.9.1	GCC/4.9.2
1.8.10	GNU/4.9.3-2.25, intel/2016.02-GCC-4.9
1.8.11	GCC/4.9.2, GCCcore/5.4.0, foss/2016a, foss/2016b, intel/2016a, intel/2016b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25
1.8.13	GCCcore/6.3.0, GCCcore/6.4.0, gimkl/2017a
1.8.14	GCCcore/6.4.0, GCCcore/7.2.0, GCCcore/7.3.0
1.8.15	GCCcore/8.2.0
1.8.16	GCCcore/8.3.0
1.8.17	GCCcore/9.3.0
1.8.20	GCCcore/10.2.0
1.9.1	GCCcore/10.3.0, GCCcore/11.2.0
1.9.4	GCCcore/11.3.0
1.9.5	GCCcore/12.2.0
1.9.7	GCCcore/12.3.0
1.9.8	GCCcore/13.2.0

DP3

DP3: streaming processing pipeline for radio interferometric data.

homepage: https://dp3.readthedocs.io/

version	toolchain
6.0	foss/2022a, foss/2023b

DRAGMAP

Dragmap is the Dragen mapper/aligner Open Source Software.

homepage: https://github.com/Illumina/DRAGMAP

version	toolchain
1.3.0	foss/2021b

Drake

Drake is a simple-to-use, extensible, text-based data workflow tool that organizes command execution around data and its dependencies.

homepage: https://github.com/Factual/drake

version	versionsuffix	toolchain
1.0.3	-Java-1.8	system

dRep

dRep is a python program which performs rapid pair-wise comparison of genome sets. One of it’s major purposes is for genome de-replication, but it can do a lot more.

homepage: https://drep.readthedocs.io/en/latest/

version	toolchain
3.0.0	foss/2021a
3.4.2	foss/2022a

drmaa-python

Distributed Resource Management Application API (DRMAA) bindings for Python.

homepage: https://github.com/pygridtools/drmaa-python

version	versionsuffix	toolchain
0.7.9	-slurm	GCCcore/12.2.0

DROP

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders

homepage: https://gagneurlab-drop.readthedocs.io

version	versionsuffix	toolchain
1.0.3	-R-4.0.3	foss/2020b
1.1.0	-R-4.0.3	foss/2020b
1.1.1	-R-4.1.2	foss/2021b

dropEst

Pipeline for initial analysis of droplet-based single-cell RNA-seq data

homepage: https://github.com/hms-dbmi/dropEst

version	versionsuffix	toolchain
0.7.1	-R-3.4.3	intel/2017b

DSA

Digital Sorting Algorithm

homepage: https://github.com/zhandong/DSA

version	versionsuffix	toolchain
1.0	-R-3.5.1	foss/2018b

dSFMT

Double precision SIMD-oriented Fast Mersenne Twister.

homepage: https://github.com/MersenneTwister-Lab/dSFMT

version	toolchain
2.2.5	GCCcore/10.2.0

DSRC

DNA Sequence Reads Compression is an application designed for compression of data files containing reads from DNA sequencing in FASTQ format. The amount of such files can be huge, e.g., a few (or tens) of gigabytes, so a need for a robust data compression tool is clear. Usually universal compression programs like gzip or bzip2 are used for this purpose, but it is obvious that a specialized tool can work better.

homepage: http://sun.aei.polsl.pl/dsrc

version	versionsuffix	toolchain
2.0rc	-linux-64-bit	system

Dsuite

Fast calculation of the ABBA-BABA statistics across many populations/species

homepage: https://github.com/millanek/Dsuite

version	toolchain
20190713	iccifort/2019.1.144-GCC-8.2.0-2.31.1
20210718	GCC/10.3.0, intel-compilers/2021.2.0

dtcmp

The Datatype Comparison (DTCMP) Library provides pre-defined and user-defined comparison operations to compare the values of two items which can be arbitrary MPI datatypes. Using these comparison operations, the library provides various routines for manipulating data, which may be distributed over the processes of an MPI communicator.

homepage: https://github.com/LLNL/dtcmp

version	toolchain
1.1.0	gompi/2019a, gompi/2020a, iimpi/2019a, iimpi/2020a
1.1.2	gompi/2020b
1.1.4	gompi/2022a, gompi/2023a

dtcwt

Dual-Tree Complex Wavelet Transform library for Python

homepage: https://github.com/rjw57/dtcwt

version	versionsuffix	toolchain
0.12.0	-Python-2.7.15	foss/2018b
0.12.0	-Python-3.7.4	intel/2019b

DualSPHysics

DualSPHysics is based on the Smoothed Particle Hydrodynamics model named SPHysics. The code is developed to study free-surface flow phenomena where Eulerian methods can be difficult to apply, such as waves or impact of dam-breaks on off-shore structures. DualSPHysics is a set of C++, CUDA and Java codes designed to deal with real-life engineering problems.

homepage: https://dual.sphysics.org/

version	versionsuffix	toolchain
5.0.175		GCC/11.2.0
5.0.175	-CUDA-%(cudaver)s	GCC/11.2.0

DUBStepR

DUBStepR (Determining the Underlying Basis using Step-wise Regression) is a feature selection algorithm for cell type identification in single-cell RNA-sequencing data.

homepage: https://github.com/prabhakarlab/DUBStepR

version	versionsuffix	toolchain
1.2.0	-R-4.1.2	foss/2021b

dune-core

The Dune core modules build the stable basis of Dune. They follow a consistent release cycle and have high requirements regarding stability and backwards compatibility. These modules build the foundation for higher-level components.

homepage: https://www.dune-project.org/groups/core/

version	toolchain
2.8.0.post1	foss/2020b

dune-fem

DUNE-FEM is a discretization module based on DUNE containing all the building blocks required to implement efficient solvers for a wide range of (systems of non linear) partial differential equations. DUNE-FEM can also be used through an extensive Python interface which brings all components of DUNE-FEM and the DUNE core modules to Python.

homepage: https://www.dune-project.org/modules/dune-fem/

version	toolchain
2.8.0.6	foss/2020b

duplex-tools

Duplex Tools contains a set of utilities for dealing with Duplex sequencing data. Tools are provided to identify and prepare duplex pairs for basecalling by Dorado (recommended) and Guppy, and for recovering simplex basecalls from incorrectly concatenated pairs.

homepage: https://github.com/nanoporetech/duplex-tools

version	toolchain
0.3.1	foss/2022a
0.3.3	foss/2022a

dx-toolkit

The DNAnexus Platform SDK - also called dx-toolkit - includes the dx command-line client; tools for building and debugging apps; utilities for working with DNA data on the DNAnexus Platform; and Python, Java, C++ and R bindings for working on the DNAnexus Platform.

homepage: https://documentation.dnanexus.com/downloads#dnanexus-platform-sdk

version	toolchain
0.350.1	GCCcore/12.2.0

dxpy

DNAnexus Platform API bindings for Python

homepage: http://autodoc.dnanexus.com/

version	versionsuffix	toolchain
0.266.1	-Python-2.7.14	intel/2018a
0.345.0		GCCcore/12.2.0

DyMat

Read and process result files from Dymola and OpenModelica with Python.

homepage: https://www.j-raedler.de/projects/DyMat

version	versionsuffix	toolchain
0.7	-2020-12-12	foss/2021b

dynesty

dynesty is a Pure Python, MIT-licensed Dynamic Nested Sampling package for estimating Bayesian posteriors and evidences.

homepage: https://dynesty.readthedocs.io/

version	toolchain
2.1.3	foss/2023a

E

E-ANTIC - e3nn - ea-utils - earthengine-api - easel - EasyBuild - EasyQC - ebGSEA - ecBuild - ecCodes - eccodes-python - ecFlow - ECL - eclib - ED2 - EDirect - edlib - EggLib - eggnog-mapper - EGTtools - eht-imaging - Eigen - EigenExa - EIGENSOFT - einops - elastix - elbencho - ELFIO - elfutils - Elk - Elmer - ELPA - ELPH - elprep - ELSI - ELSI-RCI - Emacs - EMAN2 - EMBOSS - Embree - emcee - EMU - enaBrowserTool - enchant - enchant-2 - EnergyPlus - EnsEMBLCoreAPI - entrypoints - epct - EPD - EPIC - epiScanpy - EpiSCORE - eQuilibrator - EricScript - ESL-Bundle - ESM-2 - ESMF - ESMPy - ESMValTool - eSpeak-NG - ESPResSo - Essentia - ETE - ETSF_IO - eudev - EUKulele - Evcxr-REPL - EveryBeam - EvidentialGene - evince - evmix - ExaBayes - ExaML - Excel-Writer-XLSX - ExifTool - exiv2 - Exonerate - expat - expect - expecttest - eXpress - ExpressBetaDiversity - Extrae - ExtremeLy - EZC3D

E-ANTIC

E-ANTIC is a C/C++ library to deal with real embedded number fields built on top of ANTIC (https://github.com/wbhart/antic). Its aim is to have as fast as possible exact arithmetic operations and comparisons.

homepage: https://github.com/flatsurf/e-antic

version	toolchain
0.1.2	GCC/8.2.0-2.31.1
0.1.5	GCC/8.3.0
1.3.0	gfbf/2022a

e3nn

Euclidean neural networks (e3nn) is a python library based on pytorch to create equivariant neural networks for the group O(3).

homepage: https://e3nn.org/

version	versionsuffix	toolchain
0.3.3		foss/2022a
0.3.3	-CUDA-11.7.0	foss/2022a

ea-utils

Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs.

homepage: http://expressionanalysis.github.io/ea-utils/

version	toolchain
1.04.807	foss/2016a, foss/2016b, intel/2016b

earthengine-api

Python and JavaScript bindings for calling the Earth Engine API

homepage: https://github.com/google/earthengine-api

version	versionsuffix	toolchain
0.1.143	-Python-2.7.14	intel/2018a

easel

Easel supports computational analysis of biological sequences using probabilistic models.

homepage: https://bioeasel.org/

version	toolchain
0.48	GCC/12.2.0

EasyBuild

EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.

homepage: https://easybuilders.github.io/easybuild

version	toolchain
1.0.0	system
1.0.1	system
1.0.2	system
1.1.0	system
1.2.0	system
1.3.0	system
1.4.0	system
1.5.0	system
1.6.0	system
1.7.0	system
1.8.0	system
1.8.1	system
1.8.2	system
1.9.0	system
1.10.0	system
1.11.0	system
1.11.1	system
1.12.0	system
1.12.1	system
1.13.0	system
1.14.0	system
1.15.0	system
1.15.1	system
1.15.2	system
1.16.0	system
1.16.1	system
1.16.2	system
2.0.0	system
2.1.0	system
2.1.1	system
2.2.0	system
2.3.0	system
2.4.0	system
2.5.0	system
2.6.0	system
2.7.0	system
2.8.0	system
2.8.1	system
2.8.2	system
2.9.0	system
3.0.0	system
3.0.1	system
3.0.2	system
3.1.0	system
3.1.1	system
3.1.2	system
3.2.0	system
3.2.1	system
3.3.0	system
3.3.1	system
3.4.0	system
3.4.1	system
3.5.0	system
3.5.1	system
3.5.2	system
3.5.3	system
3.6.0	system
3.6.1	system
3.6.2	system
3.7.0	system
3.7.1	system
3.8.0	system
3.8.1	system
3.9.0	system
3.9.1	system
3.9.2	system
3.9.3	system
3.9.4	system
4.0.0	system
4.0.1	system
4.1.0	system
4.1.1	system
4.1.2	system
4.2.0	system
4.2.1	system
4.2.2	system
4.3.0	system
4.3.1	system
4.3.2	system
4.3.3	system
4.3.4	system
4.4.0	system
4.4.1	system
4.4.2	system
4.5.0	system
4.5.1	system
4.5.2	system
4.5.3	system
4.5.4	system
4.5.5	system
4.6.0	system
4.6.1	system
4.6.2	system
4.7.0	system
4.7.1	system
4.7.2	system
4.8.0	system
4.8.1	system
4.8.2	system
4.9.0	system

EasyQC

EasyQC is an R-package that provides advanced functionality to (1) perform file-level QC of single genome-wide association (GWA) data-sets (2) conduct quality control across several GWA data-sets (meta-level QC) (3) simplify data-handling of large-scale GWA data-sets.

homepage: http://www.uni-regensburg.de/medizin/epidemiologie-praeventivmedizin/genetische-epidemiologie/software/

version	versionsuffix	toolchain
9.2	-R-3.3.1	intel/2016b

ebGSEA

Gene Set Enrichment Analysis is one of the most common tasks in the analysis of omic data, and is critical for biological interpretation. In the context of Epigenome Wide Association Studies (EWAS), which typically rank individual cytosines according to the level of differential methylation, enrichment analysis of biological pathways is challenging due to differences in CpG/probe density between genes.

homepage: https://github.com/aet21/ebGSEA

version	versionsuffix	toolchain
0.1.0	-R-4.2.1	foss/2022a

ecBuild

A CMake-based build system, consisting of a collection of CMake macros and functions that ease the managing of software build systems

homepage: https://ecbuild.readthedocs.io/

version	toolchain
3.7.0	system
3.8.0	system

ecCodes

ecCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).

homepage: https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home

version	versionsuffix	toolchain
2.7.3		intel/2018a
2.7.3	-Python-2.7.14	intel/2017b
2.8.2		intel/2018a
2.9.2		intel/2018b, iomkl/2018b
2.12.5		gompi/2019a
2.15.0		gompi/2019b, iimpi/2019b
2.17.0		foss/2018b, gompi/2019b
2.18.0		gompi/2020a
2.20.0		gompi/2020b
2.22.1		gompi/2021a
2.24.2		gompi/2021b, iimpi/2021b
2.27.0		gompi/2022a
2.31.0		gompi/2022b, gompi/2023a, gompi/2023b

eccodes-python

Python 3 interface to decode and encode GRIB and BUFR files via the ECMWF ecCodes library.

homepage: https://github.com/ecmwf/eccodes-python

version	versionsuffix	toolchain
1.0.0	-Python-3.7.4	foss/2019b
1.0.0	-Python-3.8.2	foss/2020a
1.1.0		foss/2020b

ecFlow

ecFlow is a client/server workflow package that enables users to run a large number of programs (with dependencies on each other and on time) in a controlled environment. It provides reasonable tolerance for hardware and software failures, combined with restart capabilities. It is used at ECMWF to run all our operational suites across a range of platforms.

homepage: https://ecflow.readthedocs.io/en/latest/index.html

version	toolchain
5.7.0	GCC/10.2.0

ECL

ECL (Embeddable Common-Lisp) is an interpreter of the Common-Lisp language as described in the X3J13 Ansi specification, featuring CLOS (Common-Lisp Object System), conditions, loops, etc, plus a translator to C, which can produce standalone executables.

homepage: https://ecl.common-lisp.dev/

version	toolchain
23.9.9	GCCcore/11.3.0

eclib

The eclib package includes mwrank (for 2-descent on elliptic curves over Q) and modular symbol code used to create the elliptic curve database.

homepage: https://github.com/JohnCremona/eclib

version	toolchain
20230424	GCC/11.3.0

ED2

The Ecosystem Demography Biosphere Model (ED2) is an integrated terrestrial biosphere model incorporating hydrology, land-surface biophysics, vegetation dynamics, and soil carbon and nitrogen biogeochemistry

homepage: https://github.com/EDmodel/ED2

version	versionsuffix	toolchain
20170201		intel/2017a
20170201	-serial	intel/2017a

EDirect

Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases from a Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in a variety of formats.

homepage: https://www.ncbi.nlm.nih.gov/books/NBK25501/

version	toolchain
19.7.20230531	GCCcore/10.3.0
20.5.20231006	GCCcore/12.2.0, GCCcore/12.3.0

edlib

Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance.

homepage: https://martinsos.github.io/edlib

version	versionsuffix	toolchain
1.3.8.post1	-Python-3.7.4	GCC/8.3.0, iccifort/2019.5.281
1.3.8.post1	-Python-3.8.2	GCC/9.3.0
1.3.8.post2	-Python-3.8.2	iccifort/2020.1.217
1.3.9		GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/11.3.0, GCC/12.2.0, GCC/12.3.0

EggLib

EggLib is a C++/Python library and program package for evolutionary genetics and genomics.

homepage: https://egglib.org

version	toolchain
2.1.10	intel/2016a
3.3.0	GCC/13.2.0

eggnog-mapper

EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Common uses of eggNOG-mapper include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.

homepage: https://github.com/eggnogdb/eggnog-mapper

version	versionsuffix	toolchain
1.0.3	-Python-2.7.14	intel/2018a
2.1.4		foss/2020b
2.1.7		foss/2021b
2.1.9		foss/2022a
2.1.10		foss/2020b

EGTtools

EGTtools provides a centralized repository with analytical and numerical methods to study/model game theoretical problems under the Evolutionary Game Theory (EGT) framework.

homepage: https://github.com/Socrats/EGTTools

version	toolchain
0.1.10.dev2	foss/2021b
0.1.11	foss/2022a

eht-imaging

Python modules for simulating and manipulating VLBI data and producing images with regularized maximum likelihood methods.

homepage: https://github.com/achael/eht-imaging

version	toolchain
1.2.2	foss/2021a

Eigen

Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.

homepage: https://eigen.tuxfamily.org

version	toolchain
3.2.3	foss/2016a, foss/2016b
3.2.5	system
3.2.6	system
3.2.7	foss/2016a, intel/2016a
3.2.8	foss/2016a, intel/2016a, system
3.2.9	foss/2016b, intel/2016b
3.2.10	intel/2016b
3.3.2	foss/2016b, intel/2016b
3.3.3	GCCcore/6.3.0, intel/2016b
3.3.4	system
3.3.5	system
3.3.7	GCCcore/9.3.0, system
3.3.8	GCCcore/10.2.0
3.3.9	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0
3.4.0	GCCcore/10.2.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

EigenExa

EigenExa, a part of KMATHLIB, is a high performance eigen-solver.

homepage: https://www.r-ccs.riken.jp/labs/lpnctrt/projects/eigenexa/

version	toolchain
2.11	intel/2020b

EIGENSOFT

The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.

homepage: http://www.hsph.harvard.edu/alkes-price/software/

version	toolchain
6.0.1	foss/2016a
6.1.1	foss/2016a
6.1.4	foss/2016b
7.2.1	foss/2018b, foss/2019a, foss/2019b, foss/2020b, foss/2021a, intel/2019a

einops

Flexible and powerful tensor operations for readable and reliable code. Supports numpy, pytorch, tensorflow, jax, and others.

homepage: https://einops.rocks/

version	toolchain
0.3.2	GCCcore/10.2.0
0.4.1	GCCcore/10.3.0, GCCcore/11.3.0
0.7.0	GCCcore/12.3.0

elastix

elastix: a toolbox for rigid and nonrigid registration of images.

homepage: http://elastix.isi.uu.nl/

version	versionsuffix	toolchain
4.9.0		foss/2018a
5.0.0	-Python-3.7.4	foss/2019b

elbencho

A distributed storage benchmark for files, objects & blocks with support for GPUs

homepage: https://github.com/breuner/elbencho

version	toolchain
2.0-3	GCC/10.3.0

ELFIO

ELFIO is a header-only C++ library intended for reading and generating files in the ELF binary format.

homepage: http://elfio.sourceforge.net

version	toolchain
3.9	system

elfutils

The elfutils project provides libraries and tools for ELF files and DWARF data.

homepage: https://elfutils.org/

version	toolchain
0.182	GCCcore/9.3.0
0.183	GCCcore/10.2.0
0.185	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/8.2.0, GCCcore/8.3.0
0.187	GCCcore/11.3.0
0.189	GCCcore/12.2.0, GCCcore/12.3.0
0.190	GCCcore/13.2.0

Elk

An all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features. Written originally at Karl-Franzens-Universität Graz as a milestone of the EXCITING EU Research and Training Network, the code is designed to be as simple as possible so that new developments in the field of density functional theory (DFT) can be added quickly and reliably.

homepage: http://elk.sourceforge.net/

version	toolchain
4.0.15	intel/2016b
4.3.6	intel/2017a
6.3.2	intel/2019b
7.0.12	foss/2020b
7.2.42	foss/2021a
8.5.2	foss/2022a

Elmer

Elmer is an open source multiphysical simulation software mainly developed by CSC - IT Center for Science (CSC). Elmer includes physical models of fluid dynamics, structural mechanics, electromagnetics, heat transfer and acoustics, for example. These are described by partial differential equations which Elmer solves by the Finite Element Method (FEM).

homepage: https://www.csc.fi/web/elmer/elmer

version	toolchain
9.0	foss/2022b

ELPA

Eigenvalue SoLvers for Petaflop-Applications.

homepage: https://elpa.mpcdf.mpg.de/

version	versionsuffix	toolchain
2015.02.002		foss/2018a, gimkl/2017a, intel/2018a
2016.05.004		intel/2016b, intel/2017a
2016.11.001.pre		foss/2018b, intel/2018b
2017.11.001		foss/2018b, intel/2018a, intel/2018b
2018.05.001		foss/2018b, intel/2018b
2018.11.001		intel/2019a
2019.11.001		foss/2019b, foss/2020a, intel/2019b, intel/2020a, iomkl/2019b
2020.05.001		intel/2020a
2020.11.001		foss/2020b, intel/2020b
2021.05.001		foss/2021a, foss/2021b, intel/2021a, intel/2021b
2021.05.002		intel/2020b
2021.11.001		foss/2021b, foss/2022a, intel/2021b, intel/2022a, intel/2022b
2022.05.001		foss/2022a, foss/2022b, intel/2022a, intel/2022b
2022.05.001	-CUDA-11.7.0	foss/2022a
2022.05.001	-CUDA-12.0.0	foss/2022b
2023.05.001		foss/2023a, intel/2023a
2023.11.001		foss/2023b, intel/2023b

ELPH

ELPH is a general-purpose Gibbs sampler for finding motifs in a set of DNA or protein sequences. The program takes as input a set containing anywhere from a few dozen to thousands of sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. We have used ELPH to find patterns such as ribosome binding sites (RBSs) and exon splicing enhancers (ESEs).

homepage: http://ccb.jhu.edu/software/ELPH/index.shtml

version	toolchain
1.0.1	foss/2018b

elprep

elPrep is a high-performance tool for analyzing .sam/.bam files (up to and including variant calling) in sequencing pipelines.

homepage: https://github.com/ExaScience/elprep

version	toolchain
5.1.1	system

ELSI

ELSI provides and enhances scalable, open-source software library solutions for electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. The ELSI infrastructure should also be useful for other challenging eigenvalue problems.

homepage: https://wordpress.elsi-interchange.org/

version	versionsuffix	toolchain
2.5.0		foss/2019b, intel/2019b
2.5.0	-PEXSI	foss/2019b, intel/2019b
2.6.4	-PEXSI	foss/2020b, intel/2020b
2.7.1	-PEXSI	foss/2021a, intel/2021a

ELSI-RCI

ELSI-RCI provides and enhances open-source software packages which iteratively solve or circumvent eigenvalue problems in self-consistent field calculations based on the Kohn-Sham density-functional theory.

homepage: https://wordpress.elsi-interchange.org/

version	toolchain
0.1.0	GCC/10.3.0, GCC/11.2.0, foss/2020b, intel-compilers/2021.2.0, intel-compilers/2021.4.0, intel/2020b

Emacs

GNU Emacs is an extensible, customizable text editor--and more. At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming language with extensions to support text editing.

homepage: https://www.gnu.org/software/emacs/

version	versionsuffix	toolchain
24.3		GCC/4.8.3
24.3	-bare	GCC/4.8.3
24.4		GCC/4.9.2
24.5		GCC/4.9.3-2.25
25.1		foss/2016a
25.3		GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.3.0
26.3		GCCcore/8.3.0
27.1		GCCcore/10.2.0, GCCcore/9.3.0
27.2		GCCcore/11.2.0
28.1		GCCcore/10.2.0
28.2		GCCcore/12.2.0

EMAN2

EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes.

homepage: https://blake.bcm.edu/emanwiki/EMAN2

version	versionsuffix	toolchain
2.3		system
2.3	-Python-2.7.15	foss/2019a, fosscuda/2019a
2.21a	-Python-2.7.14-Boost-1.63.0	foss/2018a

EMBOSS

EMBOSS is 'The European Molecular Biology Open Software Suite'. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.

homepage: http://emboss.sourceforge.net/

version	versionsuffix	toolchain
6.6.0		GCC/8.2.0-2.31.1, foss/2016b, foss/2018b, foss/2021a, foss/2021b, iccifort/2019.1.144-GCC-8.2.0-2.31.1, intel/2017a, intel/2018b
6.6.0	-Java-11	GCC/8.3.0
6.6.0	-Java-13	GCC/10.2.0
6.6.0	-X11-20170314	intel/2017a

Embree

Intel® Embree is a collection of high-performance ray tracing kernels, developed at Intel. The target users of Intel® Embree are graphics application engineers who want to improve the performance of their photo-realistic rendering application by leveraging Embree's performance-optimized ray tracing kernels. The kernels are optimized for the latest Intel® processors with support for SSE, AVX, AVX2, and AVX-512 instructions. Intel® Embree supports runtime code selection to choose the traversal and build algorithms that best matches the instruction set of your CPU. We recommend using Intel® Embree through its API to get the highest benefit from future improvements. Intel® Embree is released as Open Source under the Apache 2.0 license.

homepage: https://embree.github.io/

version	toolchain
3.4.0	iccifort/2018.1.163-GCC-6.4.0-2.28
3.13.4	system

emcee

Emcee is an extensible, pure-Python implementation of Goodman & Weare's Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler. It's designed for Bayesian parameter estimation and it's really sweet!

homepage: https://emcee.readthedocs.io/

version	versionsuffix	toolchain
2.2.1		foss/2019a
2.2.1	-Python-2.7.15	foss/2018b, intel/2018b
2.2.1	-Python-3.6.6	foss/2018b, intel/2018b
3.1.4		foss/2021b, foss/2022a

EMU

EMU infers population structure in the presence of missingness and works for both haploid, psuedo-haploid and diploid genotype datasets

homepage: http://www.popgen.dk/software/index.php/EMU

version	versionsuffix	toolchain
0.66	-Python-3.7.4	foss/2019b

enaBrowserTool

enaBrowserTools is a set of scripts that interface with the ENA web services to download data from ENA easily, without any knowledge of scripting required.

homepage: https://github.com/enasequence/enaBrowserTools/

version	versionsuffix	toolchain
1.5.4	-Python-3.7.2	GCCcore/8.2.0
1.6		GCCcore/10.3.0

enchant

Enchant is a library (and command-line program) that wraps a number of different spelling libraries and programs with a consistent interface.

homepage: https://abiword.github.io/enchant/

version	toolchain
1.6.1	intel/2017a

enchant-2

Enchant aims to provide a simple but comprehensive abstraction for dealing with different spell checking libraries in a consistent way. A client, such as a text editor or word processor, need not know anything about a specific spell-checker, and since all back-ends are plugins, new spell-checkers can be added without needing any change to the program using Enchant.

homepage: https://github.com/AbiWord/enchant

version	toolchain
2.3.3	GCCcore/11.2.0, GCCcore/11.3.0
2.6.5	GCCcore/12.3.0

EnergyPlus

EnergyPlus is a whole building energy simulation program that engineers, architects, and researchers use to model both energy consumption—for heating, cooling, ventilation, lighting and plug and process loads—and water use in buildings.

homepage: https://energyplus.net/

version	toolchain
23.2.0	foss/2022a

EnsEMBLCoreAPI

The Ensembl Core Perl API and SQL schema

homepage: https://www.ensembl.org/info/docs/api/index.html

version	versionsuffix	toolchain
96.0-r20190601	-Perl-5.28.1	foss/2019a

entrypoints

Entry points are a way for Python packages to advertise objects with some common interface.

homepage: https://github.com/takluyver/entrypoints

version	versionsuffix	toolchain
0.2.2	-Python-2.7.11	foss/2016a
0.2.2	-Python-2.7.12	foss/2016b, intel/2016b
0.2.2	-Python-3.5.1	foss/2016a
0.2.2	-Python-3.5.2	intel/2016b

epct

This is the epct (EUMETSAT Product Customisation Toolbox) Python package for the EUMETSAT Data Tailor. The EUMETSAT Data Tailor makes it possible for users to subset and aggregate EUMETSAT data products in space and time, filter layers, generate quicklooks, project onto new coordinate reference systems, and reformat into common GIS formats (netCDF, GeoTIFF, etc.).

homepage: https://gitlab.eumetsat.int/eumetlab/data-services/eumdac

version	toolchain
3.2.0	foss/2022a

EPD

The Enthought Python Distribution provides scientists with a comprehensive set of tools to perform rigorous data analysis and visualization. Python, distinguished by its flexibility, coherence, and ease-of-use, is rapidly becoming the programming language of choice for researchers worldwide. EPD extends this capacity with a powerful collection of Python libraries to enable interactive technical computing and cross-platform rapid application development.

homepage: http://www.enthought.com/products/edudownload.php

version	toolchain
7.3-2-rh5	system

EPIC

Package implementing EPIC method to estimate the proportion of immune, stromal, endothelial and cancer or other cells from bulk gene expression data.

homepage: https://gfellerlab.shinyapps.io/EPIC_1-1

version	versionsuffix	toolchain
1.1	-R-3.5.1	foss/2018b

epiScanpy

EpiScanpy is a toolkit to analyse single-cell open chromatin (scATAC-seq) and single-cell DNA methylation (for example scBS-seq) data. EpiScanpy is the epigenomic extension of the very popular scRNA-seq analysis tool Scanpy (Genome Biology, 2018) [Wolf18].

homepage: https://github.com/colomemaria/episcanpy

version	toolchain
0.3.1	foss/2021a
0.4.0	foss/2022a, foss/2023a

EpiSCORE

Epigenetic cell-type deconvolution from Single-Cell Omic Reference profiles

homepage: https://github.com/aet21/EpiSCORE

version	versionsuffix	toolchain
0.9.5-20220621	-R-4.2.1	foss/2022a

eQuilibrator

Calculation of standard thermodynamic potentials of biochemical reactions.

homepage: https://equilibrator.weizmann.ac.il/

version	toolchain
0.4.7	foss/2021a

EricScript

EricScript is a computational framework for the discovery of gene fusions in paired end RNA-seq data.

homepage: https://sites.google.com/site/bioericscript/home

version	versionsuffix	toolchain
0.5.5	-R-3.4.0	intel/2017a

ESL-Bundle

The ESL Bundle is a collection of libraries and utilities broadly used in electronic structure calculations, put together to make their use easier by researchers and scientific software developers. ESL stands for Electronic Structure Library, an initiative which distributes quality software and promotes open standards for high-performance computing applications in the field of electronic structure calculations.

homepage: https://esl.cecam.org

version	toolchain
0.6.1	foss/2020b, intel/2020b

ESM-2

ESM-2 outperforms all tested single-sequence protein language models across a range of structure prediction tasks. ESMFold harnesses the ESM-2 language model to generate accurate structure predictions end to end directly from the sequence of a protein.

homepage: https://github.com/facebookresearch/esm

version	versionsuffix	toolchain
2.0.0		foss/2021a, foss/2022b
2.0.0	-CUDA-11.3.1	foss/2021a

ESMF

The Earth System Modeling Framework (ESMF) is a suite of software tools for developing high-performance, multi-component Earth science modeling applications.

homepage: https://www.earthsystemcog.org/projects/esmf/

version	versionsuffix	toolchain
6.3.0rp1		intel/2017a
6.3.0rp1	-HDF5-1.8.18	intel/2017a
7.0.0		foss/2016a
7.0.2		intel/2017b
7.1.0r		foss/2018b, foss/2019a, intel/2018a, intel/2018b, iomkl/2018b
8.0.0		foss/2019b, intel/2019b
8.0.1		foss/2020a, foss/2020b, intel/2020a, intel/2020b
8.1.1		foss/2021a, intel/2021a
8.2.0		foss/2021b, intel/2021b
8.3.0		foss/2022a, intel/2022a
8.4.2		foss/2022a

ESMPy

Earth System Modeling Framework (ESMF) Python Interface

homepage: https://earthsystemmodeling.org/esmpy

version	versionsuffix	toolchain
8.0.0	-Python-3.7.4	intel/2019b
8.0.1		intel/2020b
8.0.1	-Python-3.8.2	foss/2020a

ESMValTool

The Earth System Model eValuation Tool (ESMValTool) is a community diagnostics and performance metrics tool for the evaluation of Earth System Models (ESMs) that allows for routine comparison of single or multiple models, either against predecessor versions or against observations.

homepage: https://www.esmvaltool.org/

version	versionsuffix	toolchain
1.1.0	-Python-2.7.14	intel/2017b

eSpeak-NG

The eSpeak NG is a compact open source software text-to-speech synthesizer for Linux, Windows, Android and other operating systems. It supports more than 100 languages and accents. It is based on the eSpeak engine created by Jonathan Duddington.

homepage: https://github.com/espeak-ng/espeak-ng

version	toolchain
1.50	gompi/2020a
1.51	gfbf/2023a

ESPResSo

A software package for performing and analyzing scientific Molecular Dynamics simulations.

homepage: https://espressomd.org/wordpress

version	versionsuffix	toolchain
4.2.1		foss/2021a, foss/2022a, foss/2023a
4.2.1	-CUDA-11.3.1	foss/2021a
4.2.1	-CUDA-11.8.0	foss/2022a

Essentia

Open-source library and tools for audio and music analysis, description and synthesis

homepage: https://essentia.upf.edu

version	versionsuffix	toolchain
2.1_beta5	-Python-2.7.15	foss/2019a

ETE

A Python framework for the analysis and visualization of trees

homepage: http://etetoolkit.org

version	versionsuffix	toolchain
3.0.0b36	-Python-2.7.12	intel/2016b
3.1.1	-Python-3.6.6	foss/2018b
3.1.2		foss/2020b, foss/2021a, foss/2021b
3.1.2	-Python-3.7.4	foss/2019b
3.1.2	-Python-3.8.2	foss/2020a
3.1.3		foss/2022b, foss/2023a

ETSF_IO

A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL.

homepage: http://www.etsf.eu/resources/software/libraries_and_tools

version	toolchain
1.0.4	foss/2017b, foss/2018a, foss/2018b, intel/2017b, intel/2018a, intel/2018b

eudev

eudev is a fork of systemd-udev with the goal of obtaining better compatibility with existing software such as OpenRC and Upstart, older kernels, various toolchains and anything else required by users and various distributions.

homepage: https://wiki.gentoo.org/wiki/Project:Eudev

version	toolchain
3.1.5	foss/2016a, gimkl/2.11.5, intel/2016a
3.2	GCCcore/4.9.3
3.2.2	GCCcore/6.4.0

EUKulele

Formalizing environmental eukaryotic taxonomic assignment

homepage: https://github.com/AlexanderLabWHOI/EUKulele

version	toolchain
2.0.6	foss/2022a

Evcxr-REPL

A Rust REPL (Read-Eval-Print loop) built using the evcxr evaluation context.

homepage: https://github.com/evcxr

version	versionsuffix	toolchain
0.14.2	-Rust-1.65.0	GCCcore/12.2.0

EveryBeam

Library that provides the antenna response pattern for several instruments, such as LOFAR (and LOBES), SKA (OSKAR), MWA, JVLA, etc.

homepage: https://everybeam.readthedocs.io/

version	toolchain
0.5.2	foss/2022a, foss/2023b

EvidentialGene

EvidentialGene is a genome informatics project for "Evidence Directed Gene Construction for Eukaryotes", for constructing high quality, accurate gene sets for animals and plants (any eukaryotes), being developed by Don Gilbert at Indiana University, gilbertd at indiana edu.

homepage: http://arthropods.eugenes.org/EvidentialGene/

version	versionsuffix	toolchain
2018.01.01	-Perl-5.24.1	intel/2017a
2022.01.14		gompi/2021b

evince

Evince is a document viewer for multiple document formats. The goal of evince is to replace the multiple document viewers that exist on the GNOME Desktop with a single simple application.

homepage: https://wiki.gnome.org/Apps/Evince

version	toolchain
45.0	GCC/12.3.0

evmix

evmix: Extreme Value Mixture Modelling, Threshold Estimation and Boundary Corrected Kernel Density Estimation

homepage: https://cran.r-project.org/web/packages/evmix

version	versionsuffix	toolchain
2.6	-R-3.3.1	intel/2016b

ExaBayes

ExaBayes is a software package for Bayesian tree inference. It is particularly suitable for large-scale analyses on computer clusters

homepage: https://cme.h-its.org/exelixis/web/software/exabayes/

version	toolchain
1.5	foss/2016b

ExaML

Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI

homepage: https://github.com/stamatak/ExaML/

version	versionsuffix	toolchain
3.0.22	-hybrid-avx	gompi/2021a

Excel-Writer-XLSX

The Excel::Writer::XLSX module can be used to create an Excel file in the 2007+ XLSX format. Multiple worksheets can be added to a workbook and formatting can be applied to cells. Text, numbers, and formulas can be written to the cells.

homepage: https://metacpan.org/pod/Excel::Writer::XLSX

version	toolchain
1.09	foss/2020b

ExifTool

Perl module (Image::ExifTool) and program (exiftool) to read EXIF information from images

homepage: https://owl.phy.queensu.ca/~phil/exiftool/

version	toolchain
12.00	GCCcore/9.3.0

exiv2

Exiv2 is a C++ library and a command line utility to manage image metadata. It provides fast and easy read and write access to the Exif, IPTC and XMP metadata of digital images in various formats. Exiv2 is available as free software and with a commercial license, and is used in many projects.

homepage: http://www.exiv2.org

version	toolchain
0.27.4	GCCcore/10.3.0
0.27.5	GCCcore/11.2.0
0.28.0	GCCcore/12.3.0

Exonerate

Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics.

homepage: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate

version	toolchain
2.4.0	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/11.3.0, GCC/12.2.0, GCC/6.4.0-2.28, GCC/8.3.0, foss/2016a, foss/2016b, iccifort/2017.4.196-GCC-6.4.0-2.28, iccifort/2019.1.144-GCC-8.2.0-2.31.1, iccifort/2019.5.281, intel/2017a

expat

Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags).

homepage: https://libexpat.github.io

version	toolchain
2.1.0	GCC/4.9.2, foss/2016a, intel/2016a
2.1.1	foss/2016a, intel/2016a
2.2.0	GCCcore/4.9.3, GCCcore/5.4.0, GCCcore/6.3.0, foss/2016a, foss/2016b, gimkl/2017a, intel/2016b
2.2.4	GCCcore/6.4.0
2.2.5	GCCcore/6.4.0, GCCcore/7.3.0
2.2.6	GCCcore/8.2.0
2.2.7	GCCcore/8.3.0
2.2.9	FCC/4.5.0, GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/9.3.0
2.4.1	GCCcore/11.2.0
2.4.8	GCCcore/11.3.0, GCCcore/12.1.0
2.4.9	GCCcore/12.2.0
2.5.0	GCCcore/12.3.0, GCCcore/13.2.0

expect

Expect is a tool for automating interactive applications such as telnet, ftp, passwd, fsck, rlogin, tip, etc. Expect really makes this stuff trivial. Expect is also useful for testing these same applications.

homepage: https://core.tcl.tk/expect/index

version	toolchain
5.45.4	GCCcore/7.3.0, GCCcore/9.3.0

expecttest

This library implements expect tests (also known as "golden" tests). Expect tests are a method of writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and the test framework automatically populates the expected output. If the output of the test changes, you can rerun the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output.

homepage: https://github.com/ezyang/expecttest

version	toolchain
0.1.3	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0
0.1.5	GCCcore/12.3.0
0.2.1	GCCcore/13.2.0

eXpress

Streaming quantification for high-throughput sequencing

homepage: https://pachterlab.github.io/eXpress

version	toolchain
1.5.1	intel/2017b

ExpressBetaDiversity

Taxon- and phylogenetic-based beta diversity measures.

homepage: https://github.com/donovan-h-parks/ExpressBetaDiversity

version	toolchain
1.0.10	GCC/12.3.0

Extrae

Extrae is the core instrumentation package developed by the Performance Tools group at BSC. Extrae is capable of instrumenting applications based on MPI, OpenMP, pthreads, CUDA1, OpenCL1, and StarSs1 using different instrumentation approaches. The information gathered by Extrae typically includes timestamped events of runtime calls, performance counters and source code references. Besides, Extrae provides its own API to allow the user to manually instrument his or her application.

homepage: https://www.bsc.es/computer-sciences/performance-tools

version	toolchain
3.4.1	foss/2017a
3.7.1	intel/2019a
3.8.0	gompi/2020b
3.8.3	gompi/2021a
4.0.4	gompi/2022a

ExtremeLy

A python package for Extreme Value Analysis.

homepage: https://github.com/SURYA-LAMICHANEY/ExtremeLy

version	toolchain
2.3.0	foss/2022a

EZC3D

EZC3D is an easy to use reader, modifier and writer for C3D format files. It is written en C++ with proper binders for Python and MATLAB/Octave scripting langages.

homepage: https://pyomeca.github.io/Documentation/ezc3d/index.html

version	toolchain
1.5.2	foss/2022a

F

f90cache - f90nml - f90wrap - Faber - FabIO - FACE - faceswap - FALCON - FANN - fast5 - FASTA - fasta-reader - fastahack - fastai - FastaIndex - FastANI - Fastaq - FastFold - fastjet - fastjet-contrib - FastME - fastml - fastp - fastparquet - fastPHASE - fastq-pair - fastq-tools - FastQ_Screen - FastQC - fastqsplitter - FastQTL - fastqz - FastRFS - fastStructure - FastTree - FastViromeExplorer - FASTX-Toolkit - fatslim - fbm - FBPIC - FCC - FCM - fdict - FDS - fdstools - FDTD_Solutions - feh - FEniCS - fermi-lite - Ferret - festival - fetchMG - FFAVES - FFC - FFLAS-FFPACK - FFmpeg - ffmpi - ffnet - ffnvcodec - fftlib - FFTW - FFTW.MPI - fgbio - FGSL - FHI-aims - FIAT - FIGARO - FigureGen - Fiji - file - filevercmp - Filtlong - find_circ - finder - findhap - findutils - fineRADstructure - fineSTRUCTURE - fio - Fiona - Firefox - FIRESTARTER - FireWorks - FIt-SNE - FIX - fixesproto - FLAC - FLAIR - flair-NLP - FLANN - FLASH - Flask - flatbuffers - flatbuffers-python - FLEUR - flex - Flexbar - FlexiBLAS - FlexiDot - Flink - FLINT - flit - flook - flowFDA - FLTK - FLUENT - Flye - FMILibrary - FMM3D - FMPy - FMRIprep - FMS - fmt - FoBiS - FoldX - fontconfig - fontsproto - forbear - FORD - foss - fosscuda - FoX - FOX-Toolkit - fplll - FPM - fpocket - fpylll - fqtrim - fqzcomp - FragGeneScan - FragPipe - FRANz - FreeBarcodes - freebayes - FreeFEM - FreeFem++ - freeglut - FreeImage - FreeSASA - FreeSurfer - FreeTDS - freetype - freetype-py - FreeXL - freud-analysis - FriBidi - FRUIT - FRUIT_processor - FSL - FSLeyes - fsom - FSON - ftfy - FTGL - fugue - Fujitsu - fullrmc - fumi_tools - funannotate - FunGAP - FUNWAVE-TVD - FUSE - FuSeq - FusionCatcher - futhark - futile - future - fxtract

f90cache

f90cache is a compiler cache. It acts as a caching pre-processor to Fortran compilers, using the -E compiler switch and a hash to detect when a compilation can be satisfied from cache. This often results in a great speedup in common compilations.

homepage: http://people.irisa.fr/Edouard.Canot/f90cache/

version	toolchain
0.96	system

f90nml

A Python module and command line tool for parsing Fortran namelist files

homepage: https://github.com/marshallward/f90nml

version	toolchain
1.4.4	GCCcore/12.2.0, GCCcore/13.2.0

f90wrap

f90wrap is a tool to automatically generate Python extension modules which interface to Fortran code that makes use of derived types. It builds on the capabilities of the popular f2py utility by generating a simpler Fortran 90 interface to the original Fortran code which is then suitable for wrapping with f2py, together with a higher-level Pythonic wrapper that makes the existance of an additional layer transparent to the final user.

homepage: https://github.com/jameskermode/f90wrap

version	toolchain
0.2.8	foss/2021a
0.2.11	foss/2022a

Faber

Faber started as a clone of Boost.Build, to experiment with a new Python frontend. Meanwhile it has evolved into a new build system, which retains most of the features found in Boost.Build, but with (hopefully !) much simplified logic, in addition of course to using Python as scripting language, rather than Jam. The original bjam engine is still in use as scheduler, though at this point that is mostly an implementation detail.

homepage: https://stefanseefeld.github.io/faber

version	toolchain
0.3	GCCcore/8.3.0

FabIO

FabIO is an I/O library for images produced by 2D X-ray detectors and written in Python. FabIO support images detectors from a dozen of companies (including Mar, Dectris, ADSC, Hamamatsu, Oxford, ...), for a total of 20 different file formats (like CBF, EDF, TIFF, ...) and offers an unified interface to their headers (as a python dictionary) and datasets (as a numpy ndarray of integers or floats).

homepage: http://www.silx.org

version	versionsuffix	toolchain
0.10.2	-Python-3.7.4	foss/2019b, fosscuda/2019b
0.11.0		foss/2020b, fosscuda/2020b
0.14.0		foss/2021b

FACE

A Fortran Ansi Colors (and Styles) Environment. A KISS pure Fortran Library for easy colorize (and stylize) strings.

homepage: https://github.com/szaghi/FACE

version	toolchain
1.1.1	GCC/10.3.0

faceswap

Faceswap is a tool that utilizes deep learning to recognize and swap faces in pictures and videos.

homepage: https://github.com/deepfakes/faceswap

version	versionsuffix	toolchain
20180212	-Python-3.6.3	foss/2017b

FALCON

Falcon: a set of tools for fast aligning long reads for consensus and assembly

homepage: https://github.com/PacificBiosciences/FALCON

version	versionsuffix	toolchain
1.8.8		intel/2017b
1.8.8	-Python-2.7.16	intel/2019b

FANN

Fast Artificial Neural Network Library is a free open source neural network library, which implements multilayer artificial neural networks in C with support for both fully connected and sparsely connected networks.

homepage: http://leenissen.dk

version	toolchain
2.2.0	GCCcore/6.4.0, intel/2018a

fast5

A lightweight C++ library for accessing Oxford Nanopore Technologies sequencing data.

homepage: http://simpsonlab.github.io/2017/02/27/packing_fast5/

version	toolchain
0.6.5	system

FASTA

The FASTA programs find regions of local or global (new) similarity between protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence.

homepage: https://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml

version	toolchain
36.3.5e	foss/2016b
36.3.8i	GCC/11.2.0, GCC/12.2.0

fasta-reader

FASTA file reader

homepage: https://github.com/EBI-Metagenomics/fasta-reader-py

version	toolchain
3.0.2	GCC/12.3.0

fastahack

Utilities for indexing and sequence extraction from FASTA files.

homepage: https://github.com/ekg/fastahack

version	toolchain
1.0.0	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.3.0, GCCcore/9.3.0

fastai

The fastai deep learning library.

homepage: https://www.fast.ai/

version	versionsuffix	toolchain
2.7.10		foss/2022a
2.7.10	-CUDA-11.7.0	foss/2022a

FastaIndex

FastA index (.fai) handler compatible with samtools faidx

homepage: https://github.com/lpryszcz/FastaIndex

version	versionsuffix	toolchain
0.11rc7	-Python-2.7.14	intel/2017b

FastANI

FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.

homepage: https://github.com/ParBLiSS/FastANI

version	toolchain
1.1	foss/2018b, intel/2018b
1.2	GCC/8.2.0-2.31.1, iccifort/2019.1.144-GCC-8.2.0-2.31.1
1.3	iccifort/2019.5.281
1.31	iccifort/2020.1.217
1.33	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/11.3.0, iccifort/2020.4.304, intel-compilers/2021.4.0
1.34	GCC/12.3.0

Fastaq

Python3 scripts to manipulate FASTA and FASTQ files.

homepage: https://github.com/sanger-pathogens/Fastaq

version	toolchain
3.17.0	GCC/10.3.0, GCC/12.3.0

FastFold

Optimizing Protein Structure Prediction Model Training and Inference on GPU Clusters

homepage: https://github.com/hpcaitech/FastFold

version	versionsuffix	toolchain
20220729	-CUDA-11.3.1	foss/2021a

fastjet

A software package for jet finding in pp and e+e- collisions

homepage: https://fastjet.fr/

version	toolchain
3.4.0	gompi/2022a
3.4.2	gompi/2023a

fastjet-contrib

3rd party extensions of FastJet

homepage: https://fastjet.hepforge.org/contrib/

version	toolchain
1.049	gompi/2022a
1.053	gompi/2023a

FastME

FastME: a comprehensive, accurate and fast distance-based phylogeny inference program.

homepage: http://www.atgc-montpellier.fr/fastme/

version	toolchain
2.1.5	foss/2016a
2.1.6.1	GCC/10.2.0, GCC/8.3.0, iccifort/2019.5.281, intel/2018a, intel/2018b
2.1.6.3	GCC/12.3.0

fastml

Maximum likelihood reconstruction of ancestral amino-acid sequences. A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites.

homepage: http://fastml.tau.ac.il/

version	toolchain
2.3	GCC/11.3.0

fastp

A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.

homepage: https://github.com/OpenGene/fastp

version	toolchain
0.19.7	foss/2018b
0.20.0	GCC/8.2.0-2.31.1, GCC/8.3.0, iccifort/2019.5.281
0.20.1	iccifort/2020.1.217
0.23.2	GCC/10.3.0, GCC/11.2.0, GCC/11.3.0
0.23.4	GCC/12.2.0, GCC/12.3.0

fastparquet

fastparquet is a python implementation of the parquet format, aiming to integrate into python-based big data work-flows. It is used implicitly by the projects Dask, Pandas and intake-parquet.

homepage: https://fastparquet.readthedocs.io/

version	toolchain
0.7.2	foss/2021a
0.8.0	foss/2021b
2023.4.0	gfbf/2022b

fastPHASE

fastPHASE: software for haplotype reconstruction, and estimating missing genotypes from population data Documentation: http://scheet.org/code/fastphase_doc_1.4.pdf

homepage: http://stephenslab.uchicago.edu/software.html#fastphase

version	toolchain
1.4.8	system

fastq-pair

Match up paired end fastq files quickly and efficiently.

homepage: https://github.com/linsalrob/fastq-pair

version	toolchain
1.0	GCCcore/8.2.0

fastq-tools

This package provides a number of small and efficient programs to perform common tasks with high throughput sequencing data in the FASTQ format. All of the programs work with typical FASTQ files as well as gzipped FASTQ files.

homepage: https://homes.cs.washington.edu/~dcjones/fastq-tools/

version	toolchain
0.8	foss/2016b, foss/2018b
0.8.3	GCC/10.3.0, GCC/11.2.0

FastQ_Screen

FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.

homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/

version	versionsuffix	toolchain
0.11.3	-Perl-5.24.0	foss/2016b
0.11.4	-Perl-5.24.0	foss/2016b
0.12.0	-Perl-5.26.1	intel/2018a
0.13.0	-Perl-5.28.0	foss/2018b
0.14.0		GCC/11.3.0

FastQC

FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.

homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

version	versionsuffix	toolchain
0.10.1	-Java-1.7.0_80	system
0.11.2	-Java-1.7.0_60	system
0.11.3	-Java-1.7.0_80	system
0.11.4	-Java-1.8.0_66	system
0.11.4	-Java-1.8.0_74	system
0.11.5	-Java-1.7.0_80	system
0.11.5	-Java-1.8.0_144	system
0.11.5	-Java-1.8.0_74	system
0.11.7	-Java-1.8.0_162	system
0.11.8	-Java-1.8	system
0.11.8	-Java-11	system
0.11.9	-Java-1.8	system
0.11.9	-Java-11	system
0.12.1	-Java-11	system

fastqsplitter

Splits fastq files evenly.

homepage: https://github.com/LUMC/fastqsplitter

version	versionsuffix	toolchain
1.2.0	-Python-3.7.2	GCCcore/8.2.0

FastQTL

FastQTL is a QTL mapper

homepage: http://fastqtl.sourceforge.net/

version	toolchain
2.184	GCC/11.2.0, foss/2018b

fastqz

fastqz is a compressor for FASTQ files. FASTQ is the output of DNA sequencing machines. It is one of the compressors described in the paper: Bonfield JK, Mahoney MV (2013) Compression of FASTQ and SAM Format Sequencing Data. (mirror) PLoS ONE 8(3): e59190. doi:10.1371/journal.pone.0059190

homepage: http://mattmahoney.net/dc/fastqz/

version	toolchain
1.5	GCC/4.8.2

FastRFS

Fast Robinson Foulds Supertrees

homepage: https://github.com/pranjalv123/FastRFS

version	toolchain
1.0-20190613	gompi/2019a

fastStructure

fastStructure is a fast algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x.

homepage: https://rajanil.github.io/fastStructure/

version	versionsuffix	toolchain
1.0	-Python-2.7.11	foss/2016a
1.0	-Python-2.7.12	foss/2016b
1.0	-Python-2.7.13	foss/2017a
1.0	-Python-2.7.15	foss/2019a

FastTree

FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.

homepage: http://www.microbesonline.org/fasttree/

version	toolchain
2.1.10	foss/2018b, intel/2017b, intel/2018a, intel/2018b
2.1.11	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0

FastViromeExplorer

Identify the viruses/phages and their abundance in the viral metagenomics data.

homepage: https://code.vt.edu/saima5/FastViromeExplorer

version	toolchain
20180422	foss/2019b

FASTX-Toolkit

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

homepage: http://hannonlab.cshl.edu/fastx_toolkit/

version	toolchain
0.0.14	GCC/10.3.0, GCC/11.2.0, GCC/11.3.0, GCC/9.3.0, GCCcore/7.3.0, foss/2016a, foss/2016b, intel/2018a

fatslim

FATSLiM stands for “Fast Analysis Toolbox for Simulations of Lipid Membranes” and its goal is to provide an efficient, yet robust, tool to extract physical parameters from MD trajectories.

homepage: https://github.com/FATSLiM/fatslim

version	versionsuffix	toolchain
0.2.1	-Python-3.6.4	foss/2018a

fbm

Exact methods for simulating fractional Brownian motion and fractional Gaussian noise in Python

homepage: https://pypi.org/project/fbm

version	versionsuffix	toolchain
0.2.0	-Python-3.6.4	intel/2018a

FBPIC

FBPIC (Fourier-Bessel Particle-In-Cell) is a Particle-In-Cell (PIC) code for relativistic plasma physics. It is especially well-suited for physical simulations of laser-wakefield acceleration and plasma-wakefield acceleration.

homepage: https://fbpic.github.io/

version	toolchain
0.20.3	fosscuda/2020b

FCC

Fujitsu Compiler based compiler toolchain.

homepage: <(none)>

version	toolchain
4.5.0	system

FCM

FCM is a set of tools for managing and building source code.

homepage: http://www.metoffice.gov.uk/research/collaboration/fcm

version	toolchain
2.3.1	system

fdict

A variable and dictionary in pure fortran for retaining any data-type and a fast hash-table dictionary.

homepage: https://github.com/zerothi/fdict

version	toolchain
0.8.0	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, iccifort/2020.4.304, intel-compilers/2021.2.0, intel-compilers/2021.4.0

FDS

Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires.

homepage: https://pages.nist.gov/fds-smv

version	versionsuffix	toolchain
6.0.1	-no-OFED	system
6.5.2		intel/2016b
6.5.3		intel/2017a
6.6.0		intel/2017b, intel/2018a
6.7.0		intel/2018a
6.7.4		intel/2020a
6.7.5		intel/2020a
6.7.6		intel/2020b
6.7.7		intel/2021b
6.7.9		intel/2022a
6.8.0		intel/2022b

fdstools

Forensic DNA Sequencing Tools Tools for characterisation and filtering of PCR stutter artefacts and other systemic noise in Next Generation Sequencing data of forensic STR markers.

homepage: https://git.lumc.nl/jerryhoogenboom/fdstools

version	versionsuffix	toolchain
20160322	-Python-2.7.11	foss/2016a

FDTD_Solutions

High performance FDTD-method Maxwell solver for the design, analysis and optimization of nanophotonic devices, processes and materials.

homepage: http://www.lumerical.com/tcad-products/fdtd/

version	toolchain
8.6.2	system
8.11.337	system
8.16.982	system
8.20.1731	system

feh

feh is an X11 image viewer aimed mostly at console users. Unlike most other viewers, it does not have a fancy GUI, but simply displays images. It is controlled via commandline arguments and configurable key/mouse actions.

homepage: https://feh.finalrewind.org/

version	toolchain
2.26	GCCcore/6.4.0

FEniCS

FEniCS is a computing platform for solving partial differential equations (PDEs).

homepage: https://fenicsproject.org/

version	versionsuffix	toolchain
2019.1.0	-Python-3.7.4	foss/2019b

fermi-lite

Standalone C library for assembling Illumina short reads in small regions.

homepage: https://github.com/lh3/fermi-lite

version	toolchain
20190320	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/12.3.0, GCCcore/9.3.0

Ferret

Ferret is an interactive computer visualization and analysis environment designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data sets.

homepage: https://ferret.pmel.noaa.gov/Ferret/

version	toolchain
7.3	intel/2017b
7.5.0	foss/2019b
7.6.0	foss/2022a

festival

University of Edinburgh's Festival Speech Synthesis Systems is a free software multi-lingual speech synthesis workbench that runs on multiple-platforms offering black box text to speech, as well as an open architecture for research in speech synthesis. It designed as a component of large speech technology systems.

homepage: <['http://festvox.org/festival/']>

version	toolchain
2.5.0	GCCcore/12.3.0, GCCcore/9.3.0

fetchMG

The program “fetchMG” was written to extract the 40 MGs from genomes and metagenomes in an easy and accurate manner.

homepage: http://vm-lux.embl.de/~mende/fetchMG/about.html

version	toolchain
1.0	GCCcore/8.3.0, GCCcore/9.3.0

FFAVES

Functional Feature Amplification Via Entropy Sorting (FFAVES). Use FFAVES to amplify the signal of groups of co-regulating genes in an unsupervised, multivariate manner. By amplifying the signal of genes with correlated expression, while filtering out genes that are randomly expressed, we can identify a subset of genes more predictive of different cell types. The output of FFAVES can then be used in our second algorithm, entropy sort feature weighting (ESFW), to create a ranked list of genes that are most likely to pertain to distinct sub-populations of cells in an scRNA-seq dataset.

homepage: https://github.com/aradley/FFAVES

version	toolchain
2022.11.1	foss/2022a

FFC

The FEniCS Form Compiler (FFC) is a compiler for finite element variational forms.

homepage: https://bitbucket.org/fenics-project/ffc

version	versionsuffix	toolchain
2018.1.0	-Python-3.6.4	foss/2018a
2019.1.0.post0	-Python-3.7.4	foss/2019b

FFLAS-FFPACK

Finite Field Linear Algebra Subroutines / Package

homepage: https://linbox-team.github.io/fflas-ffpack/

version	toolchain
2.2.0	foss/2016a
2.5.0	gfbf/2022a

FFmpeg

A complete, cross-platform solution to record, convert and stream audio and video.

homepage: https://www.ffmpeg.org/

version	toolchain
0.10.16	gimkl/2.11.5, intel/2016a
2.8.6	intel/2016a
2.8.7	foss/2016a, intel/2016a
3.0.2	foss/2016a, intel/2016a
3.1.3	foss/2016b, intel/2016b
3.2.4	gimkl/2017a
3.3.1	foss/2016b
3.3.4	intel/2017a
3.4	GCCcore/6.4.0
3.4.1	foss/2017b, intel/2017b
3.4.2	foss/2018a, intel/2018a
3.4.5	foss/2018b
4.0	foss/2018a, intel/2018a
4.0.1	intel/2018a
4.1	foss/2018b, fosscuda/2018b, intel/2018b
4.1.3	GCCcore/8.2.0
4.2.1	GCCcore/8.3.0
4.2.2	GCCcore/9.3.0
4.3.1	GCCcore/10.2.0
4.3.2	GCCcore/10.3.0, GCCcore/11.2.0
4.4.2	GCCcore/11.3.0
5.0.1	GCCcore/11.3.0
5.1.2	GCCcore/12.2.0
6.0	GCCcore/12.3.0, GCCcore/13.2.0

ffmpi

Fujitsu Compiler based compiler toolchain, including Fujitsu MPI for MPI support.

homepage: <(none)>

version	toolchain
4.5.0	system

ffnet

Feed-forward neural network solution for python

homepage: http://ffnet.sourceforge.net/

version	versionsuffix	toolchain
0.8.3	-Python-2.7.11	intel/2016a

ffnvcodec

FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present (picked up dynamically).

homepage: https://git.videolan.org/?p=ffmpeg/nv-codec-headers.git

version	toolchain
11.1.5.2	system
12.0.16.0	system
12.1.14.0	system

fftlib

A library that intercepts FFTW calls and adds features on top of it. In particular, it enables FFT plan reuse when there are multiple calls for the same geometry.

homepage: https://github.com/flwende/fftlib

version	toolchain
20170628	gompi/2020b, gompi/2022a

FFTW

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.

homepage: https://www.fftw.org

version	versionsuffix	toolchain
1.0.0	-fujitsu	FCC/4.5.0
2.1.5		intel/2016b, intel/2017a, intel/2018b
3.3.4		gmpich/2016a, gmvapich2/1.7.20, gmvapich2/2016a, gompi/2016.04, gompi/2016.06, gompi/2016.07, gompi/2016a, gompi/2016b, intel/2016a, intel/2016b
3.3.5		gompi/2016.07, gompi/2016.09, gompi/2016b, intel/2016b
3.3.6		gimpi/2017b, gimpic/2017b, gompi/2017a, gompi/2017b, gompic/2017b, intel/2016b, intel/2017a, intel/2017b, intelcuda/2017b
3.3.7		gimkl/2017a, gimpi/2018a, gmpich/2017.08, gompi/2018a, gompic/2018a, intel/2017b, intel/2018.00, intel/2018.01, intel/2018a, iomkl/2018a
3.3.7	-serial	GCC/6.4.0-2.28
3.3.8		gompi/2018.08, gompi/2018b, gompi/2019a, gompi/2019b, gompi/2020a, gompi/2020b, gompic/2018b, gompic/2019a, gompic/2019b, gompic/2020a, gompic/2020b, iimpi/2020b, intel/2018b, intel/2019a, intel/2019b, intel/2020a, intel/2020b, iomkl/2018b, iomkl/2020b, iompi/2020b
3.3.8	-amd	gompi/2020a
3.3.8	-serial	GCC/9.3.0
3.3.9		gompi/2021a, intel/2021a
3.3.10		GCC/11.3.0, GCC/12.2.0, GCC/12.3.0, GCC/13.2.0, NVHPC/22.7-CUDA-11.7.0, gompi/2021b, iimpi/2021b, iimpi/2022a, iimpi/2022b

FFTW.MPI

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.

homepage: https://www.fftw.org

version	toolchain
3.3.10	gompi/2022.05, gompi/2022.10, gompi/2022a, gompi/2022b, gompi/2023.09, gompi/2023a, gompi/2023b, nvompi/2022.07

fgbio

A set of tools to analyze genomic data with a focus on Next Generation Sequencing.

homepage: https://fulcrumgenomics.github.io/fgbio

version	toolchain
1.3.0	system

FGSL

FGSL: A Fortran interface to the GNU Scientific Library

homepage: https://www.lrz.de/services/software/mathematik/gsl/fortran/

version	toolchain
1.1.0	intel/2016b

FHI-aims

FHI-aims is an efficient, accurate all-electron, full-potential electronic structure code package for computational molecular and materials science (non-periodic and periodic systems). The code supports DFT (semilocal and hybrid) and many-body perturbation theory. FHI-aims is particularly efficient for molecular systems and nanostructures, while maintaining high numerical accuracy for all production tasks. Production calculations handle up to several thousand atoms and can efficiently use (ten) thousands of cores.

homepage: https://fhi-aims.org/

version	toolchain
200112_2	intel/2019b
221103	intel/2022a

FIAT

The FInite element Automatic Tabulator (FIAT) supports generation of arbitrary order instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating arbitrary order instances of Jacobi-type quadrature rules on the same element shapes.

homepage: https://bitbucket.org/fenics-project/fiat

version	versionsuffix	toolchain
1.6.0	-Python-2.7.11	foss/2016a, intel/2016a
2018.1.0	-Python-3.6.4	foss/2018a
2019.1.0	-Python-3.7.4	foss/2019b

FIGARO

FIGARO: An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters.

homepage: https://github.com/Zymo-Research/figaro

version	toolchain
1.1.2	intel/2020b

FigureGen

FigureGen is a Fortran program that creates images for ADCIRC files. It reads mesh files (fort.14, etc.), nodal attributes files (fort.13, etc.) and output files (fort.63, fort.64, maxele.63, etc.). It plots contours, contour lines, and vectors. Using FigureGen, you can go directly from the ADCIRC input and output files to a presentation-quality figure, for one or multiple time snaps.

homepage: https://ccht.ccee.ncsu.edu/category/software/figuregen/

version	toolchain
51-20190516	foss/2019a

Fiji

Fiji is an image processing package—a 'batteries-included' distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. This release is based on ImageJ-2.1.0 and Fiji-2.1.1

homepage: https://fiji.sc/

version	versionsuffix	toolchain
2.9.0	-Java-1.8	system
2.9.0	-Java-8	system
20170530		system
20191119-2057		system
20201104-1356		system

file

The file command is 'a file type guesser', that is, a command-line tool that tells you in words what kind of data a file contains.

homepage: https://www.darwinsys.com/file/

version	toolchain
5.17	GCC/4.8.2
5.25	intel/2016a
5.28	foss/2016b
5.30	intel/2017a
5.33	GCCcore/6.4.0
5.35	GCCcore/7.3.0
5.38	GCCcore/8.3.0, GCCcore/9.3.0
5.39	GCCcore/10.2.0
5.40	GCCcore/10.3.0
5.41	GCCcore/11.2.0
5.43	GCCcore/11.3.0, GCCcore/12.3.0

filevercmp

filevercmp function as in sort --version-sort.

homepage: https://github.com/ekg/filevercmp

version	toolchain
20141119	GCCcore/9.3.0
20191210	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.3.0

Filtlong

Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter

homepage: https://github.com/rrwick/Filtlong

version	toolchain
0.2.0	GCC/10.2.0, foss/2016b
0.2.1	GCC/10.3.0

find_circ

circRNA detection from RNA-seq reads

homepage: https://github.com/marvin-jens/find_circ

version	versionsuffix	toolchain
1.2-20170228	-Python-2.7.14	intel/2017b

finder

finder is a gene annotator pipeline which automates the process of downloading short reads, aligning them and using the assembled transcripts to generate gene annotations.

homepage: https://github.com/sagnikbanerjee15/Finder/

version	toolchain
1.1.0	foss/2021b

findhap

Find haplotypes and impute genotypes using multiple chip sets and sequence data

homepage: http://aipl.arsusda.gov/software/findhap/

version	toolchain
4	system

findutils

findutils: The GNU find, locate, updatedb, and xargs utilities

homepage: http://www.gnu.org/software/findutils/findutils.html

version	toolchain
4.4.2	GCC/4.8.2

fineRADstructure

A package for population structure inference from RAD-seq data

homepage: http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html

version	toolchain
20180709	intel/2018a
20210514	GCC/12.3.0

fineSTRUCTURE

fineSTRUCTURE is a fast and powerful algorithm for identifying population structure using dense sequencing data.

homepage: https://people.maths.bris.ac.uk/~madjl/finestructure/finestructure_info.html

version	toolchain
2.1.3	intel/2017b

fio

Flexible I/O tester

homepage: https://github.com/axboe/fio

version	toolchain
3.30	GCCcore/10.3.0
3.32	GCCcore/11.3.0
3.34	GCCcore/12.2.0
3.36	GCCcore/12.3.0

Fiona

Fiona is designed to be simple and dependable. It focuses on reading and writing data in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries, mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS packages such as pyproj, Rtree, and Shapely.

homepage: https://github.com/Toblerity/Fiona

version	versionsuffix	toolchain
1.8.13	-Python-3.7.4	foss/2019b, fosscuda/2019b, intel/2019b
1.8.13.post1	-Python-3.7.2	foss/2019a
1.8.16	-Python-3.8.2	foss/2020a
1.8.20		foss/2020b, foss/2021a, intel/2020b
1.8.21		foss/2021b, foss/2022a
1.9.2		foss/2022b
1.9.5		foss/2023a

Firefox

Firefox is a free, open source Web browser for Windows, Linux and Mac OS X. It is based on the Mozilla code base and offers customization options and features such as its capability to block pop-up windows, tabbed browsing, privacy and security measures, smart searching, and RSS live bookmarks.

homepage: https://www.mozilla.org/en-US/firefox/new/

version	toolchain
44.0.2	system

FIRESTARTER

FIRESTARTER: A Processor Stress Test Utility. FIRESTARTER maximizes the energy consumption of 64-Bit x86 processors by generating heavy load on the execution units as well as transferring data between the cores and multiple levels of the memory hierarchy.

homepage: https://github.com/tud-zih-energy/FIRESTARTER/

version	toolchain
2.0	gcccuda/2020a, gcccuda/2020b

FireWorks

FireWorks helps run calculation workflows, with a centralized workflow server controlling many worker nodes.

homepage: https://pypi.python.org/pypi/FireWorks

version	versionsuffix	toolchain
1.4.2	-Python-2.7.13	intel/2017a

FIt-SNE

t-distributed stochastic neighbor embedding (t-SNE) is widely used for visualizing single-cell RNA-sequencing (scRNA-seq) data, but it scales poorly to large datasets. We dramatically accelerate t-SNE, obviating the need for data downsampling, and hence allowing visualization of rare cell populations. Furthermore, we implement a heatmap-style visualization for scRNA-seq based on one-dimensional t-SNE for simultaneously visualizing the expression patterns of thousands of genes.

homepage: https://github.com/KlugerLab/FIt-SNE

version	toolchain
1.1.0	gompi/2018b

FIX

FIX attempts to auto-classify ICA components into "good" vs "bad" components, so that the bad components can be removed from the 4D FMRI data.

homepage: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX

version	versionsuffix	toolchain
1.06.12	-Octave-Python-3.7.2	foss/2019a

fixesproto

X.org FixesProto protocol headers.

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
5.0	foss/2016a, gimkl/2.11.5, intel/2016a

FLAC

FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning that audio is compressed in FLAC without any loss in quality.

homepage: https://xiph.org/flac/

version	toolchain
1.3.3	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0
1.3.4	GCCcore/11.3.0
1.4.2	GCCcore/12.2.0, GCCcore/12.3.0

FLAIR

FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads.

homepage: https://github.com/BrooksLabUCSC/flair

version	versionsuffix	toolchain
1.5	-Python-3.7.4	foss/2019b
1.5.1-20200630	-Python-3.7.4	foss/2019b

flair-NLP

A very simple framework for state-of-the-art NLP

homepage: https://github.com/flairNLP/flair

version	versionsuffix	toolchain
0.11.3		foss/2021a
0.11.3	-CUDA-11.3.1	foss/2021a

FLANN

FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces.

homepage: https://github.com/mariusmuja/flann/

version	versionsuffix	toolchain
1.8.4	-Python-2.7.11	intel/2016a
1.8.4	-Python-2.7.14	intel/2017b
1.8.4	-Python-3.8.2	foss/2020a
1.9.1	-Python-3.8.2	foss/2020a

FLASH

FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data.

homepage: https://ccb.jhu.edu/software/FLASH/

version	toolchain
1.2.11	GCC/8.3.0, foss/2016a, foss/2018a, foss/2018b
2.2.00	GCC/11.2.0, GCCcore/12.2.0, foss/2018b, foss/2020b

Flask

Flask is a lightweight WSGI web application framework. It is designed to make getting started quick and easy, with the ability to scale up to complex applications. This module includes the Flask extensions: Flask-Cors

homepage: https://www.palletsprojects.com/p/flask/

version	versionsuffix	toolchain
1.0.2	-Python-3.6.6	foss/2018b
1.1.2		GCCcore/10.2.0
1.1.2	-Python-3.7.4	GCCcore/8.3.0
1.1.2	-Python-3.8.2	GCCcore/9.3.0
1.1.4		GCCcore/10.3.0
2.0.2		GCCcore/11.2.0
2.2.2		GCCcore/11.3.0
2.2.3		GCCcore/12.2.0
2.3.3		GCCcore/12.3.0
3.0.0		GCCcore/13.2.0

flatbuffers

FlatBuffers: Memory Efficient Serialization Library

homepage: https://github.com/google/flatbuffers/

version	toolchain
1.12.0	GCCcore/10.2.0, GCCcore/8.3.0, GCCcore/9.3.0
2.0.0	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0
2.0.7	GCCcore/11.3.0
23.1.4	GCCcore/12.2.0
23.5.26	GCCcore/12.3.0, GCCcore/13.2.0

flatbuffers-python

Python Flatbuffers runtime library.

homepage: https://github.com/google/flatbuffers/

version	versionsuffix	toolchain
1.12		GCCcore/10.2.0
1.12	-Python-3.7.4	GCCcore/8.3.0
2.0		GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0
23.1.4		GCCcore/12.2.0
23.5.26		GCCcore/12.3.0

FLEUR

FLEUR is a feature-full, freely available FLAPW (full potential linearized augmented planewave) code, based on density-functional theory.

homepage: http://www.flapw.de/

version	toolchain
0.26e	intel/2016a

flex

Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.

homepage: http://flex.sourceforge.net/

version	toolchain
2.5.35	system
2.5.38	GCC/4.8.2
2.5.39	GCC/4.9.2, GCC/4.9.2-binutils-2.25, GCC/4.9.3, GCC/4.9.3-binutils-2.25, GCC/5.1.0-binutils-2.25, GCCcore/4.9.2, GCCcore/4.9.3, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GNU/4.9.3-2.25, foss/2016a, gimkl/2.11.5, intel/2016.02-GCC-4.9, intel/2016a, intel/2016b, system
2.6.0	GCC/4.9.2, GCCcore/4.9.3, GCCcore/4.9.4, GCCcore/5.3.0, GCCcore/5.4.0, GCCcore/6.1.0, GCCcore/6.2.0, foss/2016a, foss/2016b, gimkl/2.11.5, intel/2016a, intel/2016b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25, system
2.6.2	intel/2016b
2.6.3	GCCcore/5.4.0, GCCcore/6.3.0, GCCcore/7.1.0, gimkl/2017a, system
2.6.4	FCC/4.5.0, GCCcore/10.1.0, GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.1.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/11.4.0, GCCcore/12.1.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.1.0, GCCcore/13.2.0, GCCcore/5.5.0, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/7.4.0, GCCcore/8.1.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/8.4.0, GCCcore/9.1.0, GCCcore/9.2.0, GCCcore/9.3.0, GCCcore/9.4.0, GCCcore/9.5.0, GCCcore/system, system

Flexbar

The program Flexbar preprocesses high-throughput sequencing data efficiently

homepage: https://github.com/seqan/flexbar

version	toolchain
3.5.0	foss/2018b

FlexiBLAS

FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it.

homepage: https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release

version	toolchain
3.0.4	GCC/10.3.0, GCC/11.2.0
3.1.3	GCC/11.2.0
3.2.0	GCC/11.3.0, NVHPC/22.7-CUDA-11.7.0
3.2.1	GCC/12.2.0
3.3.1	GCC/12.3.0, GCC/13.2.0

FlexiDot

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

homepage: https://github.com/molbio-dresden/flexidot

version	versionsuffix	toolchain
1.06	-Python-2.7.15	foss/2018b

Flink

Apache Flink is a framework and distributed processing engine for stateful computations over unbounded and bounded data streams. Flink has been designed to run in all common cluster environments, perform computations at in-memory speed and at any scale.

homepage: https://flink.apache.org/

version	versionsuffix	toolchain
1.11.2	-bin-scala_2.11	system

FLINT

FLINT (Fast Library for Number Theory) is a C library in support of computations in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides various low-level routines for fast arithmetic. FLINT is extensively documented and tested.

homepage: https://www.flintlib.org/

version	toolchain
2.5.2	GCC/7.3.0-2.30, GCC/8.2.0-2.31.1, GCC/8.3.0, iccifort/2018.3.222-GCC-7.3.0-2.30
2.7.1	GCC/10.3.0
2.8.4	foss/2021b
2.9.0	gfbf/2022a, gfbf/2022b
3.1.1	gfbf/2023b

flit

A simple packaging tool for simple packages.

homepage: https://github.com/pypa/flit

version	toolchain
3.9.0	GCCcore/12.3.0, GCCcore/13.2.0

flook

The fortran-Lua-hook library.

homepage: https://github.com/ElectronicStructureLibrary/flook

version	toolchain
0.8.1	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/11.3.0, iccifort/2020.4.304, intel-compilers/2021.2.0, intel-compilers/2021.4.0

flowFDA

R package for analysing flow cytometry experiments with model based clustering, functional principal component analysis

homepage: https://github.com/FMKerckhof/flowFDA

version	versionsuffix	toolchain
0.99-20220602	-R-4.2.1	foss/2022a

FLTK

FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.

homepage: https://www.fltk.org

version	toolchain
1.3.3	foss/2016a, foss/2016b, intel/2016a, intel/2016b
1.3.4	foss/2017b, foss/2018a, foss/2018b, fosscuda/2017b, fosscuda/2018a, fosscuda/2018b, intel/2017a, intel/2017b, intel/2018a, intel/2018b, intelcuda/2017b
1.3.5	GCC/8.2.0-2.31.1, GCC/8.3.0, GCCcore/10.2.0, GCCcore/9.3.0
1.3.6	GCCcore/10.3.0
1.3.7	GCCcore/11.2.0
1.3.8	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0

FLUENT

ANSYS FLUENT software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants.

homepage: https://www.ansys.com/products/fluids/ansys-fluent

version	toolchain
14.5	system
15.0.7	system
16.0	system
17.1	system
18.0	system
18.1	system
18.2	system
2019R3	system
2021R1	system
2021R2	system

Flye

Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies.

homepage: https://github.com/fenderglass/Flye

version	versionsuffix	toolchain
2.4	-Python-2.7.15	intel/2018b
2.6	-Python-3.7.2	foss/2019a
2.6	-Python-3.7.4	intel/2019b
2.8.1	-Python-3.8.2	intel/2020a
2.8.2	-Python-3.8.2	foss/2020a
2.8.3		GCC/10.2.0, iccifort/2020.4.304
2.9		GCC/10.3.0, intel-compilers/2021.2.0
2.9.1		GCC/11.2.0
2.9.2		GCC/11.3.0
2.9.3		GCC/10.3.0, GCC/12.3.0

FMILibrary

FMI library is intended as a foundation for applications interfacing FMUs (Functional Mockup Units) that follow FMI Standard. This version of the library supports FMI 1.0 and FMI2.0. See http://www.fmi-standard.org/

homepage: https://jmodelica.org/

version	toolchain
2.0.3	intel/2018b

FMM3D

Flatiron Institute Fast Multipole Libraries: a set of libraries to compute N-body interactions governed by the Laplace and Helmholtz equations, to a specified precision, in three dimensions, on a multi-core shared-memory machine.

homepage: https://fmm3d.readthedocs.io

version	toolchain
20211018	foss/2020b

FMPy

FMPy is a free Python library to simulate Functional Mock-up Units (FMUs).

homepage: https://github.com/CATIA-Systems/FMPy

version	toolchain
0.3.2	foss/2021a

FMRIprep

FMRIprep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting.

homepage: https://fmriprep.readthedocs.io

version	versionsuffix	toolchain
1.1.8	-Python-3.6.6	foss/2018b
1.4.1	-Python-3.6.6	foss/2018b

FMS

The Flexible Modeling System (FMS) is a software framework for supporting the efficient development, construction, execution, and scientific interpretation of atmospheric, oceanic, and climate system models.

homepage: https://github.com/NOAA-GFDL/FMS

version	toolchain
2022.02	gompi/2022a, iimpi/2022a

fmt

fmt (formerly cppformat) is an open-source formatting library.

homepage: http://fmtlib.net/

version	toolchain
3.0.1	foss/2016b, intel/2016b
3.0.2	GCCcore/6.4.0, intel/2017a
5.3.0	GCCcore/7.3.0, GCCcore/8.2.0
6.2.1	GCCcore/9.3.0
7.0.3	GCCcore/9.3.0
7.1.1	GCCcore/11.2.0
8.1.1	GCCcore/11.2.0
9.1.0	GCCcore/11.3.0, GCCcore/12.2.0
10.0.0	GCCcore/12.3.0
10.1.0	GCCcore/12.3.0
10.2.0	GCCcore/13.2.0

FoBiS

A Fortran Building System for automatic building modern Fortran projects

homepage: https://github.com/szaghi/FoBiS

version	toolchain
3.0.5	GCCcore/10.3.0

FoldX

FoldX is used to provide a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes.

homepage: http://foldx.crg.es/

version	toolchain
2.5.2	system
3.0-beta5.1	system
3.0-beta6	system
3.0-beta6.1	system

fontconfig

Fontconfig is a library designed to provide system-wide font configuration, customization and application access.

homepage: https://www.freedesktop.org/wiki/Software/fontconfig/

version	versionsuffix	toolchain
2.11.94		foss/2016a, intel/2016a
2.11.95		foss/2016a, intel/2016a
2.12.1		GCCcore/5.4.0, GCCcore/6.3.0, foss/2016b, gimkl/2017a, intel/2016b
2.12.1	-libpng-1.6.29	GCCcore/6.3.0
2.12.4		GCCcore/6.4.0
2.12.6		GCCcore/6.4.0
2.13.0		GCCcore/6.4.0, GCCcore/7.3.0
2.13.1		GCCcore/8.2.0, GCCcore/8.3.0
2.13.92		GCCcore/10.2.0, GCCcore/9.3.0
2.13.93		GCCcore/10.3.0
2.13.94		GCCcore/11.2.0
2.14.0		GCCcore/11.3.0
2.14.1		GCCcore/12.2.0
2.14.2		GCCcore/12.3.0, GCCcore/13.2.0

fontsproto

X11 font extension wire protocol

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
2.1.3	foss/2016a, gimkl/2.11.5, intel/2016a

forbear

A Fortran Library for building and running fancy progress bar

homepage: https://github.com/szaghi/forbear

version	toolchain
1.2.0	GCC/10.3.0

FORD

FORD is an automatic documentation generator for modern Fortran programs

homepage: https://github.com/Fortran-FOSS-Programmers/ford/wiki

version	toolchain
6.1.1	GCCcore/10.2.0
6.1.6	GCCcore/10.3.0
6.1.15	GCCcore/11.3.0

foss

GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.

homepage: https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain

version	toolchain
2016.04	system
2016.06	system
2016.07	system
2016.09	system
2016a	system
2016b	system
2017a	system
2017b	system
2018.08	system
2018a	system
2018b	system
2019a	system
2019b	system
2020a	system
2020b	system
2021a	system
2021b	system
2022.05	system
2022.10	system
2022a	system
2022b	system
2023.09	system
2023a	system
2023b	system

fosscuda

GCC based compiler toolchain with CUDA support, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.

homepage: <(none)>

version	toolchain
2017b	system
2018a	system
2018b	system
2019a	system
2019b	system
2020a	system
2020b	system

FoX

FoX is an XML library written in Fortran 95. It allows software developers to read, write and modify XML documents from Fortran applications without the complications of dealing with multi-language development.

homepage: http://homepages.see.leeds.ac.uk/~earawa/FoX/

version	toolchain
4.1.2	GCC/11.2.0, GCC/9.3.0, intel/2017b, intel/2018a

FOX-Toolkit

FOX is a C++ based Toolkit for developing Graphical User Interfaces easily and effectively. It offers a wide, and growing, collection of Controls, and provides state of the art facilities such as drag and drop, selection, as well as OpenGL widgets for 3D graphical manipulation. FOX also implements icons, images, and user-convenience features such as status line help, and tooltips.

homepage: https://www.fox-toolkit.org/

version	toolchain
1.6.57	GCCcore/11.2.0, GCCcore/9.3.0

fplll

fplll contains implementations of several lattice algorithms. The implementation relies on floating-point orthogonalization, and the 1982 paper from Lenstra, Lenstra Jr. and Lovasz (LLL) is central to the code, hence the name.

homepage: https://github.com/fplll/fplll

version	toolchain
5.4.5	GCCcore/11.3.0

FPM

Effing package management! Build packages for multiple platforms (deb, rpm, etc) with great ease and sanity.

homepage: https://github.com/jordansissel/fpm

version	versionsuffix	toolchain
1.3.3	-Ruby-2.1.6	system
1.15.1		GCCcore/12.2.0

fpocket

The fpocket suite of programs is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level.

homepage: https://github.com/Discngine/fpocket

version	toolchain
3.1.4.2	gompi/2020a

fpylll

A Python wrapper for fplll.

homepage: https://pypi.org/project/fpylll

version	toolchain
0.5.9	foss/2022a

fqtrim

fqtrim is a versatile stand-alone utility that can be used to trim adapters, poly-A tails, terminal unknown bases (Ns) and low quality 3' regions in reads from high-throughput next-generation sequencing machines.

homepage: http://ccb.jhu.edu/software/fqtrim/

version	toolchain
0.9.4	intel/2016b
0.9.5	intel/2017a

fqzcomp

Fqzcomp is a basic fastq compressor, designed primarily for high performance. Despite that it is comparable to bzip2 for compression levels.

homepage: http://sourceforge.net/projects/fqzcomp/

version	toolchain
4.6	GCC/4.8.2

FragGeneScan

FragGeneScan is an application for finding (fragmented) genes in short reads.

homepage: http://omics.informatics.indiana.edu/FragGeneScan/

version	toolchain
1.31	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/8.2.0, foss/2018b

FragPipe

FragPipe is a Java Graphical User Interface (GUI) for a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data.

homepage: https://fragpipe.nesvilab.org

version	versionsuffix	toolchain
20.0	-Java-11	system

FRANz

A fast and flexible parentage inference program for natural populations.

homepage: https://www.bioinf.uni-leipzig.de/Software/FRANz

version	toolchain
2.0.0	foss/2018a

FreeBarcodes

A package for the generation and decoding of FREE divergence error-correcting DNA barcodes

homepage: https://github.com/hawkjo/freebarcodes

version	toolchain
3.0.a5	foss/2021b

freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

homepage: https://github.com/freebayes/freebayes

version	versionsuffix	toolchain
1.3.5		GCC/10.2.0
1.3.5	-Python-3.8.2	GCC/9.3.0
1.3.6	-R-4.1.0	foss/2021a
1.3.6	-R-4.1.2	foss/2021b
1.3.7	-R-4.3.2	gfbf/2023a

FreeFEM

FreeFEM offers a fast interpolation algorithm and a language for the manipulation of data on multiple meshes.

homepage: https://freefem.org

version	versionsuffix	toolchain
4.5	-Python-3.7.4	foss/2019b

FreeFem++

FreeFem++ is a partial differential equation solver. It has its own language. freefem scripts can solve multiphysics non linear systems in 2D and 3D.

homepage: http://www.freefem.org/

version	versionsuffix	toolchain
3.58	-downloaded-deps	foss/2017b
3.60	-downloaded-deps	intel/2018a
3.61-1	-downloaded-deps	intel/2018a

freeglut

freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library.

homepage: http://freeglut.sourceforge.net/

version	versionsuffix	toolchain
3.0.0		GCCcore/8.2.0, foss/2016a, foss/2016b, foss/2017b, foss/2018a, foss/2018b, intel/2016a, intel/2016b, intel/2017a, intel/2017b, intel/2018a
3.0.0	-Mesa-11.2.1	foss/2016a, intel/2016a
3.2.1		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/8.3.0, GCCcore/9.3.0
3.2.2		GCCcore/11.3.0
3.4.0		GCCcore/12.2.0, GCCcore/12.3.0

FreeImage

FreeImage is an Open Source library project for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. FreeImage is easy to use, fast, multithreading safe.

homepage: http://freeimage.sourceforge.net

version	toolchain
3.18.0	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/7.3.0, GCCcore/8.3.0, GCCcore/9.3.0

FreeSASA

FreeSASA is a command line tool, C-library and Python module for calculating solvent accessible surface areas (SASA).

homepage: https://freesasa.github.io

version	toolchain
2.0.3	GCC/8.3.0

FreeSurfer

FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data.

homepage: https://surfer.nmr.mgh.harvard.edu/

version	versionsuffix	toolchain
5.3.0	-centos4_x86_64	system
5.3.0	-centos6_x86_64	system
6.0.0	-centos6_x86_64	system
6.0.1	-centos6_x86_64	system
7.1.1	-centos6_x86_64	system
7.1.1	-centos7_x86_64	system
7.1.1	-centos8_x86_64	system
7.2.0	-centos7_x86_64	system
7.2.0	-centos8_x86_64	system
7.2.0	-ubuntu18_amd64	system
7.3.2	-centos7_x86_64	system
7.3.2	-centos8_x86_64	system
7.4.0	-centos8_x86_64	system
7.4.0	-ubuntu20_amd64	system
7.4.0	-ubuntu22_amd64	system
7.4.1	-centos7_x86_64	system
7.4.1	-centos8_x86_64	system
7.4.1	-ubuntu20_amd64	system
7.4.1	-ubuntu22_amd64	system

FreeTDS

FreeTDS is a set of libraries for Unix and Linux that allows your programs to natively talk to Microsoft SQL Server and Sybase databases.

homepage: https://www.freetds.org/

version	toolchain
1.3.3	GCCcore/10.3.0

freetype

FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well.

homepage: https://freetype.org

version	versionsuffix	toolchain
2.6.2		foss/2016a, gimkl/2.11.5, intel/2016a
2.6.3		foss/2016a, intel/2016a
2.6.5		GCCcore/4.9.3, GCCcore/5.4.0, foss/2016b, intel/2016b
2.7		foss/2016b, intel/2016b
2.7.1		GCCcore/5.4.0, GCCcore/6.3.0, gimkl/2017a, intel/2016b
2.7.1	-libpng-1.6.29	GCCcore/6.3.0
2.8		GCCcore/6.4.0
2.8.1		GCCcore/6.4.0
2.9		GCCcore/6.4.0
2.9.1		GCCcore/7.3.0, GCCcore/8.2.0
2.10.1		GCCcore/8.3.0, GCCcore/9.3.0
2.10.3		GCCcore/10.2.0
2.10.4		GCCcore/10.3.0
2.11.0		GCCcore/11.2.0
2.12.1		GCCcore/11.3.0, GCCcore/12.2.0
2.13.0		GCCcore/12.3.0
2.13.2		GCCcore/13.2.0

freetype-py

Python binding for the freetype library

homepage: https://github.com/rougier/freetype-py

version	versionsuffix	toolchain
2.2.0	-Python-3.7.4	GCCcore/8.3.0

FreeXL

FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet.

homepage: https://www.gaia-gis.it/fossil/freexl/index

version	toolchain
1.0.2	foss/2016b, intel/2016b
1.0.3	GCCcore/6.4.0
1.0.5	GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0
1.0.6	GCCcore/11.2.0

freud-analysis

The freud Python library provides a simple, flexible, powerful set of tools for analyzing trajectories obtained from molecular dynamics or Monte Carlo simulations. High performance, parallelized C++ is used to compute standard tools such as radial distribution functions, correlation functions, order parameters, and clusters, as well as original analysis methods including potentials of mean force and torque (PMFTs) and local environment matching. The freud library supports many input formats and outputs NumPy arrays, enabling integration with the scientific Python ecosystem for many typical materials science workflows.

homepage: https://github.com/glotzerlab/freud

version	toolchain
2.6.2	foss/2020b

FriBidi

The Free Implementation of the Unicode Bidirectional Algorithm.

homepage: https://github.com/fribidi/fribidi

version	toolchain
1.0.1	foss/2018a, intel/2018a
1.0.2	GCCcore/6.4.0
1.0.5	GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0
1.0.9	GCCcore/9.3.0
1.0.10	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0
1.0.12	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0
1.0.13	GCCcore/13.2.0

FRUIT

FORTRAN Unit Test Framework (FRUIT)

homepage: https://fortranxunit.sourceforge.io

version	versionsuffix	toolchain
3.4.3	-Ruby-2.5.1	foss/2018a, intel/2018a

FRUIT_processor

FORTRAN Unit Test Framework (FRUIT)

homepage: https://fortranxunit.sourceforge.io

version	versionsuffix	toolchain
3.4.3	-Ruby-2.5.1	foss/2018a, intel/2018a

FSL

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.

homepage: https://www.fmrib.ox.ac.uk/fsl/

version	versionsuffix	toolchain
5.0.9		intel/2016a
5.0.9	-Mesa-11.2.1	intel/2016a
5.0.9	-centos6_64	system
5.0.10		foss/2017b, intel/2017a, intel/2017b
5.0.11		foss/2018b
5.0.11	-Python-3.6.6	foss/2018b
6.0.1	-Python-2.7.15	foss/2019a
6.0.1	-Python-3.7.2	foss/2019a
6.0.2	-Python-2.7.15	foss/2018b, foss/2019a
6.0.2	-Python-2.7.15-CUDA-9.2.88	foss/2018b
6.0.2	-Python-3.7.2	foss/2019a
6.0.3	-Python-3.7.4	foss/2019b
6.0.4	-Python-3.7.4	foss/2019b
6.0.5.1		foss/2021a

FSLeyes

FSLeyes is the FSL image viewer.

homepage: https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes

version	versionsuffix	toolchain
0.15.0	-Python-2.7.13	intel/2017a

fsom

A tiny C library for managing SOM (Self-Organizing Maps) neural networks.

homepage: https://github.com/ekg/fsom

version	toolchain
20141119	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/9.3.0
20151117	GCCcore/11.3.0, GCCcore/12.3.0

FSON

Fortran 95 JSON Parser

homepage: https://github.com/josephalevin/fson

version	toolchain
1.0.5	GCC/10.2.0

ftfy

ftfy (fixes text for you) fixes Unicode that’s broken in various ways. The goal of ftfy is to take in bad Unicode and output good Unicode, for use in your Unicode-aware code. This is different from taking in non-Unicode and outputting Unicode, which is not a goal of ftfy. It also isn’t designed to protect you from having to write Unicode-aware code. ftfy helps those who help themselves.

homepage: http://ftfy.readthedocs.org

version	toolchain
6.1.1	GCCcore/11.3.0

FTGL

FTGL is a free open source library to enable developers to use arbitrary fonts in their OpenGL (www.opengl.org) applications.

homepage: https://github.com/frankheckenbach/ftgl

version	toolchain
2.1.3-rc5	GCCcore/10.2.0, GCCcore/8.2.0, foss/2017b, foss/2018a, fosscuda/2018b, intel/2017b
2.4.0	GCCcore/11.3.0

fugue

Fugue is a unified interface for distributed computing that lets users execute Python, Pandas, and SQL code on Spark, Dask, and Ray with minimal rewrites. Fugue is most commonly used for: Parallelizing or scaling existing Python and Pandas code by bringing it to Spark, Dask, or Ray with minimal rewrites. Using FugueSQL to define end-to-end workflows on top of Pandas, Spark, and Dask DataFrames. FugueSQL is an enhanced SQL interface that can invoke Python code.

homepage: https://github.com/fugue-project/fugue

version	toolchain
0.8.7	foss/2022a

Fujitsu

Toolchain using Fujitsu compilers and libraries.

homepage: <(none)>

version	toolchain
21.05	system

fullrmc

Reverse Monte Carlo (RMC) is probably best known for its applications in condensed matter physics and solid state chemistry. fullrmc which stands for FUndamental Library Language for Reverse Monte Carlo is different than traditional RMC but a stochastic modelling method to solve an inverse problem whereby an atomic/molecular model is adjusted until its atoms position havei the greatest consistency with a set of experimental data.

homepage: https://bachiraoun.github.io/fullrmc

version	versionsuffix	toolchain
3.2.0	-Python-2.7.14	intel/2018a

fumi_tools

This tool is intended to deduplicate UMIs from single-end and paired-end sequencing data. Reads are considered identical when their UMIs have the same sequence, they have the same length and map at the same position.

homepage: https://ccb-gitlab.cs.uni-saarland.de/tobias/fumi_tools

version	versionsuffix	toolchain
0.18.2		GCC/10.3.0, GCC/11.2.0
0.18.2	-Python-3.6.6	foss/2018b

funannotate

funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes)

homepage: https://funannotate.readthedocs.io

version	toolchain
1.8.13	foss/2021b

FunGAP

Fungal Genome Annotation Pipeline using evidence-based gene model evaluation.

homepage: https://github.com/CompSynBioLab-KoreaUniv/FunGAP

version	toolchain
1.1.1	foss/2022a

FUNWAVE-TVD

FUNWAVE–TVD is the TVD version of the fully nonlinear Boussinesq wave model (FUNWAVE) initially developed by Kirby et al.

homepage: https://fengyanshi.github.io

version	versionsuffix	toolchain
3.1-20170525		intel/2017a
3.1-20170525	-no-storm	intel/2017a

FUSE

The reference implementation of the Linux FUSE (Filesystem in Userspace) interface

homepage: https://github.com/libfuse/libfuse

version	toolchain
3.2.6	intel/2018a
3.4.1	foss/2018a
3.14.1	GCCcore/11.3.0, GCCcore/12.2.0

FuSeq

FuSeq is a novel method to discover fusion genes from paired-end RNA sequencing data.

homepage: https://github.com/nghiavtr/FuSeq

version	toolchain
1.1.2	gompi/2019b

FusionCatcher

FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data (paired-end or single-end reads from Illumina NGS platforms like Solexa/HiSeq/NextSeq/MiSeq/MiniSeq) from diseased samples.

homepage: https://github.com/ndaniel/fusioncatcher

version	versionsuffix	toolchain
1.20	-Python-2.7.16	foss/2019b
1.30	-Python-2.7.16	foss/2019b

futhark

Futhark is a small programming language designed to be compiled to efficient parallel code. It is a statically typed, data-parallel, and purely functional array language in the ML family, and comes with a heavily optimising ahead-of-time compiler that presently generates GPU code via CUDA and OpenCL, although the language itself is hardware-agnostic and can also run on multicore CPUs

homepage: https://futhark-lang.org/

version	toolchain
0.19.5	system

futile

The FUTILE project (Fortran Utilities for the Treatment of Innermost Level of Executables) is a set of modules and wrapper that encapsulate the most common low-level operations of a Fortran code.

homepage: https://launchpad.net/futile

version	toolchain
1.8.3	foss/2020b, foss/2021a, foss/2021b, foss/2022a, intel/2020b, intel/2021a, intel/2021b

future

python-future is the missing compatibility layer between Python 2 and Python 3.

homepage: https://python-future.org/

version	versionsuffix	toolchain
0.16.0	-Python-2.7.14	foss/2018a, intel/2017b, intel/2018a
0.16.0	-Python-2.7.15	foss/2018b, intel/2018b
0.16.0	-Python-3.6.3	intel/2017b
0.16.0	-Python-3.6.6	foss/2018b

fxtract

Extract sequences from a fastx (fasta or fastq) file given a subsequence.

homepage: https://github.com/ctSkennerton/fxtract

version	toolchain
2.3	GCCcore/8.2.0

G

G-PhoCS - g2clib - g2lib - g2log - Gaia - GAMESS-US - gap - GapCloser - GapFiller - gappa - GAPPadder - GARLI - garnett - GAT - GATB-Core - GATE - GATK - Gaussian - gawk - gbasis - Gblocks - GBprocesS - gbs2ploidy - gc - GC3Pie - GCC - GCCcore - gcccuda - gcloud - GConf - gcsfs - GCTA - Gctf - GD - GDAL - GDB - gdbgui - gdbm - gdc-client - GDCHART - GDCM - GDGraph - gdist - Gdk-Pixbuf - GDRCopy - Gdspy - Geant4 - Geant4-data - gearshifft - GEGL - GEM - GEM-library - gemelli - GEMMA - gemmi - gencore_variant_detection - GeneMark-ET - GenerativeModels - gengetopt - GenMap - Genome_Profiler - GenomeComb - GenomeMapper - genomepy - GenomeTester4 - GenomeThreader - GenomeTools - GenomeWorks - GenotypeHarmonizer - genozip - gensim - geocube - geopandas - geopy - georges - GEOS - geosphere - Gerris - GETORB - GetOrganelle - gettext - gexiv2 - gfbf - GFF3-toolkit - GffCompare - gffread - gffutils - gflags - GFOLD - gh - GHC - Ghostscript - GI-DocGen - giac - Gibbs2 - giflib - gifsicle - GIMIC - gimkl - GimmeMotifs - GIMP - gimpi - gimpic - GIMPS - giolf - giolfc - Giotto-Suite - git - git-annex - git-extras - git-lfs - GitPython - Givaro - Giza - GKeyll - GKlib-METIS - gkmSVM - GL2PS - Glade - glew - GLFW - GLI - GLib - glib-networking - glibc - GLibmm - GLIMMER - GlimmerHMM - GLIMPSE - GLM - GLM-AED - GlobalArrays - Globus-CLI - GlobusConnectPersonal - glog - GLPK - glproto - Glucose - GMAP-GSNAP - GMP - GMP-ECM - gmpich - gmpolf - gmpy2 - gmsh - GMT - gmvapich2 - gmvolf - GNU - gnuplot - GnuTLS - Go - goalign - GOATOOLS - gobff - GObject-Introspection - goblf - GOBNILP - Godon - gofasta - golf - gomkl - gompi - gompic - google-java-format - googletest - gotree - GP2C - GPAW - GPAW-setups - gperf - gperftools - gpustat - GPy - GPyOpt - GPyTorch - Grace - Gradle - gradunwarp - graph-tool - GraphDB - Graphene - GraphicsMagick - graphite2 - GraPhlAn - GraphMap - GraphMap2 - Graphviz - graphviz-python - GRASP - GRASP-suite - GRASS - Greenlet - Grep - gretl - grib_api - grid - GRIDSS - GRIT - GRNBoost - groff - GroIMP - GROMACS - GromacsWrapper - Groovy - gRPC - GSD - GSEA - gsettings-desktop-schemas - GSL - gSOAP - gspell - gsport - GST-plugins-bad - GST-plugins-base - GStreamer - gsutil - gsw - GTDB-Tk - GTK+ - GTK2 - GTK3 - GTK4 - GtkSourceView - GTOOL - GTS - gubbins - guenomu - GUIDANCE - Guile - GULP - Gurobi - GUSHR - gzip

G-PhoCS

G-PhoCS is a software package for inferring ancestral population sizes, population divergence times, and migration rates from individual genome sequences. G-PhoCS accepts as input a set of multiple sequence alignments from separate neutrally evolving loci along the genome. Parameter inference is done in a Bayesian manner, using a Markov Chain Monte Carlo (MCMC) to jointly sample model parameters and genealogies at the input loci.

homepage: http://compgen.cshl.edu/GPhoCS/

version	toolchain
1.2.3	iccifort/2019.1.144-GCC-8.2.0-2.31.1

g2clib

Library contains GRIB2 encoder/decoder ('C' version).

homepage: https://github.com/NOAA-EMC/NCEPLIBS-g2c

version	toolchain
1.6.0	GCCcore/8.3.0, GCCcore/9.3.0, foss/2018b, intel/2017a, intel/2017b, intel/2018a, intel/2018b
1.6.3	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0
1.7.0	GCCcore/11.3.0

g2lib

Library contains GRIB2 encoder/decoder and search/indexing routines.

homepage: https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/

version	toolchain
1.4.0	intel/2017a, intel/2017b, intel/2018a
3.1.0	GCCcore/8.3.0, GCCcore/9.3.0, foss/2018b, intel/2018b
3.2.0	GCCcore/10.2.0, GCCcore/10.3.0

g2log

g2log, efficient asynchronous logger using C++11

homepage: https://sites.google.com/site/kjellhedstrom2//g2log-efficient-background-io-processign-with-c11

version	toolchain
1.0	GCCcore/8.3.0, foss/2016b

Gaia

Gaia is a C++ library with python bindings which implements similarity measures and classifications on the results of audio analysis, and generates classification models that Essentia can use to compute high-level description of music.

homepage: https://github.com/MTG/gaia

version	versionsuffix	toolchain
2.4.5	-Python-2.7.15	GCCcore/8.2.0

GAMESS-US

The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package.

homepage: http://www.msg.chem.iastate.edu/gamess/index.html

version	versionsuffix	toolchain
20141205-R1		intel/2016a
20170420-R1		intel/2016b
20170420-R1	-sockets	intel/2016b
20180214-R1		foss/2016b
20180214-R1	-sockets	foss/2016b

gap

GAP is a system for computational discrete algebra, with particular emphasis on Computational Group Theory.

homepage: https://www.gap-system.org

version	toolchain
4.9.3	intel/2018b
4.11.0	foss/2019a
4.12.2	foss/2022a

GapCloser

GapCloser is designed to close the gaps emerging during the scaffolding process by SOAPdenovo or other assembler, using the abundant pair relationships of short reads.

homepage: https://sourceforge.net/projects/soapdenovo2/files/GapCloser/

version	toolchain
1.12-r6	foss/2018a, intel/2017b

GapFiller

GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. It can be used for both DNA and RNA and it has been tested on Illumina data.

homepage: https://sourceforge.net/projects/gapfiller

version	toolchain
2.1.1	intel/2017a
2.1.2	GCC/11.3.0

gappa

gappa is a collection of commands for working with phylogenetic data. Its main focus are evolutionary placements of short environmental sequences on a reference phylogenetic tree. Such data is typically produced by tools like EPA-ng, RAxML-EPA or pplacer and usually stored in jplace files.

homepage: https://github.com/lczech/gappa

version	toolchain
0.7.1	GCC/10.3.0

GAPPadder

GAPPadder is tool for closing gaps on draft genomes with short sequencing data

homepage: https://github.com/simoncchu/GAPPadder

version	versionsuffix	toolchain
20170601	-Python-2.7.18	foss/2021b

GARLI

GARLI, Genetic Algorithm for Rapid Likelihood Inference is a program for inferring phylogenetic trees. Using an approach similar to a classical genetic algorithm, it rapidly searches the space of evolutionary trees and model parameters to find the solution maximizing the likelihood score. It implements nucleotide, amino acid and codon-based models of sequence evolution, and runs on all platforms.

homepage: https://code.google.com/archive/p/garli/

version	toolchain
2.01	gompi/2019a

garnett

Garnett is a software package that faciliates automated cell type classification from single-cell expression data.

homepage: https://cole-trapnell-lab.github.io/garnett

version	versionsuffix	toolchain
0.1.20	-R-4.0.3	foss/2020b

GAT

The Genomic Association Tester (GAT) is a tool for computing the significance of overlap between multiple sets of genomic intervals. GAT estimates significance based on simulation.

homepage: https://gat.readthedocs.io/

version	versionsuffix	toolchain
1.2.2	-Python-2.7.11	foss/2016a

GATB-Core

GATB-Core is a high-performance and low memory footprint C++ library that provides a set of highly efficient algorithms to analyse NGS data sets

homepage: https://gatb.inria.fr/software/gatb-core

version	toolchain
1.4.2	gompi/2022a

GATE

GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography

homepage: http://www.opengatecollaboration.org/

version	versionsuffix	toolchain
6.2	-Python-2.7.11	intel/2016a
7.1	-Python-2.7.11	intel/2016a
7.2	-Python-2.7.11	intel/2016a
8.0	-Python-2.7.14	foss/2017b, intel/2017b
8.0	-Python-2.7.14-Geant4-10.04	intel/2017b
8.1.p01	-Python-2.7.15	foss/2018b
8.2	-Python-2.7.14	foss/2017b, intel/2017b
8.2	-Python-2.7.15	foss/2018b
9.0	-Python-3.7.4	foss/2019b
9.1		foss/2021b
9.2		foss/2021b, foss/2022a

GATK

The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

homepage: https://www.broadinstitute.org/gatk/

version	versionsuffix	toolchain
1.0.5083		system
2.5-2	-Java-1.7.0_10	system
2.6-5	-Java-1.7.0_10	system
2.7-4		system
2.7-4	-Java-1.7.0_10	system
2.8-1	-Java-1.7.0_10	system
3.0-0	-Java-1.7.0_10	system
3.3-0	-Java-1.7.0_21	system
3.3-0	-Java-1.7.0_80	system
3.3-0	-Java-1.8.0_66	system
3.5	-Java-1.8.0_66	system
3.5	-Java-1.8.0_74	system
3.6	-Java-1.8.0_92	system
3.7	-Java-1.8.0_112	system
3.8-0	-Java-1.8.0_144	system
4.0.1.2	-Java-1.8	system
4.0.4.0	-Python-2.7.14	intel/2018a
4.0.4.0	-Python-3.6.4	intel/2018a
4.0.5.1	-Python-3.6.4	foss/2018a
4.0.7.0	-Python-2.7.14	intel/2018a
4.0.7.0	-Python-3.6.4	intel/2018a
4.0.8.1	-Python-2.7.15	foss/2018b
4.0.8.1	-Python-3.6.6	foss/2018b
4.0.10.0	-Python-3.6.6	foss/2018b
4.0.12.0	-Python-3.6.6	foss/2018b
4.1.0.0	-Python-3.6.6	foss/2018b
4.1.2.0	-Java-1.8	GCCcore/8.2.0
4.1.3.0	-Java-1.8	GCCcore/8.3.0
4.1.4.1	-Java-1.8	GCCcore/8.3.0
4.1.4.1	-Java-11	GCCcore/8.3.0
4.1.5.0	-Java-1.8	GCCcore/9.3.0
4.1.5.0	-Java-11	GCCcore/9.3.0
4.1.8.1	-Java-1.8	GCCcore/9.3.0
4.2.0.0	-Java-1.8	GCCcore/10.2.0
4.2.0.0	-Java-11	GCCcore/10.2.0
4.2.3.0	-Java-11	GCCcore/11.2.0
4.2.5.0	-Java-11	GCCcore/11.2.0
4.2.6.1	-Java-11	GCCcore/10.3.0, GCCcore/11.2.0
4.3.0.0	-Java-11	GCCcore/11.3.0
4.4.0.0	-Java-17	GCCcore/12.2.0, GCCcore/12.3.0
4.5.0.0	-Java-17	GCCcore/12.3.0

Gaussian

Gaussian provides state-of-the-art capabilities for electronic structure modeling. Gaussian 09 is licensed for a wide variety of computer systems. All versions of Gaussian 09 contain every scientific/modeling feature, and none imposes any artificial limitations on calculations other than your computing resources and patience. This is the official gaussian AVX2 build.

homepage: https://www.gaussian.com/

version	versionsuffix	toolchain
09.e.01	-AVX	system
16.A.03	-AVX2	system

gawk

The awk utility interprets a special-purpose programming language that makes it possible to handle simple data-reformatting jobs with just a few lines of code.

homepage: https://www.gnu.org/software/gawk

version	toolchain
5.1.0	GCC/10.2.0
5.1.1	GCC/10.3.0, GCC/11.2.0, GCC/11.3.0
5.3.0	GCC/12.2.0, GCC/13.2.0

gbasis

Python library for analytical evaluation and integration of Gaussian-type basis functions and related quantities.

homepage: https://github.com/theochem/gbasis

version	toolchain
20210904	intel/2022a

Gblocks

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

homepage: https://www.biologiaevolutiva.org/jcastresana/Gblocks.html

version	toolchain
0.91b	system

GBprocesS

GBprocesS allows for the extraction of genomic inserts from NGS data for GBS experiments. Preprocessing is performed in different stages that are part of a linear pipeline where the steps are performed in order. GBprocesS provides a flexible way to adjust the functionality to your needs, as the operations required and the execution order vary depending on the GBS protocol used.

homepage: https://gbprocess.readthedocs.io/

version	versionsuffix	toolchain
2.3	-Python-3.8.2	intel/2020a
4.0.0.post1		foss/2022a

gbs2ploidy

Inference of Ploidy from (Genotyping-by-Sequencing) GBS Data

homepage: https://cran.r-project.org/web/packages/gbs2ploidy

version	versionsuffix	toolchain
1.0	-R-3.4.3	intel/2017b

gc

The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new.

homepage: https://hboehm.info/gc/

version	toolchain
7.4.4	GCC/4.9.3-2.25, foss/2016a
7.6.0	GCCcore/6.4.0
7.6.4	GCCcore/7.3.0
7.6.10	GCCcore/8.2.0
7.6.12	GCCcore/8.3.0, GCCcore/9.3.0
8.0.4	GCCcore/10.3.0
8.2.0	GCCcore/11.2.0
8.2.2	GCCcore/10.2.0, GCCcore/11.3.0
8.2.4	GCCcore/12.3.0

GC3Pie

GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution environments.

homepage: https://gc3pie.readthedocs.org

version	toolchain
2.4.2	system
2.5.0	system
2.5.2	system

GCC

The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).

homepage: http://gcc.gnu.org/

version	versionsuffix	toolchain
4.8.1		system
4.8.1	-CLooG	system
4.8.2		system
4.8.2	-CLooG	system
4.8.2	-CLooG-multilib	system
4.8.2	-multilib	system
4.8.3		system
4.8.3	-CLooG-multilib	system
4.8.4		system
4.8.4	-CLooG	system
4.8.4	-CLooG-multilib	system
4.8.5		system
4.9.0		system
4.9.0	-CLooG	system
4.9.0	-CLooG-multilib	system
4.9.1		system
4.9.1	-CLooG	system
4.9.1	-CLooG-multilib	system
4.9.2		system
4.9.2	-CLooG	system
4.9.2	-CLooG-multilib	system
4.9.2	-binutils-2.25	system
4.9.3		system
4.9.3	-2.25	system
4.9.3	-binutils-2.25	system
4.9.4	-2.25	system
5.1.0		system
5.1.0	-binutils-2.25	system
5.2.0		system
5.3.0		system
5.3.0	-2.26	system
5.4.0	-2.26	system
5.5.0	-2.26	system
6.1.0	-2.27	system
6.2.0	-2.27	system
6.3.0	-2.27	system
6.3.0	-2.28	system
6.4.0	-2.28	system
7.1.0	-2.28	system
7.2.0	-2.29	system
7.3.0	-2.30	system
7.4.0	-2.31.1	system
8.1.0	-2.30	system
8.2.0	-2.31.1	system
8.3.0		system
8.3.0	-2.32	system
8.4.0		system
9.1.0	-2.32	system
9.2.0		system
9.2.0	-2.32	system
9.3.0		system
9.4.0		system
9.5.0		system
10.1.0		system
10.2.0		system
10.3.0		system
11.1.0		system
11.2.0		system
11.3.0		system
11.4.0		system
12.1.0		system
12.2.0		system
12.3.0		system
13.1.0		system
13.2.0		system
system		system
system	-2.29	system

GCCcore

The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).

homepage: http://gcc.gnu.org/

version	toolchain
4.9.2	system
4.9.3	system
4.9.4	system
5.3.0	system
5.4.0	system
5.5.0	system
6.1.0	system
6.2.0	system
6.3.0	system
6.4.0	system
6.5.0	system
7.1.0	system
7.2.0	system
7.3.0	system
7.4.0	system
8.1.0	system
8.2.0	system
8.3.0	system
8.4.0	system
9.1.0	system
9.2.0	system
9.3.0	system
9.4.0	system
9.5.0	system
10.1.0	system
10.2.0	system
10.3.0	system
11.1.0	system
11.2.0	system
11.3.0	system
11.4.0	system
12.1.0	system
12.2.0	system
12.3.0	system
13.1.0	system
13.2.0	system
system	system

gcccuda

GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.

homepage: <(none)>

version	toolchain
2016.08	system
2017b	system
2018a	system
2018b	system
2019a	system
2019b	system
2020a	system
2020b	system

gcloud

Libraries and tools for interacting with Google Cloud products and services.

homepage: https://cloud.google.com/sdk

version	toolchain
382.0.0	system

GConf

GConf is a system for storing application preferences. It is intended for user preferences; not configuration of something like Apache, or arbitrary data storage.

homepage: https://projects.gnome.org/gconf/

version	toolchain
3.2.6	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/8.2.0, GCCcore/8.3.0, foss/2016a, foss/2018b, intel/2016a, intel/2016b, intel/2017a, intel/2017b

gcsfs

Pythonic file-system interface for Google Cloud Storage.

homepage: https://github.com/fsspec/gcsfs

version	toolchain
2023.12.2.post1	foss/2023a

GCTA

GCTA (Genome-wide Complex Trait Analysis) is a software package, which was initially developed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for a complex trait but has been extensively extended for many other analyses of data from genome-wide association studies (GWASs).

homepage: https://yanglab.westlake.edu.cn/software/gcta/

version	toolchain
1.94.0beta	foss/2021b, gfbf/2022a
1.94.1	gfbf/2022a, gfbf/2023a

Gctf

Gctf: real-time CTF determination and correction, Kai Zhang, 2016

homepage: https://www.mrc-lmb.cam.ac.uk/kzhang/

version	toolchain
1.06	system

GD

GD.pm - Interface to Gd Graphics Library

homepage: https://github.com/lstein/Perl-GD

version	versionsuffix	toolchain
2.66	-Perl-5.24.0	foss/2016b
2.68	-Perl-5.26.1	GCCcore/6.4.0
2.69	-Perl-5.28.0	GCCcore/7.3.0
2.71		GCCcore/9.3.0
2.73		GCCcore/10.3.0
2.75		GCCcore/11.3.0

GDAL

GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.

homepage: https://www.gdal.org

version	versionsuffix	toolchain
2.0.2		foss/2016a, intel/2016a
2.1.0		foss/2016a, foss/2016b, intel/2016b
2.1.1		foss/2016a
2.1.1	-Python-2.7.12	intel/2016b
2.1.2	-Python-2.7.12	intel/2016b
2.1.3	-Python-2.7.12	foss/2016b, intel/2016b
2.1.3	-Python-2.7.13	intel/2017a
2.1.3	-Python-3.6.1	intel/2017a
2.2.0	-Python-2.7.13-HDF5-1.8.18	intel/2017a
2.2.0	-Python-2.7.13-HDF5-HDF	intel/2017a
2.2.0	-Python-3.6.1	intel/2017a
2.2.2	-Python-2.7.14	intel/2017b
2.2.2	-Python-2.7.14-HDF5-1.8.19	intel/2017b
2.2.3	-Python-2.7.14	foss/2017b, foss/2018a, intel/2017b, intel/2018a
2.2.3	-Python-2.7.15	foss/2018b
2.2.3	-Python-3.6.3	foss/2017b
2.2.3	-Python-3.6.4	foss/2018a, intel/2018a, iomkl/2018a
2.2.3	-Python-3.6.6	foss/2018b, intel/2018b
2.4.4		foss/2021b, intel/2021b
3.0.0	-Python-2.7.15	foss/2019a, intel/2019a
3.0.0	-Python-3.7.2	foss/2019a, intel/2019a
3.0.2	-Python-3.7.4	foss/2019b, fosscuda/2019b, intel/2019b
3.0.4	-Python-3.8.2	foss/2020a, intel/2020a
3.2.1		foss/2020b, fosscuda/2020b, intel/2020b
3.3.0		foss/2021a
3.3.2		foss/2021b
3.5.0		foss/2022a
3.6.2		foss/2022b
3.7.1		foss/2023a

GDB

The GNU Project Debugger

homepage: https://www.gnu.org/software/gdb/gdb.html

version	versionsuffix	toolchain
7.8.2		GCC/4.9.2
7.9		GCC/4.9.2
7.10.1	-Python-2.7.11	foss/2016a, intel/2016a
7.11	-Python-2.7.11	foss/2016a, intel/2016a
7.11.1	-Python-2.7.12	foss/2016b, intel/2016b
8.0.1	-Python-2.7.14	foss/2017b
8.0.1	-Python-3.6.3	foss/2017b
8.1	-Python-2.7.14	foss/2018a
8.1.1	-Python-2.7.14	intel/2018a
8.3	-Python-3.7.2	GCCcore/8.2.0
9.1	-Python-3.7.4	GCCcore/8.3.0
10.1		GCCcore/10.2.0
10.2		GCCcore/10.3.0
10.2	-Python-3.8.2	GCCcore/9.3.0
11.1		GCCcore/11.2.0
12.1		GCCcore/11.3.0
13.2		GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

gdbgui

Browser-based frontend to gdb (gnu debugger). Add breakpoints, view the stack, visualize data structures, and more in C, C++, Go, Rust, and Fortran. Run gdbgui from the terminal and a new tab will open in your browser.

homepage: https://gdbgui.com

version	versionsuffix	toolchain
0.13.1.2	-Python-3.7.2	GCCcore/8.2.0

gdbm

GNU dbm (or GDBM, for short) is a library of database functions that use extensible hashing and work similar to the standard UNIX dbm. These routines are provided to a programmer needing to create and manipulate a hashed database.

homepage: https://www.gnu.org.ua/software/gdbm/gdbm.html

version	toolchain
1.18.1	foss/2020a
1.21	GCCcore/10.2.0

gdc-client

The gdc-client provides several convenience functions over the GDC API which provides general download/upload via HTTPS.

homepage: https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool

version	versionsuffix	toolchain
1.0.1	-Python-2.7.12	intel/2016b
1.3.0	-Python-2.7.14	foss/2018a, intel/2017b
1.3.0	-Python-2.7.15	foss/2018b
1.6.0		GCCcore/10.2.0

GDCHART

Easy to use C API, high performance library to create charts and graphs in PNG, GIF and WBMP format.

homepage: http://users.fred.net/brv/chart

version	toolchain
0.11.5dev	GCCcore/8.2.0

GDCM

Grassroots DICOM: Cross-platform DICOM implementation

homepage: https://sourceforge.net/projects/gdcm

version	toolchain
2.8.8	GCCcore/6.4.0
2.8.9	GCCcore/7.3.0
3.0.4	GCCcore/8.2.0
3.0.5	GCCcore/8.3.0
3.0.8	GCCcore/10.2.0, GCCcore/9.3.0
3.0.20	GCCcore/11.3.0
3.0.21	GCCcore/12.2.0

GDGraph

GDGraph is a Perl package to generate charts

homepage: https://metacpan.org/release/GDGraph

version	versionsuffix	toolchain
1.54	-Perl-5.26.1	intel/2018a
1.54	-Perl-5.28.0	foss/2018b
1.56		GCCcore/11.3.0

gdist

The gdist module is a Cython interface to a C++ library (http://code.google.com/p/geodesic/) for computing geodesic distance which is the length of shortest line between two vertices on a triangulated mesh in three dimensions, such that the line lies on the surface.

homepage: https://pypi.python.org/pypi/gdist

version	versionsuffix	toolchain
1.0.3	-Python-2.7.11	intel/2016a

Gdk-Pixbuf

The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3.

homepage: https://docs.gtk.org/gdk-pixbuf/

version	toolchain
2.32.3	intel/2016a
2.35.1	foss/2016a, intel/2016a
2.36.0	foss/2016b, intel/2016b
2.36.8	intel/2017a
2.36.10	intel/2017a
2.36.11	foss/2017b, foss/2018a, fosscuda/2018b, intel/2017b, intel/2018a
2.36.12	foss/2018b, fosscuda/2018b
2.38.1	GCCcore/8.2.0
2.38.2	GCCcore/8.3.0
2.40.0	GCCcore/10.2.0, GCCcore/9.3.0
2.42.6	GCCcore/10.3.0, GCCcore/11.2.0
2.42.8	GCCcore/11.3.0
2.42.10	GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

GDRCopy

A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology.

homepage: https://github.com/NVIDIA/gdrcopy

version	versionsuffix	toolchain
2.1	-CUDA-11.0.2	GCCcore/9.3.0
2.1	-CUDA-11.1.1	GCCcore/10.2.0
2.1	-CUDA-11.2.1	GCCcore/10.2.0
2.2		GCCcore/10.2.0, GCCcore/10.3.0
2.3		GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0
2.3.1		GCCcore/12.3.0
2.4		GCCcore/13.2.0

Gdspy

Gdspy is a Python module for creation and manipulation of GDSII stream files.

homepage: https://github.com/heitzmann/gdspy

version	toolchain
1.6.13	foss/2022a

Geant4

Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.

homepage: https://geant4.cern.ch

version	toolchain
9.5.p02	intel/2016a
9.6.p04	intel/2016a
10.01.p03	intel/2016a
10.02.p01	intel/2016a
10.03.p03	foss/2017b, intel/2017b
10.04	intel/2017b
10.5	foss/2017b, foss/2018b, intel/2017b, intel/2018b
10.6	foss/2019b
10.6.2	foss/2020a
10.7.1	GCC/10.2.0, GCC/11.2.0
11.0.0	GCC/11.2.0
11.0.1	GCC/11.2.0
11.0.2	GCC/11.2.0, GCC/11.3.0
11.1.2	GCC/11.3.0

Geant4-data

Datasets for Geant4.

homepage: https://geant4.cern.ch/

version	toolchain
11.1	system
20201103	system
20210510	system

gearshifft

Benchmark Suite for Heterogenuous FFT Implementations

homepage: https://github.com/mpicbg-scicomp/gearshifft

version	toolchain
0.4.0	foss/2019a

GEGL

GEGL (Generic Graphics Library) is a data flow based image processing framework, providing floating point processing and non-destructive image processing capabilities to GNU Image Manipulation Program (GIMP) and other projects.

homepage: https://www.gegl.org

version	toolchain
0.4.30	GCCcore/10.3.0

GEM

GEM (Gene-Environment interaction analysis for Millions of samples) is a software program for large-scale gene-environment interaction testing in samples from unrelated individuals. It enables genome-wide association studies in up to millions of samples while allowing for multiple exposures, control for genotype-covariate interactions, and robust inference.

homepage: https://github.com/large-scale-gxe-methods/GEM

version	toolchain
1.5.1	foss/2022a, foss/2022b

GEM-library

Next-generation sequencing platforms (Illumina/Solexa, ABI/SOLiD, etc.) call for powerful and very optimized tools to index/analyze huge genomes. The GEM library strives to be a true "next-generation" tool for handling any kind of sequence data, offering state-of-the-art algorithms and data structures specifically tailored to this demanding task. At the moment, efficient indexing and searching algorithms based on the Burrows-Wheeler transform (BWT) have been implemented. The library core is written in C for maximum speed, with concise interfaces to higher-level programming languages like OCaml and Python. Many high-performance standalone programs (mapper, splice mapper, etc.) are provided along with the library; in general, new algorithms and tools can be easily implemented on the top of it.

homepage: http://algorithms.cnag.cat/wiki/The_GEM_library

version	versionsuffix	toolchain
20130406-045632	_pre-release-3_Linux-x86_64	system

gemelli

Gemelli is a tool box for running both Robust Aitchison PCA (RPCA) and Compositional Tensor Factorization (CTF) on sparse compositional omics datasets.

homepage: https://github.com/biocore/gemelli

version	toolchain
0.0.9	foss/2022a

GEMMA

Genome-wide Efficient Mixed Model Association

homepage: https://github.com/genetics-statistics/GEMMA

version	toolchain
0.97	foss/2016b, foss/2017a
0.98.1	foss/2018b
0.98.5	foss/2020a, foss/2021b, foss/2022b

gemmi

Gemmi is a library, accompanied by a set of programs, developed primarily for use in macromolecular crystallography (MX). For working with: macromolecular models (content of PDB, PDBx/mmCIF and mmJSON files), refinement restraints (CIF files), reflection data (MTZ and mmCIF formats), data on a 3D grid (electron density maps, masks, MRC/CCP4 format) crystallographic symmetry. Parts of this library can be useful in structural bioinformatics (for symmetry- aware analysis of protein models), and in other molecular-structure sciences that use CIF files (we have the fastest open-source CIF parser).

homepage: https://gemmi.readthedocs.io/

version	toolchain
0.4.5	GCCcore/10.2.0

gencore_variant_detection

This is a bundled install of many software packages for doing variant detection analysis.

homepage: https://nyuad-cgsb.github.io/variant_detection/public/index.html

version	toolchain
1.0	system

GeneMark-ET

Eukaryotic gene prediction suite with automatic training

homepage: http://exon.gatech.edu/GeneMark

version	toolchain
4.38	GCCcore/8.2.0
4.57	GCCcore/8.3.0
4.65	GCCcore/10.2.0
4.71	GCCcore/11.2.0, GCCcore/11.3.0

GenerativeModels

homepage: https://monai.io/

version	versionsuffix	toolchain
0.2.1	-CUDA-11.7.0	foss/2022a

gengetopt

Gengetopt is a tool to write command line option parsing code for C programs.

homepage: https://www.gnu.org/software/gengetopt/gengetopt.html

version	toolchain
2.23	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.3.0, GCCcore/9.3.0

GenMap

GenMap - Fast and Exact Computation of Genome Mappability

homepage: https://github.com/cpockrandt/genmap

version	toolchain
1.3.0	GCCcore/11.2.0

Genome_Profiler

Genome Profiler (GeP) is a program to perform whole-genome multilocus sequence typing (wgMLST) analysis for bacterial isolates

homepage: https://sourceforge.net/projects/genomeprofiler/

version	versionsuffix	toolchain
2.1	-Perl-5.24.0	foss/2016b

GenomeComb

Genomecomb is a package designed to analyze, combine, annotate and query genome as well as transcriptome sequencing data.

homepage: https://github.com/derijkp/genomecomb

version	versionsuffix	toolchain
0.106.0	-x86_64	system

GenomeMapper

GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. This version is used to align against a single reference. If you are unsure which one is the appropriate GenomeMapper, you might want to use this one.

homepage: https://1001genomes.org/software/genomemapper_singleref.html

version	toolchain
0.4.4	foss/2016a

genomepy

genomepy is designed to provide a simple and straightforward way to download and use genomic data

homepage: https://github.com/vanheeringen-lab/genomepy

version	toolchain
0.15.0	foss/2022a

GenomeTester4

A toolkit for performing set operations - union, intersection and complement - on k-mer lists.

homepage: https://github.com/bioinfo-ut/GenomeTester4

version	toolchain
4.0	intel/2018a

GenomeThreader

GenomeThreader is a software tool to compute gene structure predictions.

homepage: https://genomethreader.org

version	versionsuffix	toolchain
1.7.1	-Linux_x86_64-64bit	system
1.7.3	-Linux_x86_64-64bit	system

GenomeTools

A comprehensive software library for efficient processing of structured genome annotations.

homepage: http://genometools.org

version	versionsuffix	toolchain
1.5.10		foss/2018b
1.5.10	-Python-2.7.15	foss/2018b
1.6.1		GCC/10.2.0, GCC/8.3.0, GCC/9.3.0
1.6.1	-Python-2.7.16	GCC/8.3.0
1.6.2		GCC/10.3.0, GCC/11.3.0, GCC/12.2.0

GenomeWorks

SDK for GPU accelerated genome assembly and analysis

homepage: https://github.com/clara-parabricks/GenomeWorks

version	toolchain
2021.02.2	fosscuda/2020b

GenotypeHarmonizer

The Genotype Harmonizer is an easy to use command-line tool that allows harmonization of genotype data stored using different file formats with different and potentially unknown strands.

homepage: https://github.com/molgenis/systemsgenetics/wiki/Genotype-Harmonizer

version	versionsuffix	toolchain
1.4.14	-Java-1.7.0_80	system

genozip

Genozip is a compressor for genomic files - it compresses FASTQ, SAM/BAM/CRAM, VCF, FASTA and others.

homepage: https://genozip.com

version	toolchain
13.0.5	GCCcore/11.2.0

gensim

Gensim is a Python library for topic modelling, document indexing and similarity retrieval with large corpora.

homepage: https://radimrehurek.com/gensim

version	versionsuffix	toolchain
0.13.2	-Python-2.7.11	foss/2016a
3.8.3		foss/2020b, intel/2020b
4.2.0		foss/2021a

geocube

Tool to convert geopandas vector data into rasterized xarray data.

homepage: https://corteva.github.io/geocube

version	versionsuffix	toolchain
0.0.14	-Python-3.8.2	foss/2020a
0.4.3		foss/2023a

geopandas

GeoPandas is a project to add support for geographic data to pandas objects. It currently implements GeoSeries and GeoDataFrame types which are subclasses of pandas.Series and pandas.DataFrame respectively. GeoPandas objects can act on shapely geometry objects and perform geometric operations.

homepage: https://github.com/geopandas/geopandas

version	versionsuffix	toolchain
0.7.0	-Python-3.7.4	foss/2019b, fosscuda/2019b
0.8.0	-Python-3.7.2	foss/2019a
0.8.1	-Python-3.7.4	intel/2019b
0.8.1	-Python-3.8.2	foss/2020a
0.10.2		foss/2021a
0.11.0		foss/2021b
0.12.2		foss/2022a, foss/2022b
0.14.2		foss/2023a

geopy

geopy is a Python client for several popular geocoding web services. geopy makes it easy for Python developers to locate the coordinates of addresses, cities, countries, and landmarks across the globe using third-party geocoders and other data sources.

homepage: https://geopy.readthedocs.io/

version	versionsuffix	toolchain
1.11.0	-Python-3.6.1	intel/2017a
2.1.0		GCCcore/10.2.0
2.4.1		GCCcore/12.3.0

georges

Georges the lemur opinionated particle accelerator modeling Python package. Also a thin wrapper over MAD-X/PTC, BDSim and G4Beamline.

homepage: https://github.com/ULB-Metronu/georges

version	versionsuffix	toolchain
2019.2		foss/2021a
2019.2	-Python-3.7.4	foss/2019b

GEOS

GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)

homepage: https://trac.osgeo.org/geos

version	versionsuffix	toolchain
3.5.0	-Python-2.7.11	intel/2016a
3.5.0	-Python-2.7.12	intel/2016b
3.6.1	-Python-2.7.12	foss/2016b, intel/2016b
3.6.1	-Python-2.7.13	intel/2017a
3.6.1	-Python-3.6.1	intel/2017a
3.6.2	-Python-2.7.14	foss/2017b, foss/2018a, intel/2017b, intel/2018a
3.6.2	-Python-2.7.15	foss/2018b
3.6.2	-Python-3.6.2	foss/2017b
3.6.2	-Python-3.6.3	foss/2017b, intel/2017b, intel/2018.01
3.6.2	-Python-3.6.4	foss/2018a, intel/2018a, iomkl/2018a
3.6.2	-Python-3.6.6	foss/2018b, intel/2018b
3.7.2	-Python-2.7.15	foss/2019a, intel/2019a
3.7.2	-Python-3.7.2	foss/2019a, intel/2019a
3.8.0		GCC/8.3.0
3.8.0	-Python-3.7.4	GCC/8.3.0, iccifort/2019.5.281
3.8.1	-Python-3.8.2	GCC/9.3.0, iccifort/2020.1.217
3.9.1		GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, iccifort/2020.4.304, intel-compilers/2021.4.0
3.10.3		GCC/11.3.0
3.11.1		GCC/12.2.0
3.12.0		GCC/12.3.0

geosphere

Spherical trigonometry for geographic applications. That is, compute distances and related measures for angular (longitude/latitude) locations.

homepage: https://cran.r-project.org/web/packages/geosphere/index.html

version	versionsuffix	toolchain
1.5-18	-R-4.2.1	foss/2022a

Gerris

Gerris is a Free Software program for the solution of the partial differential equations describing fluid flow

homepage: http://gfs.sourceforge.net/wiki/index.php/Main_Page

version	toolchain
20131206	foss/2017b, gompi/2023a

GETORB

GETORB software package contains programs to handle the orbital data records (ODRs)

homepage: http://www.deos.tudelft.nl/ers/precorbs/tools/getorb_pack.shtml

version	toolchain
2.3.2	intel/2017a

GetOrganelle

This toolkit assemblies organelle genome from genomic skimming data.

homepage: https://github.com/Kinggerm/GetOrganelle

version	versionsuffix	toolchain
1.7.2	-Python-3.8.2	foss/2020a
1.7.4-pre2		foss/2020b
1.7.5.3		foss/2021b
1.7.6.1		foss/2021b
1.7.7.0		foss/2022a

gettext

GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation

homepage: https://www.gnu.org/software/gettext/

version	versionsuffix	toolchain
0.18.2		system
0.19.4		GCC/4.9.2, system
0.19.6		GNU/4.9.3-2.25, foss/2016a, gimkl/2.11.5, intel/2016a, system
0.19.7		foss/2016a, intel/2016a, system
0.19.8		GCCcore/4.9.3, GCCcore/5.4.0, foss/2016.04, foss/2016b, intel/2016b, system
0.19.8.1		GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, system
0.19.8.1	-libxml2-2.9.7	GCCcore/6.4.0
0.20.1		GCCcore/8.3.0, GCCcore/9.3.0, system
0.21		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, system
0.21.1		GCCcore/12.2.0, GCCcore/12.3.0, system
0.22		GCCcore/13.2.0, system

gexiv2

gexiv2 is a GObject wrapper around the Exiv2 photo metadata library.

homepage: https://wiki.gnome.org/Projects/gexiv2

version	toolchain
0.12.2	GCCcore/10.3.0

gfbf

GNU Compiler Collection (GCC) based compiler toolchain, including FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.

homepage: <(none)>

version	toolchain
2022a	system
2022b	system
2023.09	system
2023a	system
2023b	system

GFF3-toolkit

Python programs for processing GFF3 files

homepage: https://gff3toolkit.readthedocs.io

version	toolchain
2.1.0	foss/2022a

GffCompare

GffCompare provides classification and reference annotation mapping and matching statistics for RNA-Seq assemblies (transfrags) or other generic GFF/GTF files.

homepage: https://ccb.jhu.edu/software/stringtie/gffcompare.shtml

version	toolchain
0.10.1	foss/2016b
0.10.6	GCCcore/7.3.0
0.11.6	GCCcore/8.3.0, GCCcore/9.3.0
0.12.2	GCC/10.3.0
0.12.6	GCC/11.2.0

gffread

GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.

homepage: https://github.com/gpertea/gffread

version	toolchain
0.9.12	foss/2016b
0.10.6	GCCcore/7.3.0
0.11.6	GCCcore/8.3.0, GCCcore/9.3.0
0.12.7	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/12.2.0

gffutils

Gffutils is a Python package for working with and manipulating the GFF and GTF format files typically used for genomic annotations.

homepage: https://github.com/daler/gffutils

version	toolchain
0.12	foss/2022b

gflags

The gflags package contains a C++ library that implements commandline flags processing. It includes built-in support for standard types such as string and the ability to define flags in the source file in which they are used.

homepage: https://github.com/gflags/gflags

version	toolchain
2.1.2	foss/2016a
2.2.1	GCCcore/6.4.0, intel/2017a, intel/2017b
2.2.2	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0

GFOLD

Generalized fold change for ranking differentially expressed genes from RNA-seq data

homepage: http://www.tongji.edu.cn/~zhanglab/GFOLD/index.html

version	toolchain
1.1.4	intel/2016a

gh

gh is GitHub on the command line.

homepage: https://github.com/cli/cli

version	toolchain
1.3.1	system
2.20.2	system

GHC

The Glorious/Glasgow Haskell Compiler

homepage: https://haskell.org/ghc/

version	versionsuffix	toolchain
6.12.3		system
8.6.5	-x86_64	system
9.2.2	-x86_64	system
9.4.6	-x86_64	system

Ghostscript

Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that.

homepage: https://ghostscript.com

version	versionsuffix	toolchain
9.19		intel/2016a, intel/2016b
9.20		foss/2016b, intel/2016b
9.21		intel/2017a
9.22		GCCcore/6.4.0, foss/2017b, intel/2017b
9.22	-cairo-1.14.12	GCCcore/6.4.0
9.23		GCCcore/6.4.0, GCCcore/7.3.0
9.23	-cairo-1.14.12	GCCcore/6.4.0
9.27		GCCcore/8.2.0
9.50		GCCcore/8.3.0
9.52		GCCcore/9.3.0
9.53.3		GCCcore/10.2.0
9.54.0		GCCcore/10.3.0, GCCcore/11.2.0
9.56.1		GCCcore/11.3.0
10.0.0		GCCcore/12.2.0
10.01.2		GCCcore/12.3.0
10.02.1		GCCcore/13.2.0

GI-DocGen

GI-DocGen is a document generator for GObject-based libraries. GObject is the base type system of the GNOME project. GI-Docgen reuses the introspection data generated by GObject-based libraries to generate the API reference of these libraries, as well as other ancillary documentation.

homepage: https://gitlab.gnome.org/GNOME/gi-docgen

version	toolchain
2023.3	GCCcore/12.3.0

giac

Giac is a C++ library, it is the CAS computing kernel. It may be used inside other C++ programs, and also Python, Java and Javascript programs.

homepage: https://www-fourier.ujf-grenoble.fr/~parisse/giac.html

version	toolchain
1.9.0-69	gfbf/2022a

Gibbs2

Gibbs2 is a program for the calculation of thermodynamic properties in periodic solids under arbitrary conditions of temperature and pressure. Gibbs2 uses the results of periodic solid-state quantum-mechanical calculations, specifically the energy-volume curve and possibly the harmonic phonon frequencies, to compute the thermodynamic properties of the solid within the framework of the quasiharmonic approximation.

homepage: https://aoterodelaroza.github.io/gibbs2/

version	toolchain
1.0	GCC/10.3.0

giflib

giflib is a library for reading and writing gif images. It is API and ABI compatible with libungif which was in wide use while the LZW compression algorithm was patented.

homepage: http://giflib.sourceforge.net/

version	toolchain
5.1.4	GCCcore/7.3.0, GCCcore/8.2.0
5.2.1	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0, GCCcore/8.3.0, GCCcore/9.3.0

gifsicle

Gifsicle is a command-line tool for creating, editing, and getting information about GIF images and animations. Making a GIF animation with gifsicle is easy.

homepage: https://github.com/kohler/gifsicle

version	toolchain
1.92	GCCcore/8.2.0
1.93	GCCcore/11.3.0

GIMIC

The GIMIC program calculates magnetically induced currents in molecules. You need to provide this program with a density matrix in atomic-orbital (AO) basis and three (effective) magnetically perturbed AO density matrices in the proper format. Currently ACES2, Turbomole, G09, QChem, FERMION++, and LSDalton can produce these matrices.

homepage: http://gimic.readthedocs.io

version	versionsuffix	toolchain
2.2.1		foss/2022a
2018.04.20	-Python-2.7.14	intel/2018a

gimkl

GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI and MKL

homepage: <(none)>

version	toolchain
2.11.5	system
2017a	system
2018b	system

GimmeMotifs

Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments

homepage: https://github.com/vanheeringen-lab/gimmemotifs

version	toolchain
0.17.2	foss/2022a

GIMP

GIMP is a cross-platform image editor available for GNU/Linux, OS X, Windows and more operating systems.

homepage: https://www.gimp.org

version	toolchain
2.10.24	GCC/10.3.0

gimpi

GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI.

homepage: <(none)>

version	toolchain
2.11.5	system
2017a	system
2017b	system
2018a	system
2018b	system

gimpic

GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including IntelMPI for MPI support with CUDA features enabled.

homepage: <(none)>

version	toolchain
2017b	system

GIMPS

GIMPS: Great Internet Mersenne Prime Search; it can be useful for limited stress testing of nodes, in user space

homepage: http://www.mersenne.org/

version	toolchain
p95v279	GCC/4.8.2
p95v279.linux64	system

giolf

GNU Compiler Collection (GCC) based compiler toolchain, including IntelMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.

homepage: <(none)>

version	toolchain
2017b	system
2018a	system

giolfc

GCC based compiler toolchain with CUDA support, and including IntelMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.

homepage: <(none)>

version	toolchain
2017b	system

Giotto-Suite

Giotto Suite is focused on building a modular platform for analyzing spatial-omics technologies and strives to be interoperable with other popular spatial analysis tools and classes. Using established packages optimized for large(r) data, Giotto Suite adopts fast and memory efficient methods to create an interactive analysis.

homepage: https://github.com/drieslab/Giotto

version	versionsuffix	toolchain
3.0.1	-R-4.2.1	foss/2022a

git

Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.

homepage: http://git-scm.com/

version	versionsuffix	toolchain
1.8.5.6		GCC/4.9.2
2.2.2		GCC/4.9.2
2.4.1		GCC/4.9.2
2.8.0		foss/2016a
2.12.2		foss/2016b
2.13.1		foss/2016b
2.14.1		GCCcore/6.4.0
2.16.1		foss/2018a
2.18.0		GCCcore/7.3.0
2.19.1		GCCcore/7.3.0
2.21.0		GCCcore/8.2.0
2.21.0	-nodocs	GCCcore/8.2.0
2.23.0		GCCcore/8.3.0
2.23.0	-nodocs	GCCcore/8.3.0, GCCcore/9.3.0
2.28.0	-nodocs	GCCcore/10.2.0
2.32.0	-nodocs	GCCcore/10.3.0
2.33.1	-nodocs	GCCcore/11.2.0
2.36.0	-nodocs	GCCcore/11.3.0
2.38.1	-nodocs	GCCcore/12.2.0
2.41.0	-nodocs	GCCcore/12.3.0
2.42.0		GCCcore/13.2.0

git-annex

git-annex allows managing large files with git, without storing the file contents in git. It can sync, backup, and archive your data, offline and online. Checksums and encryption keep your data safe and secure. Bring the power and distributed nature of git to bear on your large files with git-annex.

homepage: https://git-annex.branchable.com

version	toolchain
10.20230802	GCCcore/12.2.0, GCCcore/12.3.0

git-extras

Extra useful scripts for git

homepage: https://github.com/tj/git-extras

version	toolchain
5.1.0	foss/2016a

git-lfs

Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com

homepage: https://git-lfs.github.com

version	toolchain
1.1.1	system
2.7.1	system
2.11.0	system
3.2.0	system
3.4.0	system
3.4.1	system
3.5.1	system

GitPython

GitPython is a python library used to interact with Git repositories

homepage: https://github.com/gitpython-developers/GitPython

version	versionsuffix	toolchain
2.1.11	-Python-3.6.6	foss/2018b, intel/2018b
2.1.15		system
3.0.3	-Python-3.7.2	GCCcore/8.2.0
3.1.0	-Python-3.7.4	GCCcore/8.3.0
3.1.9	-Python-3.8.2	GCCcore/9.3.0
3.1.14		GCCcore/10.2.0
3.1.18		GCCcore/10.3.0
3.1.24		GCCcore/11.2.0
3.1.27		GCCcore/11.3.0
3.1.31		GCCcore/12.2.0
3.1.40		GCCcore/12.3.0
3.1.42		GCCcore/13.2.0

Givaro

C++ library for arithmetic and algebraic computations

homepage: https://github.com/linbox-team/givaro

version	toolchain
4.0.1	foss/2016a
4.2.0	GCCcore/11.3.0

Giza

Giza is an open, lightweight scientific plotting library built on top of cairo that provides uniform output to multiple devices.

homepage: https://danieljprice.github.io/giza/

version	toolchain
1.1.0	foss/2018b

GKeyll

Gkeyll v2.0 (pronounced as in the book “The Strange Case of Dr. Jekyll and Mr. Hyde”) is a computational plasma physics code mostly written in C/C++ and LuaJIT. Gkeyll contains solvers for gyrokinetic equations, Vlasov-Maxwell equations, and multi-fluid equations. Gkeyll contains ab-initio and novel implementations of a number of algorithms, and perhaps is unique in using a JIT compiled typeless dynamic language for as its main implementation language.

homepage: https://gkeyll.readthedocs.io

version	versionsuffix	toolchain
20220803	-Python-3.8.2	foss/2020a

GKlib-METIS

A library of various helper routines and frameworks used by many of the lab's software

homepage: https://github.com/KarypisLab/GKlib

version	toolchain
5.1.1	GCCcore/11.3.0

gkmSVM

Gapped-Kmer Support Vector Machine.

homepage: https://cran.r-project.org/web/packages/gkmSVM/index.html

version	versionsuffix	toolchain
0.82.0	-R-4.2.1	foss/2022a

GL2PS

GL2PS: an OpenGL to PostScript printing library

homepage: https://www.geuz.org/gl2ps/

version	versionsuffix	toolchain
1.3.9		foss/2016a, foss/2016b, intel/2016a, intel/2016b
1.3.9	-Mesa-11.2.1	foss/2016a, intel/2016a
1.4.0		GCCcore/8.3.0, foss/2017b, foss/2018a, foss/2018b, foss/2019a, intel/2017a, intel/2017b, intel/2018a
1.4.2		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/9.3.0

Glade

Glade is a RAD tool to enable quick & easy development of user interfaces for the GTK+ toolkit and the GNOME desktop environment.

homepage: https://glade.gnome.org/

version	versionsuffix	toolchain
3.8.5	-Python-2.7.11	intel/2016a
3.8.5	-Python-2.7.14	intel/2017b
3.8.6	-Python-2.7.14	intel/2018a
3.8.6	-Python-2.7.15	foss/2018b

glew

The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. GLEW provides efficient run-time mechanisms for determining which OpenGL extensions are supported on the target platform.

homepage: https://github.com/nigels-com/glew

version	versionsuffix	toolchain
2.1.0		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0, foss/2018b
2.2.0	-egl	GCCcore/10.2.0, GCCcore/11.2.0, GCCcore/11.3.0
2.2.0	-glx	GCCcore/10.2.0, GCCcore/11.2.0
2.2.0	-osmesa	GCCcore/10.2.0, GCCcore/11.2.0, GCCcore/11.3.0

GLFW

GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop

homepage: https://www.glfw.org

version	toolchain
3.2.1	intel/2018a
3.3.2	GCCcore/9.3.0
3.3.3	GCCcore/10.2.0
3.3.4	GCCcore/10.3.0, GCCcore/11.2.0
3.3.8	GCCcore/11.3.0
3.4	GCCcore/12.2.0

GLI

Graphics Language Interpreter

homepage: https://pgi-jcns.fz-juelich.de/portal/pages/gli.html

version	toolchain
4.5.31	GCCcore/10.2.0, GCCcore/12.2.0

GLib

GLib is one of the base libraries of the GTK+ project

homepage: https://www.gtk.org/

version	toolchain
2.42.1	GCC/4.9.2
2.44.0	GCC/4.9.2
2.47.5	foss/2016a, gimkl/2.11.5, intel/2016a
2.48.0	foss/2016a, intel/2016a
2.49.5	foss/2016b, intel/2016b
2.52.0	foss/2017a, intel/2017a
2.53.5	GCCcore/6.3.0, GCCcore/6.4.0
2.54.2	GCCcore/6.4.0
2.54.3	GCCcore/6.4.0, GCCcore/7.3.0
2.60.1	GCCcore/8.2.0
2.62.0	GCCcore/8.3.0
2.64.1	GCCcore/9.3.0
2.66.1	GCCcore/10.2.0
2.68.2	GCCcore/10.3.0
2.69.1	GCCcore/11.2.0
2.72.1	GCCcore/11.3.0
2.75.0	GCCcore/12.2.0
2.77.1	GCCcore/12.3.0
2.78.1	GCCcore/13.2.0

glib-networking

Network extensions for GLib

homepage: https://gitlab.gnome.org/GNOME/glib-networking

version	toolchain
2.68.1	GCCcore/10.3.0
2.72.1	GCCcore/11.2.0, GCCcore/11.3.0

glibc

The GNU C Library project provides the core libraries for the GNU system and GNU/Linux systems, as well as many other systems that use Linux as the kernel.

homepage: https://www.gnu.org/software/libc/

version	toolchain
2.17	GCCcore/6.4.0
2.26	GCCcore/6.4.0
2.30	GCCcore/8.3.0

GLibmm

C++ bindings for Glib

homepage: https://www.gtk.org/

version	toolchain
2.49.7	GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0
2.66.4	GCCcore/10.3.0

GLIMMER

Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.

homepage: http://ccb.jhu.edu/software/glimmer/index.shtml

version	toolchain
3.02b	foss/2016b, foss/2018b

GlimmerHMM

GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model. Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models.

homepage: https://ccb.jhu.edu/software/glimmerhmm

version	toolchain
3.0.4	foss/2016b, foss/2018b
3.0.4c	GCC/10.2.0, GCC/11.2.0, GCC/8.3.0

GLIMPSE

GLIMPSE2 is a set of tools for phasing and imputation for low-coverage sequencing datasets

homepage: https://github.com/odelaneau/GLIMPSE

version	toolchain
2.0.0	GCC/10.3.0, GCC/11.3.0, GCC/12.2.0

GLM

OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications.

homepage: https://github.com/g-truc/glm

version	toolchain
0.9.7.6	intel/2016a
0.9.8.3	GCCcore/5.4.0, GCCcore/7.3.0
0.9.9.0	GCCcore/6.4.0
0.9.9.8	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/8.3.0

GLM-AED

The General Lake Model (GLM) is a water balance and one-dimensional vertical stratification hydrodynamic model, which is dynamically coupled with the AED water quality modelling library. GLM-AED is suitable for simulating conditions in a wide range of natural and engineered lakes, including shallow (well-mixed) and deep (stratified) systems. The model has been successfully applied to systems from the scale of individual ponds and wetlands, to actively operated reservoirs, upto the scale of the Great Lakes.

homepage: https://github.com/AquaticEcoDynamics/glm-aed

version	toolchain
3.3.0a5	gompi/2021b

GlobalArrays

Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model

homepage: https://hpc.pnl.gov/globalarrays

version	versionsuffix	toolchain
5.7		intel/2018b
5.7	-peigs	intel/2019a
5.7.2		intel/2019b
5.7.2	-peigs	intel/2019b
5.8		intel/2020a, intel/2021a, iomkl/2021a
5.8.1		intel/2022a
5.8.2		intel/2022a, intel/2023a

Globus-CLI

A Command Line Wrapper over the Globus SDK for Python, which provides an interface to Globus services from the shell, and is suited to both interactive and simple scripting use cases.

homepage: https://docs.globus.org/cli/

version	toolchain
1.11.0	GCCcore/8.3.0
3.1.1	GCCcore/10.2.0
3.2.0	GCCcore/10.3.0
3.6.0	GCCcore/11.2.0

GlobusConnectPersonal

Globus Connect Personal turns your laptop or other personal computer into a Globus endpoint with a just a few clicks. With Globus Connect Personal you can share and transfer files to/from a local machine—campus server, desktop computer or laptop—even if it's behind a firewall and you don't have administrator privileges.

homepage: https://www.globus.org/globus-connect-personal

version	toolchain
2.3.6	system

glog

A C++ implementation of the Google logging module.

homepage: https://github.com/google/glog

version	toolchain
0.3.4	foss/2016a
0.3.5	GCCcore/6.4.0, intel/2017a, intel/2017b
0.4.0	GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
0.5.0	GCCcore/10.2.0
0.6.0	GCCcore/11.3.0

GLPK

The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.

homepage: https://www.gnu.org/software/glpk/

version	toolchain
4.58	foss/2016a, intel/2016a
4.60	GCCcore/5.4.0, intel/2016b
4.61	intel/2017a
4.65	GCCcore/10.2.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
5.0	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

glproto

X protocol and ancillary headers

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.4.17	foss/2016a, gimkl/2.11.5, intel/2016a

Glucose

Glucose is based on a new scoring scheme (well, not so new now, it was introduced in 2009) for the clause learning mechanism of so called Modern SAT solvers (it is based on our IJCAI'09 paper). It is designed to be parallel, since v4.0.

homepage: https://www.labri.fr/perso/lsimon/glucose/

version	toolchain
4.1	GCC/9.3.0

GMAP-GSNAP

GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program

homepage: http://research-pub.gene.com/gmap/

version	toolchain
2016-05-01	foss/2016a
2016-11-07	foss/2016b
2018-05-11	intel/2018a
2018-07-04	intel/2018a
2019-03-15	foss/2018b
2019-09-12	GCC/8.3.0
2020-12-17	GCC/9.3.0
2021-12-17	GCC/11.2.0
2023-02-17	GCC/11.3.0
2023-04-20	GCC/10.3.0, GCC/12.2.0

GMP

GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.

homepage: https://gmplib.org/

version	toolchain
4.3.2	system
5.1.3	GCC/4.8.2
6.0.0	GCC/4.9.2
6.0.0a	GCC/4.8.4, GCC/4.9.2, GNU/4.9.3-2.25
6.1.0	GCC/4.9.3-2.25, foss/2016a, gimkl/2.11.5, intel/2016.02-GCC-4.9, intel/2016a, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25
6.1.1	GCC/5.4.0-2.26, GCCcore/5.4.0, GCCcore/6.3.0, foss/2016.04, foss/2016a, foss/2016b, intel/2016b
6.1.2	GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, foss/2016b
6.2.0	GCCcore/10.2.0, GCCcore/9.3.0
6.2.1	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0
6.3.0	GCCcore/13.2.0

GMP-ECM

Yet another implementation of the Elliptic Curve Method.

homepage: https://gitlab.inria.fr/zimmerma/ecm

version	toolchain
7.0.5	GCCcore/11.3.0

gmpich

gcc and GFortran based compiler toolchain, including MPICH for MPI support.

homepage: <(none)>

version	toolchain
2016a	system
2017.08	system

gmpolf

gcc and GFortran based compiler toolchain, MPICH for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.

homepage: <(none)>

version	toolchain
2016a	system
2017.10	system

gmpy2

GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x

homepage: https://github.com/aleaxit/gmpy

version	versionsuffix	toolchain
2.0.8	-Python-2.7.13	intel/2017a
2.0.8	-Python-2.7.14	foss/2017b, intel/2017b
2.0.8	-Python-3.6.3	foss/2017b, intel/2017b
2.1.0b1	-Python-2.7.14	foss/2017b, intel/2017b
2.1.0b1	-Python-3.6.3	foss/2017b, intel/2017b
2.1.0b4		GCC/8.3.0
2.1.0b5		GCC/10.2.0, GCC/10.3.0, GCC/9.3.0, iccifort/2020.4.304
2.1.2		GCC/11.2.0, GCC/11.3.0, intel-compilers/2021.4.0, intel-compilers/2022.1.0
2.1.5		GCC/12.2.0, GCC/12.3.0, GCC/13.2.0

gmsh

Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor.

homepage: https://gmsh.info/

version	versionsuffix	toolchain
3.0.6	-Python-2.7.14	foss/2017b
3.0.6	-Python-3.6.6	foss/2018b
4.2.2	-Python-3.6.6	foss/2018b
4.5.6	-Python-2.7.16	intel/2019b
4.5.6	-Python-3.7.4	foss/2019b
4.7.1	-Python-3.8.2	foss/2020a, intel/2020a
4.8.4	-Python-3.6.4	foss/2018a
4.9.0		foss/2021a
4.11.1		foss/2022a

GMT

GMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another 40 more specialized and discipline-specific tools.

homepage: https://www.generic-mapping-tools.org/

version	toolchain
4.5.17	foss/2018a
5.4.1	intel/2017a
5.4.3	foss/2018a, intel/2017b
5.4.5	foss/2019a
6.2.0	foss/2019b, foss/2020b

gmvapich2

GNU Compiler Collection (GCC) based compiler toolchain, including MVAPICH2 for MPI support.

homepage: <(none)>

version	toolchain
1.7.20	system
2016a	system

gmvolf

GNU Compiler Collection (GCC) based compiler toolchain, including MVAPICH2 for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.

homepage: <(none)>

version	toolchain
1.7.20	system
2016a	system

GNU

Compiler-only toolchain with GCC and binutils.

homepage: http://www.gnu.org/software/

version	toolchain
4.9.2-2.25	system
4.9.3-2.25	system
5.1.0-2.25	system

gnuplot

Portable interactive, function plotting utility

homepage: http://gnuplot.sourceforge.net

version	toolchain
5.0.3	foss/2016a, intel/2016a
5.0.5	foss/2016b, intel/2016b
5.0.6	intel/2017a
5.2.2	foss/2017b, foss/2018a, intel/2017b, intel/2018a
5.2.5	foss/2018b
5.2.6	GCCcore/8.2.0, foss/2018b, fosscuda/2018b
5.2.8	GCCcore/8.3.0, GCCcore/9.3.0
5.4.1	GCCcore/10.2.0
5.4.2	GCCcore/10.3.0, GCCcore/11.2.0
5.4.4	GCCcore/11.3.0
5.4.6	GCCcore/12.2.0
5.4.8	GCCcore/12.3.0

GnuTLS

GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them. It provides a simple C language application programming interface (API) to access the secure communications protocols as well as APIs to parse and write X.509, PKCS #12, OpenPGP and other required structures. It is aimed to be portable and efficient with focus on security and interoperability.

homepage: https://www.gnutls.org

version	toolchain
3.3.21	intel/2016a
3.4.7	GNU/4.9.3-2.25
3.4.11	foss/2016a
3.7.2	GCCcore/10.3.0
3.7.3	GCCcore/11.2.0
3.7.8	GCCcore/11.3.0

Go

Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.

homepage: http://www.golang.org

version	toolchain
1.2.1	GCC/4.8.2
1.4.2	GCC/4.8.4
1.5	GCC/4.8.4
1.8.1	system
1.11.5	system
1.12	system
1.12.1	GCCcore/7.3.0
1.13.1	system
1.14	system
1.14.1	system
1.16.3	system
1.16.5	system
1.16.6	system
1.17.3	system
1.17.6	system
1.18.1	system
1.18.3	system
1.20.4	system
1.21.1	system
1.21.2	system
1.21.6	system
1.22.1	system

goalign

Goalign is a set of command line tools to manipulate multiple alignments.

homepage: https://github.com/evolbioinfo/goalign

version	toolchain
0.3.2	system

GOATOOLS

A Python library for Gene Ontology analyses

homepage: https://github.com/tanghaibao/goatools

version	toolchain
1.1.6	foss/2020b
1.3.1	foss/2021b, foss/2022a

gobff

GCC and GFortran based compiler toolchain with OpenMPI, BLIS, libFLAME, ScaLAPACK and FFTW.

homepage: <(none)>

version	versionsuffix	toolchain
2020.06	-amd	system
2020.11		system
2020b		system
2021a		system

GObject-Introspection

GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library.

homepage: https://gi.readthedocs.io/en/latest/

version	versionsuffix	toolchain
1.47.1		foss/2016a, intel/2016a
1.48.0		foss/2016a, intel/2016a
1.49.1		foss/2016b, intel/2016b
1.52.0		intel/2017a
1.53.5	-Python-2.7.13	intel/2017a
1.53.5	-Python-2.7.14	foss/2017b, intel/2017b
1.53.5	-Python-3.6.1	intel/2017a
1.54.1	-Python-2.7.14	foss/2018a, intel/2018a
1.54.1	-Python-2.7.15	foss/2018b, fosscuda/2018b
1.54.1	-Python-3.6.6	fosscuda/2018b
1.58.3	-Python-2.7.16	GCCcore/8.3.0
1.60.1	-Python-3.7.2	GCCcore/8.2.0
1.63.1	-Python-3.7.4	GCCcore/8.3.0
1.64.0	-Python-3.8.2	GCCcore/9.3.0
1.66.1		GCCcore/10.2.0
1.68.0		GCCcore/10.3.0, GCCcore/11.2.0
1.72.0		GCCcore/11.3.0
1.74.0		GCCcore/12.2.0
1.76.1		GCCcore/12.3.0
1.78.1		GCCcore/13.2.0

goblf

GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, BLIS (BLAS support), LAPACK, FFTW and ScaLAPACK.

homepage: <(none)>

version	toolchain
2018b	system
2020b	system

GOBNILP

GOBNILP (Globally Optimal Bayesian Network learning using Integer Linear Programming) is a C program which learns Bayesian networks from complete discrete data or from local scores.

homepage: https://www.cs.york.ac.uk/aig/sw/gobnilp/

version	toolchain
1.6.3	GCC/11.3.0

Godon

Godon is codon models software written in Go.

homepage: https://bitbucket.org/Davydov/godon/

version	versionsuffix	toolchain
20210913	-x86_64	system

gofasta

Some functions for dealing with alignments, developed to handle SARS-CoV-2 data as part of the COG-UK project.

homepage: https://github.com/cov-ert/gofasta

version	toolchain
0.0.5	system

golf

GNU Compiler Collection (GCC) based compiler toolchain, including OpenBLAS (BLAS and LAPACK support) and FFTW.

homepage: <(none)>

version	toolchain
2018a	system
2020a	system

gomkl

GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL

homepage: <(none)>

version	toolchain
2018b	system
2019a	system
2020a	system
2020b	system
2021a	system
2021b	system
2022a	system
2023a	system

gompi

GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.

homepage: <(none)>

version	versionsuffix	toolchain
2016.04		system
2016.06		system
2016.07		system
2016.09		system
2016a		system
2016b		system
2017a		system
2017b		system
2018.08		system
2018a		system
2018b		system
2019a		system
2019b		system
2020a		system
2020b		system
2021a		system
2021b		system
2022.05		system
2022.10		system
2022a		system
2022b		system
2023.09		system
2023a		system
2023b		system
system	-2.29	system

gompic

GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled.

homepage: <(none)>

version	toolchain
2017b	system
2018a	system
2018b	system
2019a	system
2019b	system
2020a	system
2020b	system

google-java-format

Reformats Java source code to comply with Google Java Style.

homepage: https://github.com/google/google-java-format

version	versionsuffix	toolchain
1.7	-Java-1.8	system

googletest

Google's framework for writing C++ tests on a variety of platforms

homepage: https://github.com/google/googletest

version	toolchain
1.8.0	GCCcore/6.3.0, GCCcore/6.4.0, foss/2016b, intel/2016b
1.8.1	GCCcore/8.2.0
1.10.0	GCCcore/10.2.0, GCCcore/8.3.0, GCCcore/9.3.0
1.11.0	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0
1.12.1	GCCcore/12.2.0
1.13.0	GCCcore/12.3.0
1.14.0	GCCcore/13.2.0

gotree

GoTree is a set of command line tools to manipulate phylogenetic trees.

homepage: https://github.com/evolbioinfo/gotree

version	toolchain
0.4.0	system

GP2C

The gp2c compiler is a package for translating GP routines into the C programming language, so that they can be compiled and used with the PARI system or the GP calculator.

homepage: http://pari.math.u-bordeaux.fr/pub/pari/manuals/gp2c/gp2c.html

version	toolchain
0.0.9pl5	foss/2016a

GPAW

GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or atom-centered basis-functions.

homepage: https://wiki.fysik.dtu.dk/gpaw/

version	versionsuffix	toolchain
1.4.0	-Python-3.6.6	foss/2018b, intel/2018b
19.8.1	-ASE-3.18.0-Python-3.6.6	foss/2018b, intel/2018b
19.8.1	-Python-3.7.2	foss/2019a, intel/2019a
20.1.0	-Python-3.7.4	foss/2019b, intel/2019b
20.10.0		foss/2020b, intel/2020b
20.10.0	-ASE-3.20.1-Python-3.7.4	foss/2019b, intel/2019b
21.1.0	-ASE-3.21.1	foss/2020b, intel/2020b
21.6.0		foss/2021a
21.6.0	-ASE-3.22.0	foss/2020b, intel/2020b
22.8.0		foss/2021b, foss/2022a, intel/2021b, intel/2022a
23.9.1		foss/2022a, foss/2023a, intel/2022a
24.1.0		foss/2022a, foss/2023a, intel/2022a, intel/2023a

GPAW-setups

PAW setups for the GPAW Density Functional Theory package. Users can install setups manually using 'gpaw install-data' or use setups from this package. The versions of GPAW and GPAW-setups can be intermixed. Compared to version 0.9.20000, version 24.1.0 contains an new improved Cr setup with 14 electrons, which can be manually selected. Otherwise no changes are made, so no results will change.

homepage: https://wiki.fysik.dtu.dk/gpaw/

version	toolchain
0.8.7929	system
0.9.9672	system
0.9.11271	system
0.9.20000	system
24.1.0	system

gperf

GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.

homepage: https://www.gnu.org/software/gperf/

version	toolchain
3.0.4	GCCcore/4.9.3, GCCcore/5.4.0, foss/2016a, gimkl/2.11.5, intel/2016a, intel/2016b, intel/2017a
3.1	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0

gperftools

gperftools is a collection of a high-performance multi-threaded malloc() implementation, plus some pretty nifty performance analysis tools. Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler.

homepage: https://github.com/gperftools/gperftools

version	toolchain
2.5	foss/2016a, intel/2016b
2.6.3	GCCcore/6.4.0, GCCcore/7.3.0
2.7.90	GCCcore/8.3.0
2.8	GCCcore/9.3.0
2.9.1	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0
2.10	GCCcore/11.3.0
2.12	GCCcore/12.3.0
2.13	GCCcore/13.2.0
2.14	GCCcore/12.2.0

gpustat

A simple command-line utility for querying and monitoring GPU status

homepage: https://github.com/wookayin/gpustat

version	versionsuffix	toolchain
0.5.0	-Python-2.7.15	fosscuda/2018b
0.6.0		GCCcore/10.3.0, gcccuda/2020b
0.6.0	-Python-3.7.4	fosscuda/2019b
1.0.0b1		GCCcore/11.2.0
1.1		GCCcore/11.3.0

GPy

GPy is a Gaussian Process (GP) framework written in Python

homepage: https://sheffieldml.github.io/GPy

version	toolchain
1.10.0	foss/2021b

GPyOpt

GPyOpt is a Python open-source library for Bayesian Optimization

homepage: https://sheffieldml.github.io/GPyOpt

version	toolchain
1.2.6	intel/2020b

GPyTorch

GPyTorch is a Gaussian process library implemented using PyTorch.

homepage: https://gpytorch.ai

version	versionsuffix	toolchain
1.3.0		foss/2020b
1.9.1	-CUDA-11.3.1	foss/2021a
1.10	-CUDA-11.7.0	foss/2022a

Grace

Grace is a WYSIWYG tool to make two-dimensional plots of numerical data.

homepage: https://plasma-gate.weizmann.ac.il/Grace/

version	versionsuffix	toolchain
5.1.25		foss/2016a, foss/2021a, foss/2021b, intel/2016a
5.1.25	-5build1	foss/2017b, foss/2018a, foss/2019a, foss/2019b, intel/2017b, intel/2019a, intel/2019b

Gradle

Complete Gradle install. From mobile apps to microservices, from small startups to big enterprises, Gradle helps teams build, automate and deliver better software, faster.

homepage: https://gradle.org

version	versionsuffix	toolchain
4.5.1		system
6.1.1		system
6.9.1		system
8.6	-Java-17	system

gradunwarp

Gradient Unwarping. This is the Human Connectome Project fork of the no longer maintained original.

homepage: https://github.com/Washington-University/gradunwarp

version	versionsuffix	toolchain
1.1.0	-HCP-Python-2.7.15	foss/2019a
1.2.0	-HCP-Python-2.7.15	foss/2019a
1.2.0	-HCP-Python-3.7.2	foss/2019a

graph-tool

Graph-tool is an efficient Python module for manipulation and statistical analysis of graphs (a.k.a. networks). Contrary to most other python modules with similar functionality, the core data structures and algorithms are implemented in C++, making extensive use of template metaprogramming, based heavily on the Boost Graph Library. This confers it a level of performance that is comparable (both in memory usage and computation time) to that of a pure C/C++ library.

homepage: https://graph-tool.skewed.de/

version	versionsuffix	toolchain
2.26	-Python-3.6.3	foss/2017b
2.27	-Python-3.6.6	foss/2018b
2.55		foss/2022a

GraphDB

GraphDB is an enterprise ready Semantic Graph Database, compliant with W3C Standards. Semantic graph databases (also called RDF triplestores) provide the core infrastructure for solutions where modelling agility, data integration, relationship exploration and cross-enterprise data publishing and consumption are important.

homepage: https://graphdb.ontotext.com/

version	toolchain
10.1.5	system

Graphene

Graphene is a a thin layer of types for graphic libraries

homepage: https://ebassi.github.io/graphene/

version	toolchain
1.6.0	intel/2017a
1.10.8	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

GraphicsMagick

GraphicsMagick is the swiss army knife of image processing.

homepage: https://www.graphicsmagick.org/

version	toolchain
1.3.23	foss/2016a, intel/2016a
1.3.25	intel/2016b, intel/2017a
1.3.28	foss/2018a
1.3.31	foss/2018b
1.3.34	foss/2019a, foss/2019b
1.3.36	GCCcore/11.2.0, foss/2020b

graphite2

Graphite is a "smart font" system developed specifically to handle the complexities of lesser-known languages of the world.

homepage: https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home

version	toolchain
1.3.14	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0, GCCcore/8.3.0

GraPhlAn

GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. It focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.

homepage: https://segatalab.github.io/tools/graphlan

version	versionsuffix	toolchain
1.1.3	-Python-2.7.16	foss/2019b

GraphMap

A highly sensitive and accurate mapper for long, error-prone reads

homepage: https://github.com/isovic/graphmap

version	toolchain
0.5.2	foss/2019b

GraphMap2

A highly sensitive and accurate mapper for long, error-prone reads

homepage: https://github.com/lbcb-sci/graphmap2

version	toolchain
0.6.4	foss/2019b

Graphviz

Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains.

homepage: https://www.graphviz.org/

version	versionsuffix	toolchain
2.38.0		foss/2016b, intel/2016b
2.40.1		foss/2018b, intel/2018a
2.40.1	-Python-2.7.15	foss/2018b
2.42.2		foss/2019b
2.42.2	-Java-11	GCCcore/8.3.0
2.42.2	-Python-3.7.4	foss/2019b
2.44.1	-Java-11	GCCcore/9.3.0
2.44.1	-Java-11-Python-3.8.2	GCCcore/9.3.0
2.47.0	-Java-11	GCCcore/10.2.0
2.47.2		GCCcore/10.3.0
2.50.0		GCCcore/11.2.0
5.0.0		GCCcore/11.3.0
8.1.0		GCCcore/12.2.0, GCCcore/12.3.0

graphviz-python

Simple Python interface for Graphviz

homepage: https://pypi.python.org/pypi/graphviz

version	versionsuffix	toolchain
0.5.1	-Python-2.7.12	foss/2016b, intel/2016b
0.5.1	-Python-3.5.2	intel/2016b
0.8.2	-Python-3.6.4	intel/2018a
0.20.1		GCCcore/11.3.0, GCCcore/12.3.0

GRASP

The General Relativistic Atomic Structure Package (GRASP) is a set of Fortran 90 programs for performing fully-relativistic electron structure calculations of atoms.

homepage: https://compas.github.io/grasp/

version	toolchain
2018	foss/2019b

GRASP-suite

GRASP-suite is a collection of tools and tutorials to perform and analyse ancestral sequence reconstruction.

homepage: https://github.com/bodenlab/GRASP-suite/

version	versionsuffix	toolchain
2023-05-09	-Java-17	system

GRASS

The Geographic Resources Analysis Support System - used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization

homepage: https://grass.osgeo.org

version	versionsuffix	toolchain
7.6.0	-Python-2.7.15	foss/2018b
7.8.3	-Python-3.7.4	fosscuda/2019b
8.2.0		foss/2021b

Greenlet

The greenlet package is a spin-off of Stackless, a version of CPython that supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single or a few OS-level threads) and are synchronized with data exchanges on "channels". A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs.

homepage: https://github.com/python-greenlet/greenlet

version	versionsuffix	toolchain
0.4.9	-Python-2.7.11	intel/2016a
0.4.9	-Python-3.5.1	intel/2016a
0.4.11	-Python-2.7.12	intel/2016b
0.4.12	-Python-2.7.14	intel/2017b
2.0.2		GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0
3.0.2		GCCcore/12.3.0
3.0.3		GCCcore/13.2.0

Grep

The grep command searches one or more input files for lines containing a match to a specified pattern. By default, grep prints the matching lines.

homepage: http://www.gnu.org/software/grep/

version	toolchain
2.21	GCC/4.9.2

gretl

A cross-platform software package for econometric analysis

homepage: http://gretl.sourceforge.net

version	toolchain
2020a	foss/2019a

grib_api

The ECMWF GRIB API is an application program interface accessible from C, FORTRAN and Python programs developed for encoding and decoding WMO FM-92 GRIB edition 1 and edition 2 messages. A useful set of command line tools is also provided to give quick access to GRIB messages.

homepage: https://software.ecmwf.int/wiki/display/GRIB/Home

version	toolchain
1.16.0	intel/2016a
1.21.0	foss/2017a
1.24.0	foss/2017b, intel/2017a, intel/2017b

grid

Grid is a free and open-source Python library for numerical integration, interpolation and differentiation of interest for the quantum chemistry community.

homepage: https://grid.qcdevs.org/

version	toolchain
20220610	intel/2022a

GRIDSS

GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants based on alignment-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair evidence.

homepage: https://github.com/PapenfussLab/gridss/wiki/GRIDSS-Documentation

version	versionsuffix	toolchain
2.13.2	-Java-11	foss/2021b

GRIT

GRIT - A tool for the integrative analysis of RNA-seq type assays

homepage: https://github.com/nboley/grit

version	versionsuffix	toolchain
2.0.5	-Python-2.7.12	intel/2016b

GRNBoost

XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, flexible and portable.

homepage: https://github.com/dmlc/xgboost

version	versionsuffix	toolchain
20171009	-Java-1.8.0_152	intel/2017b

groff

Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output.

homepage: https://www.gnu.org/software/groff

version	toolchain
1.22.4	FCC/4.5.0, GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.1.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/8.3.0, GCCcore/9.3.0
1.23.0	GCCcore/13.2.0

GroIMP

GroIMP (Growth Grammar-related Interactive Modelling Platform) is a 3D-modelling platform.

homepage: http://www.grogra.de/software/groimp

version	toolchain
1.5	system

GROMACS

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

homepage: http://www.gromacs.org

version	versionsuffix	toolchain
5.1.2	-hybrid	foss/2016a, intel/2016a
5.1.2	-hybrid-dp	intel/2016a
5.1.2	-mt	foss/2016a
5.1.4	-hybrid	foss/2016b
5.1.4	-mt	foss/2016b
2016	-hybrid	foss/2016b
2016	-mt	foss/2016b
2016.1	-PLUMED	foss/2017a
2016.2		foss/2017a
2016.3		foss/2017a, intel/2017a
2016.3	-GPU-enabled	foss/2016b
2016.4		foss/2017b, fosscuda/2017b, giolf/2017b, intel/2017a, intel/2017b, intelcuda/2017b
2016.5		intel/2018a
2018		foss/2018a
2018.1	-PLUMED	foss/2018b
2018.2		foss/2017b, foss/2018b, fosscuda/2017b, fosscuda/2018b, intel/2017b, intelcuda/2017b
2018.3		foss/2018b, fosscuda/2018b
2018.4	-PLUMED-2.5.0	foss/2018b, fosscuda/2018b
2019		foss/2018b, fosscuda/2018b
2019.2		fosscuda/2019a
2019.3		foss/2019a, foss/2019b, fosscuda/2019a, fosscuda/2019b
2019.4		foss/2019b, fosscuda/2019b
2019.4	-PLUMED-2.5.4	foss/2019b, fosscuda/2019b
2019.6		fosscuda/2019b
2020		foss/2019b, fosscuda/2019b
2020.1	-Python-3.8.2	foss/2020a
2020.3		fosscuda/2019b
2020.4	-Python-3.8.2	foss/2020a
2020.5	-Python-3.8.2	fosscuda/2020a
2021		foss/2020b, fosscuda/2020b
2021.2		fosscuda/2020b
2021.3		foss/2021a
2021.3	-CUDA-11.3.1	foss/2021a
2021.3	-CUDA-11.3.1-PLUMED-2.7.2	foss/2021a
2021.3	-PLUMED-2.7.2	foss/2021a
2021.5		foss/2021b
2021.5	-CUDA-11.4.1	foss/2021b
2021.5	-CUDA-11.4.1-PLUMED-2.8.0	foss/2021b
2021.5	-PLUMED-2.8.0	foss/2021b
2023.1		foss/2022a
2023.1	-CUDA-11.7.0	foss/2022a
2023.3		foss/2022a, foss/2023a
2023.3	-CUDA-11.7.0	foss/2022a
2023.3	-CUDA-12.1.1-PLUMED-2.9.0	foss/2023a
2024.1		foss/2023b

GromacsWrapper

GromacsWrapper is a python package that wraps system calls to Gromacs tools into thin classes. This allows for fairly seamless integration of the gromacs tools into python scripts.

homepage: https://gromacswrapper.readthedocs.org

version	versionsuffix	toolchain
0.8.0	-Python-3.7.2	fosscuda/2019a

Groovy

Groovy is a powerful, optionally typed and dynamic language, with static-typing and static compilation capabilities, for the Java platform aimed at improving developer productivity thanks to a concise, familiar and easy to learn syntax.

homepage: https://groovy-lang.org

version	versionsuffix	toolchain
2.5.9	-Java-11	system
4.0.3	-Java-11	system

gRPC

gRPC is a modern, open source, high-performance remote procedure call (RPC) framework that can run anywhere. gRPC enables client and server applications to communicate transparently, and simplifies the building of connected systems.

homepage: https://grpc.io/

version	toolchain
1.44.0	GCCcore/11.2.0
1.57.0	GCCcore/12.3.0
1.62.1	GCCcore/13.2.0

GSD

The GSD file format is the native file format for HOOMD-blue. GSD files store trajectories of the HOOMD-blue system state in a binary file with efficient random access to frames. GSD allows all particle and topology properties to vary from one frame to the next. Use the GSD Python API to specify the initial condition for a HOOMD-blue simulation or analyze trajectory output with a script. Read a GSD trajectory with a visualization tool to explore the behavior of the simulation.

homepage: https://gsd.readthedocs.io

version	toolchain
3.2.0	foss/2022a

GSEA

Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes).

homepage: https://www.gsea-msigdb.org/gsea/index.jsp

version	toolchain
4.0.3	system

gsettings-desktop-schemas

gsettings-desktop-schemas contains a collection of GSettings schemas for settings shared by various components of a desktop.

homepage: https://gitlab.gnome.org/GNOME/gsettings-desktop-schemas

version	toolchain
3.34.0	GCCcore/8.2.0

GSL

The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.

homepage: https://www.gnu.org/software/gsl/

version	toolchain
1.16	foss/2016a, intel/2016a
2.1	GCC/5.4.0-2.26, foss/2016a, foss/2016b, iccifort/2016.3.210-GCC-5.4.0-2.26, intel/2016a, intel/2016b
2.2.1	intel/2016a, intel/2016b
2.3	foss/2016b, foss/2017a, intel/2016b, intel/2017a
2.4	GCCcore/6.4.0
2.5	GCC/7.3.0-2.30, GCC/8.2.0-2.31.1, iccifort/2018.3.222-GCC-7.3.0-2.30, iccifort/2019.1.144-GCC-8.2.0-2.31.1
2.6	GCC/10.2.0, GCC/8.3.0, GCC/9.3.0, iccifort/2019.5.281, iccifort/2020.1.217, iccifort/2020.4.304
2.7	GCC/10.3.0, GCC/11.2.0, GCC/11.3.0, GCC/12.2.0, GCC/12.3.0, GCC/13.2.0, intel-compilers/2021.2.0, intel-compilers/2021.4.0, intel-compilers/2022.1.0

gSOAP

The gSOAP toolkit is a C and C++ software development toolkit for SOAP and REST XML Web services and generic C/C++ XML data bindings. The toolkit analyzes WSDLs and XML schemas (separately or as a combined set) and maps the XML schema types and the SOAP/REST XML messaging protocols to easy-to-use and efficient C and C++ code. It also supports exposing (legacy) C and C++ applications as XML Web services by auto-generating XML serialization code and WSDL specifications. Or you can simply use it to automatically convert XML to/from C and C++ data. The toolkit supports options to generate pure ANSI C or C++ with or without STL.

homepage: http://www.cs.fsu.edu/~engelen/soap.html

version	toolchain
2.8.48	GCCcore/6.3.0
2.8.100	GCCcore/8.3.0

gspell

gspell provides a flexible API to add spell-checking to a GTK application.

homepage: https://gitlab.gnome.org/GNOME/gspell

version	toolchain
1.12.2	GCCcore/12.3.0

gsport

GSPORT command-line tool for accessing GenomeScan Customer Portal

homepage: https://github.com/genomescan/gsport

version	versionsuffix	toolchain
1.4.2	-Python-3.7.4	GCCcore/8.3.0

GST-plugins-bad

GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.

homepage: https://gstreamer.freedesktop.org/

version	toolchain
1.20.2	GCC/11.3.0
1.22.5	GCC/12.2.0, GCC/12.3.0

GST-plugins-base

GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.

homepage: https://gstreamer.freedesktop.org/

version	toolchain
0.10.36	foss/2016a, foss/2017b, foss/2018b, intel/2016a, intel/2016b, intel/2017a, intel/2017b
1.6.4	foss/2016a
1.8.3	foss/2016a
1.16.0	GCC/8.2.0-2.31.1
1.16.2	GCC/8.3.0
1.18.4	GCC/10.2.0, GCC/10.3.0
1.18.5	GCC/11.2.0
1.20.2	GCC/11.3.0
1.22.1	GCC/12.2.0
1.22.5	GCC/12.3.0

GStreamer

GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.

homepage: https://gstreamer.freedesktop.org/

version	toolchain
0.10.36	foss/2016a, foss/2017b, foss/2018b, intel/2016a, intel/2016b, intel/2017a, intel/2017b
1.6.4	foss/2016a
1.8.3	foss/2016a
1.15.1	fosscuda/2018b
1.16.0	GCC/8.2.0-2.31.1
1.16.2	GCC/8.3.0
1.18.4	GCC/10.2.0, GCC/10.3.0
1.18.5	GCC/11.2.0
1.20.2	GCC/11.3.0
1.22.1	GCC/12.2.0
1.22.5	GCC/12.3.0

gsutil

gsutil is a Python application that lets you access Cloud Storage from the command line.

homepage: https://cloud.google.com/storage/docs/gsutil

version	toolchain
5.10	GCCcore/11.2.0

gsw

This Python implementation of the Thermodynamic Equation of Seawater 2010 (TEOS-10) is based primarily on numpy ufunc wrappers of the GSW-C implementation. This library replaces the original python-gsw pure-python implementation.. The primary reasons for this change are that by building on the C implementation we reduce code duplication and we gain an immediate update to the 75-term equation. Additional benefits include a major increase in speed, a reduction in memory usage, and the inclusion of more functions. The penalty is that a C (or MSVC C++ for Windows) compiler is required to build the package from source.

homepage: https://github.com/TEOS-10/GSW-python

version	toolchain
3.6.16	foss/2022a

GTDB-Tk

A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

homepage: https://github.com/Ecogenomics/GTDBTk

version	versionsuffix	toolchain
0.2.2	-Python-2.7.15	intel/2018b
0.3.2	-Python-2.7.15	foss/2019a, intel/2019a
1.0.2	-Python-3.7.4	intel/2019b
1.3.0	-Python-3.8.2	intel/2020a
1.5.0		intel/2020b
1.7.0		foss/2020b, foss/2021a, intel/2020b
2.0.0		foss/2021a, intel/2021b
2.1.1		foss/2021b
2.3.2		foss/2022a, foss/2023a

GTK+

The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.

homepage: https://developer.gnome.org/gtk+/stable/

version	toolchain
2.24.28	intel/2016a
2.24.30	foss/2016a, intel/2016a
2.24.31	foss/2016b, intel/2016b, intel/2017a
2.24.32	foss/2017b, foss/2018a, foss/2018b, intel/2017b, intel/2018a
2.24.33	GCCcore/10.3.0
3.22.30	fosscuda/2018b
3.24.8	GCCcore/8.2.0
3.24.13	GCCcore/8.3.0
3.24.17	GCCcore/9.3.0
3.24.23	GCCcore/10.2.0

GTK2

The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.

homepage: https://www.gtk.org

version	toolchain
2.24.33	GCCcore/10.3.0, GCCcore/11.3.0

GTK3

GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction.

homepage: https://developer.gnome.org/gtk3/stable/

version	toolchain
3.24.29	GCCcore/10.3.0
3.24.31	GCCcore/11.2.0
3.24.33	GCCcore/11.3.0
3.24.35	GCCcore/12.2.0
3.24.37	GCCcore/12.3.0
3.24.39	GCCcore/13.2.0

GTK4

GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction.

homepage: https://docs.gtk.org/gtk4/

version	toolchain
4.7.0	GCC/11.3.0
4.11.3	GCC/12.2.0
4.13.1	GCC/12.3.0

GtkSourceView

GtkSourceView is a GNOME library that extends GtkTextView, the standard GTK+ widget for multiline text editing. GtkSourceView adds support for syntax highlighting, undo/redo, file loading and saving, search and replace, a completion system, printing, displaying line numbers, and other features typical of a source code editor.

homepage: https://wiki.gnome.org/Projects/GtkSourceView

version	toolchain
3.24.11	GCCcore/10.2.0, GCCcore/8.2.0
4.4.0	GCCcore/8.2.0

GTOOL

GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE.

homepage: http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html

version	toolchain
0.7.5	system

GTS

GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles.

homepage: http://gts.sourceforge.net/

version	toolchain
0.7.6	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/8.3.0, GCCcore/9.3.0, foss/2016a, foss/2016b, foss/2018b, foss/2019b, foss/2020a, intel/2016a, intel/2016b, intel/2018a
20121130	foss/2017b

gubbins

Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences.

homepage: https://sanger-pathogens.github.io/gubbins

version	toolchain
2.4.0	system

guenomu

guenomu is a software written in C that estimates the species tree for a given set of gene families.

homepage: https://bitbucket.org/leomrtns/guenomu

version	versionsuffix	toolchain
2019.07.05	-mpi	iimpi/2019a

GUIDANCE

GUIDANCE is a software package for aligning biological sequences (DNA or amino acids) using either MAFFT, PRANK, or CLUSTALW, and calculating confidence scores for each column, sequence and residue in the alignment.

homepage: https://taux.evolseq.net/guidance/

version	toolchain
2.02	GCC/12.3.0

Guile

Guile is a programming language, designed to help programmers create flexible applications that can be extended by users or other programmers with plug-ins, modules, or scripts.

homepage: https://www.gnu.org/software/guile/

version	toolchain
1.8.8	GCCcore/5.4.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0, GNU/4.9.3-2.25, foss/2016a, foss/2016b, foss/2017a, intel/2016a, intel/2016b
2.0.11	GCC/4.9.3-2.25, foss/2016a
2.2.2	GCCcore/6.4.0
2.2.4	GCCcore/7.3.0, GCCcore/9.3.0
2.2.7	GCCcore/10.3.0
3.0.7	GCCcore/11.2.0
3.0.8	GCCcore/11.3.0
3.0.9	GCCcore/10.2.0, GCCcore/12.3.0

GULP

GULP is a program for performing a variety of types of simulation on materials using boundary conditions of 0-D (molecules and clusters), 1-D (polymers), 2-D (surfaces, slabs and grain boundaries), or 3-D (periodic solids)Band Unfolding code for Plane-wave based calculations

homepage: https://gulp.curtin.edu.au/gulp/

version	toolchain
5.1	intel/2019a
6.1	foss/2021b

Gurobi

The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms.

homepage: https://www.gurobi.com

version	versionsuffix	toolchain
6.5.1		system
6.5.2		system
7.0.1		system
7.5.2		system
7.5.2	-Python-3.6.4	intel/2018a
8.1.1		system
9.0.0		system
9.0.0	-Python-3.6.6	foss/2018b, intel/2018b
9.0.0	-Python-3.7.4	GCCcore/8.3.0
9.0.1		system
9.0.1	-Python-3.8.2	GCCcore/9.3.0
9.0.3		GCCcore/10.2.0, system
9.1.0		system
9.1.1		GCCcore/10.2.0
9.1.2		GCCcore/10.2.0, GCCcore/10.3.0, system
9.5.0		GCCcore/10.3.0, GCCcore/11.2.0
9.5.2		GCCcore/11.3.0
10.0.1		GCCcore/11.3.0, GCCcore/12.2.0
11.0.0		GCCcore/12.3.0

GUSHR

Assembly-free construction of UTRs from short read RNA-Seq data on the basis of coding sequence annotation.

homepage: https://github.com/Gaius-Augustus/GUSHR

version	toolchain
2020-09-28	foss/2021b

gzip

gzip (GNU zip) is a popular data compression program as a replacement for compress

homepage: http://www.gnu.org/software/gzip/

version	toolchain
1.8	GCCcore/5.4.0, GCCcore/6.3.0, GCCcore/6.4.0
1.9	GCCcore/7.3.0
1.10	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
1.12	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0
1.13	GCCcore/13.2.0

H

h4toh5 - H5hut - h5netcdf - h5py - Hadoop - HAL - hampel - hanythingondemand - HAPGEN2 - HarfBuzz - Harminv - harmony - hatchling - HBase - HD-BET - HDBSCAN - HDDM - HDF - HDF-EOS - HDF-EOS2 - HDF-EOS5 - HDF5 - hdf5storage - HDFView - hdWGCNA - HEALPix - Health-GPS - heaptrack - hector - HeFFTe - Hello - help2man - HepMC - HepMC3 - HF-Datasets - HH-suite - HiC-Pro - hic-straw - HiCExplorer - HiCMatrix - hierfstat - hifiasm - HighFive - Highway - HIP - hipify-clang - HIPS - hipSYCL - hiredis - HISAT2 - histolab - hivtrace - hl7apy - HLAminer - HMMER - HMMER2 - hmmlearn - HOME - HOOMD-blue - Horovod - horton - how_are_we_stranded_here - HPCC - HPCG - HPCX - HPDBSCAN - HPL - htop - HTSeq - HTSlib - HTSplotter - hub - humann - hunspell - hwloc - Hybpiper - Hydra - Hyperopt - HyperQueue - hyperspy - HyPhy - HyPo - hypothesis - Hypre

h4toh5

The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects.

homepage: http://www.hdfgroup.org/h4toh5/

version	versionsuffix	toolchain
2.2.2	-linux-x86_64-static	system
2.2.3		foss/2018b, gompi/2019b, gompi/2020b
2.2.5		gompi/2022a

H5hut

HDF5 Utility Toolkit: High-Performance I/O Library for Particle-based Simulations

homepage: https://amas.psi.ch/H5hut/

version	toolchain
1.99.13	intel/2016b

h5netcdf

A Python interface for the netCDF4 file-format that reads and writes local or remote HDF5 files directly via h5py or h5pyd, without relying on the Unidata netCDF library.

homepage: https://h5netcdf.org/

version	toolchain
1.1.0	foss/2021b
1.2.0	foss/2022a, foss/2023a

h5py

HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.

homepage: https://www.h5py.org/

version	versionsuffix	toolchain
2.5.0	-Python-2.7.11-HDF5-1.8.16	foss/2016a, intel/2016a
2.5.0	-Python-2.7.11-HDF5-1.8.16-serial	foss/2016a, intel/2016a
2.5.0	-Python-3.5.1-HDF5-1.8.16	foss/2016a
2.6.0	-Python-2.7.11	intel/2016a
2.6.0	-Python-2.7.12-HDF5-1.10.0-patch1	foss/2016b, intel/2016b
2.6.0	-Python-2.7.12-HDF5-1.8.17	foss/2016b, intel/2016b
2.6.0	-Python-2.7.12-HDF5-1.8.18	foss/2016b, intel/2016b
2.6.0	-Python-3.5.2-HDF5-1.10.0-patch1	foss/2016b, intel/2016b
2.6.0	-Python-3.5.2-HDF5-1.8.17	intel/2016b
2.6.0	-Python-3.5.2-HDF5-1.8.18	foss/2016b, intel/2016b
2.7.0	-Python-2.7.12	intel/2016b
2.7.0	-Python-2.7.13	intel/2017a
2.7.0	-Python-2.7.13-HDF5-1.10.1	foss/2017a
2.7.0	-Python-2.7.13-HDF5-1.8.19	foss/2017a
2.7.0	-Python-3.6.1	intel/2017a
2.7.0	-Python-3.6.1-HDF5-1.10.0-patch1	intel/2017a
2.7.0	-Python-3.6.1-HDF5-1.10.1	foss/2017a
2.7.0	-Python-3.6.1-HDF5-1.8.19	foss/2017a
2.7.1	-Python-2.7.13	intel/2017a
2.7.1	-Python-2.7.14	foss/2017b, foss/2018a, fosscuda/2017b, intel/2017b, intel/2018a
2.7.1	-Python-2.7.14-serial	intel/2018a
2.7.1	-Python-3.6.1	intel/2017a
2.7.1	-Python-3.6.3	foss/2017b, fosscuda/2017b, intel/2017b
2.7.1	-Python-3.6.4	foss/2018a, intel/2018a
2.8.0	-Python-2.7.15	foss/2018b, fosscuda/2018b, intel/2018b
2.8.0	-Python-2.7.15-serial	intel/2018b
2.8.0	-Python-3.6.6	foss/2018b, fosscuda/2018b, intel/2018b
2.9.0		foss/2019a, fosscuda/2019a, intel/2019a, intelcuda/2019a
2.10.0	-Python-2.7.18	intel/2020a
2.10.0	-Python-3.7.4	foss/2019b, fosscuda/2019b, intel/2019b, intelcuda/2019b
2.10.0	-Python-3.8.2	foss/2020a, fosscuda/2020a, intel/2020a, intelcuda/2020a
2.10.0	-serial-Python-3.7.4	foss/2019b
3.1.0		foss/2020b, fosscuda/2020b, intel/2020b, intelcuda/2020b
3.2.1		foss/2021a, gomkl/2021a
3.6.0		foss/2021b, intel/2021b
3.7.0		foss/2022a, intel/2022a
3.8.0		foss/2022b
3.9.0		foss/2023a

Hadoop

Hadoop MapReduce by Cloudera

homepage: https://archive.cloudera.com/cdh5/cdh/5/

version	versionsuffix	toolchain
2.4.0	-seagate-722af1-native	system
2.5.0-cdh5.3.1	-native	system
2.6.0-cdh5.4.5	-native	system
2.6.0-cdh5.7.0	-native	system
2.6.0-cdh5.8.0	-native	system
2.6.0-cdh5.12.0	-native	system
2.9.2	-native	GCCcore/7.3.0
2.10.0	-native	GCCcore/8.3.0
2.10.0	-native-Java-1.8	GCCcore/10.2.0

HAL

HAL is a structure to efficiently store and index multiple genome alignments and ancestral reconstructions. HAL is a graph-based representation which provides several advantages over matrix/block-based formats such as MAF, such as improved scalability and the ability to perform queries with respect to an arbitrary reference or subtree. This package includes the HAL API and several analysis and conversion tools which are described below. HAL files are presently stored in either HDF5 or mmap format, but we note that the tools and most of the API are format-independent, so other databases could be implemented in the future.

homepage: https://github.com/ComparativeGenomicsToolkit/hal

version	toolchain
2.1	foss/2020b

hampel

The Hampel filter is generally used to detect anomalies in data with a timeseries structure. It basically consists of a sliding window of a parameterizable size. For each window, each observation will be compared with the Median Absolute Deviation (MAD). The observation will be considered an outlier in the case in which it exceeds the MAD by n times (the parameter n is also parameterizable).

homepage: https://github.com/MichaelisTrofficus/hampel_filter

version	toolchain
0.0.5	foss/2022a

hanythingondemand

HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. It uses the Torque resource manager to do node allocation.

homepage: https://github.com/hpcugent/hanythingondemand

version	versionsuffix	toolchain
3.0.0	-cli	system
3.0.1	-cli	system
3.0.2	-cli	system
3.0.3	-cli	system
3.0.4	-cli	system
3.1.0	-Python-2.7.11	intel/2016a
3.1.0	-cli	system
3.1.1	-Python-2.7.11	intel/2016a
3.1.1	-cli	system
3.1.2	-Python-2.7.11	intel/2016a
3.1.2	-cli	system
3.1.3	-Python-2.7.12	intel/2016b
3.1.3	-cli	system
3.1.4	-Python-2.7.12	intel/2016b
3.1.4	-cli	system
3.2.0	-Python-2.7.12	intel/2016b
3.2.0	-cli	system
3.2.2	-Python-2.7.12	intel/2016b
3.2.2	-cli	system

HAPGEN2

'HAPGEN2' simulates case control datasets at SNP markers.

homepage: https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html

version	toolchain
2.2.0	system

HarfBuzz

HarfBuzz is an OpenType text shaping engine.

homepage: https://www.freedesktop.org/wiki/Software/HarfBuzz

version	toolchain
1.1.3	foss/2016a, intel/2016a
1.2.7	foss/2016a, intel/2016a
1.3.1	foss/2016b, intel/2016b, intel/2017a
1.5.1	intel/2017a
1.7.1	foss/2017b, intel/2017b
1.7.5	foss/2018a, intel/2018a
1.9.0	fosscuda/2018b
2.2.0	foss/2018b, fosscuda/2018b
2.4.0	GCCcore/8.2.0
2.6.4	GCCcore/8.3.0, GCCcore/9.3.0
2.6.7	GCCcore/10.2.0
2.8.1	GCCcore/10.3.0
2.8.2	GCCcore/11.2.0
4.2.1	GCCcore/11.3.0
5.3.1	GCCcore/12.2.0, GCCcore/12.3.0
8.2.2	GCCcore/13.2.0

Harminv

Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.

homepage: https://github.com/stevengj/harminv

version	toolchain
1.4	foss/2016a
1.4.1	foss/2017b, foss/2018a, intel/2018a, intel/2020a
1.4.2	foss/2020b

harmony

Harmony is a general-purpose R package with an efficient algorithm for integrating multiple data sets.

homepage: https://portals.broadinstitute.org/harmony

version	versionsuffix	toolchain
0.1.0-20210528	-R-4.0.3	foss/2020b
1.0.0-20200224	-R-4.0.0	foss/2020a

hatchling

Extensible, standards compliant build backend used by Hatch, a modern, extensible Python project manager.

homepage: https://hatch.pypa.io

version	toolchain
1.18.0	GCCcore/12.3.0, GCCcore/13.2.0

HBase

Apache HBase. is the Hadoop database, a distributed, scalable, big data store.

homepage: http://hbase.apache.org/

version	toolchain
1.0.2	system

HD-BET

Tool for brain extraction.

homepage: https://github.com/MIC-DKFZ/HD-BET

version	versionsuffix	toolchain
20220318		foss/2021a
20220318	-CUDA-11.3.1	foss/2021a

HDBSCAN

The hdbscan library is a suite of tools to use unsupervised learning to find clusters, or dense regions, of a dataset. The primary algorithm is HDBSCAN* as proposed by Campello, Moulavi, and Sander. The library provides a high performance implementation of this algorithm, along with tools for analysing the resulting clustering.

homepage: http://hdbscan.readthedocs.io/en/latest/

version	versionsuffix	toolchain
0.8.24	-Python-3.7.4	foss/2019b
0.8.27		foss/2021a
0.8.29		foss/2022a

HDDM

HDDM is a Python toolbox for hierarchical Bayesian parameter estimation of the Drift Diffusion Model (via PyMC).

homepage: http://ski.clps.brown.edu/hddm_docs

version	versionsuffix	toolchain
0.6.1	-Python-3.6.6	intel/2018b
0.7.5	-Python-2.7.16	intel/2019b
0.7.5	-Python-3.7.4	intel/2019b

HDF

HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.

homepage: https://www.hdfgroup.org/products/hdf4/

version	versionsuffix	toolchain
4.2.11		intel/2016a
4.2.12		intel/2017a
4.2.13		GCCcore/6.4.0
4.2.13	-no-netcdf	intel/2017a
4.2.14		GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0
4.2.15		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/9.3.0
4.2.16		GCCcore/12.3.0
4.2.16-2		GCCcore/12.3.0, GCCcore/13.2.0

HDF-EOS

HDF-EOS libraries are software libraries built on HDF libraries. It supports three data structures for remote sensing data: Grid, Point and Swath.

homepage: https://hdfeos.org/

version	toolchain
2.20	GCCcore/10.2.0, GCCcore/7.3.0, GCCcore/8.3.0

HDF-EOS2

HDF-EOS libraries are software libraries built on HDF libraries. It supports three data structures for remote sensing data: Grid, Point and Swath.

homepage: https://hdfeos.org/

version	toolchain
3.0	GCCcore/11.3.0

HDF-EOS5

HDF-EOS libraries are software libraries built on HDF libraries. It supports three data structures for remote sensing data: Grid, Point and Swath.

homepage: https://hdfeos.org/

version	toolchain
1.16	foss/2018b, gompi/2019b, gompi/2020b

HDF5

HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.

homepage: https://portal.hdfgroup.org/display/support

version	versionsuffix	toolchain
1.8.10	-serial	GCC/4.8.1
1.8.11	-serial	GCC/4.8.1
1.8.12		foss/2018b, intel/2016b
1.8.13		foss/2018b
1.8.16		foss/2016a, intel/2016.02-GCC-4.9, intel/2016a, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25
1.8.16	-serial	foss/2016a, gimkl/2.11.5, intel/2016a
1.8.17		foss/2016a, foss/2016b, intel/2016a, intel/2016b
1.8.17	-serial	GCC/5.4.0-2.26, foss/2016a, intel/2016b
1.8.18		foss/2016b, foss/2017a, gimkl/2017a, intel/2016b, intel/2017.01, intel/2017a
1.8.18	-serial	intel/2017a
1.8.19		foss/2017a, foss/2017b, intel/2017a, intel/2017b
1.8.20		foss/2018a, gmpolf/2017.10, intel/2017b, intel/2018a
1.10.0-patch1		foss/2016b, intel/2016b, intel/2017.01, intel/2017a
1.10.1		foss/2017a, foss/2017b, foss/2018a, fosscuda/2017b, intel/2017a, intel/2017b, intel/2018.00, intel/2018.01, intel/2018a, intelcuda/2017b, iomkl/2017b, iomkl/2018a
1.10.2		PGI/18.4-GCC-6.4.0-2.28, foss/2018b, fosscuda/2018b, intel/2018b, iomkl/2018b
1.10.5		gompi/2019a, gompi/2019b, gompic/2019a, gompic/2019b, iimpi/2019a, iimpi/2019b, iimpic/2019a, iimpic/2019b, iompi/2019b
1.10.5	-serial	GCC/8.3.0
1.10.6		gompi/2020a, gompic/2020a, iimpi/2020a, iimpic/2020a, iompi/2020a
1.10.7		gompi/2020b, gompi/2021a, gompic/2020b, iimpi/2020b, iimpi/2021a, iimpic/2020b, iompi/2021a
1.10.8		gompi/2021b, gompi/2022a
1.12.0		gompi/2020a, iimpi/2020a
1.12.1		gompi/2021a, gompi/2021b, iimpi/2021b
1.12.2		gompi/2022a, iimpi/2022a, nvompi/2022.07
1.12.2	-serial	GCC/11.3.0, NVHPC/22.7-CUDA-11.7.0
1.13.1		gompi/2022a, iimpi/2022a
1.13.1	-serial	GCC/11.3.0
1.14.0		gompi/2022b, gompi/2023a, iimpi/2022b, iimpi/2023a
1.14.3		gompi/2023b, iimpi/2023b

hdf5storage

This Python package provides high level utilities to read/write a variety of Python types to/from HDF5 (Heirarchal Data Format) formatted files. This package also provides support for MATLAB MAT v7.3 formatted files, which are just HDF5 files with a different extension and some extra meta-data. All of this is done without pickling data. Pickling is bad for security because it allows arbitrary code to be executed in the interpreter. One wants to be able to read possibly HDF5 and MAT files from untrusted sources, so pickling is avoided in this package.

homepage: https://pythonhosted.org/hdf5storage/

version	toolchain
0.1.15	foss/2019a, fosscuda/2019a

HDFView

HDFView is a visual tool for browsing and editing HDF4 and HDF5 files.

homepage: https://support.hdfgroup.org/products/java/hdfview/

version	versionsuffix	toolchain
2.14	-Java-1.8.0_152-centos6	system
2.14	-Java-1.8.0_152-centos7	system

hdWGCNA

hdWGCNA is an R package for performing weighted gene co-expression network analysis (WGCNA) in high dimensional transcriptomics data such as single-cell RNA-seq or spatial transcriptomics. hdWGCNA is highly modular and can construct context-specific co-expression networks across cellular and spatial hierarchies. hdWGNCA identifies modules of highly co-expressed genes and provides context for these modules via statistical testing and biological knowledge sources. hdWGCNA uses datasets formatted as Seurat objects.

homepage: https://smorabit.github.io/hdWGCNA/

version	versionsuffix	toolchain
0.3.00	-R-4.3.2	foss/2023a

HEALPix

Hierarchical Equal Area isoLatitude Pixelation of a sphere.

homepage: http://healpix.sourceforge.net/

version	toolchain
3.50	GCCcore/7.3.0, GCCcore/8.2.0

Health-GPS

Health-GPS microsimulation is part of the STOP project, and supports researchers and policy makers in the analysis of the health and economic impacts of alternative measures to tackle chronic diseases and obesity in children. The model reproduces the characteristics of a population and simulates key individual event histories associated with key components of relevant behaviours, such as physical activity, and diseases such as diabetes or cancer. To run the test-jobs with HealthGPS.Tests the data-directory, found in your installation folder, must be in the current path.

homepage: https://github.com/imperialCHEPI/healthgps

version	toolchain
1.1.3.0	GCCcore/11.3.0
1.2.2.0	GCCcore/11.3.0

heaptrack

A heap memory profiler for Linux.

homepage: http://milianw.de/blog/heaptrack-a-heap-memory-profiler-for-linux

version	toolchain
1.1.0	foss/2016b

hector

This is the repository for Hector, an open source, object-oriented, simple global climate carbon-cycle model. It runs essentially instantaneously while still representing the most critical global scale earth system processes, and is one of a class of models heavily used for for emulating complex climate models and uncertainty analyses.

homepage: https://github.com/JGCRI/hector

version	toolchain
2.5.0	GCC/11.2.0

HeFFTe

Highly Efficient FFT for Exascale (HeFFTe) library

homepage: https://icl.utk.edu/fft

version	toolchain
1.0	foss/2020a
2.4.0	foss/2023b

Hello

The GNU Hello program produces a familiar, friendly greeting. Yes, this is another implementation of the classic program that prints "Hello, world!" when you run it. However, unlike the minimal version often seen, GNU Hello processes its argument list to modify its behavior, supports greetings in many languages, and so on.

homepage: https://www.gnu.org/software/hello/

version	toolchain
2.10	GCCcore/8.2.0

help2man

help2man produces simple manual pages from the '--help' and '--version' output of other commands.

homepage: https://www.gnu.org/software/help2man/

version	toolchain
1.47.4	GCCcore/5.4.0, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.1.0, GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/system, gimkl/2017a, intel/2016b, system
1.47.5	GCCcore/5.5.0
1.47.6	GCCcore/8.1.0
1.47.7	GCCcore/8.2.0
1.47.8	GCCcore/7.4.0, GCCcore/8.3.0, GCCcore/8.4.0
1.47.10	GCCcore/9.1.0, GCCcore/9.2.0
1.47.12	GCCcore/9.3.0
1.47.15	GCCcore/10.1.0
1.47.16	GCCcore/10.2.0
1.48.3	FCC/4.5.0, GCCcore/10.3.0, GCCcore/11.1.0, GCCcore/11.2.0, GCCcore/9.4.0
1.49.2	GCCcore/11.3.0, GCCcore/12.1.0, GCCcore/12.2.0, GCCcore/9.5.0
1.49.3	GCCcore/11.4.0, GCCcore/12.3.0, GCCcore/13.1.0, GCCcore/13.2.0

HepMC

HepMC is a standard for storing Monte Carlo event data.

homepage: http://hepmc.web.cern.ch/hepmc/

version	toolchain
2.06.11	gompi/2022a

HepMC3

HepMC is a standard for storing Monte Carlo event data.

homepage: http://hepmc.web.cern.ch/hepmc/

version	toolchain
3.2.5	GCC/11.3.0
3.2.6	GCC/12.3.0

HF-Datasets

The largest hub of ready-to-use datasets for ML models with fast, easy-to-use and efficient data manipulation tools.

homepage: https://github.com/huggingface/datasets

version	toolchain
2.18.0	gfbf/2023a

HH-suite

The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).

homepage: https://github.com/soedinglab/hh-suite

version	versionsuffix	toolchain
3.0-beta.3		intel/2018a
3.2.0		foss/2019b, fosscuda/2019b
3.3.0		foss/2020a, gompi/2020b, gompi/2021a, gompi/2021b, gompi/2022a, gompic/2020b
3.3.0	-Python-3.7.4	gompic/2019b

HiC-Pro

HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps.

homepage: https://nservant.github.io/HiC-Pro

version	versionsuffix	toolchain
2.9.0	-Python-2.7.12	foss/2016b
3.1.0	-R-4.2.1	foss/2022a

hic-straw

Straw is a library which allows rapid streaming of contact data from .hic files.

homepage: https://github.com/aidenlab/straw

version	toolchain
1.3.1	foss/2022a

HiCExplorer

HiCexplorer addresses the common tasks of Hi-C analysis from processing to visualization.

homepage: http://hicexplorer.readthedocs.org/

version	versionsuffix	toolchain
2.1.1	-Python-3.6.4	foss/2018a
3.7.2		foss/2022a

HiCMatrix

This library implements the central class of HiCExplorer to manage Hi-C interaction matrices.

homepage: https://github.com/deeptools/HiCMatrix

version	toolchain
17	foss/2022a

hierfstat

Estimates hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in the hierarchy.

homepage: https://cran.r-project.org/package=hierfstat

version	versionsuffix	toolchain
0.5-7	-R-4.0.0-Python-3.8.2	foss/2020a

hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads.

homepage: https://github.com/chhylp123/hifiasm

version	toolchain
0.15.2	GCCcore/10.3.0, GCCcore/9.3.0
0.16.1	GCCcore/10.3.0
0.19.5	GCCcore/11.2.0
0.19.7	GCCcore/12.2.0

HighFive

HighFive is a modern header-only C++11 friendly interface for libhdf5.

homepage: https://github.com/BlueBrain/HighFive

version	toolchain
2.6.2	gompi/2021a, gompi/2022a
2.7.1	gompi/2023a

Highway

Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same operation to 'lanes'.

homepage: https://github.com/google/highway

version	toolchain
0.12.2	GCCcore/10.2.0, GCCcore/10.3.0
1.0.3	GCCcore/11.3.0, GCCcore/12.2.0
1.0.4	GCCcore/11.3.0, GCCcore/12.3.0
1.0.7	GCCcore/13.2.0

HIP

HIP is a C++ Runtime API and Kernel Language that allows developers to create portable applications for AMD and NVIDIA GPUs from single source code.

homepage: https://github.com/ROCm-Developer-Tools/HIP

version	versionsuffix	toolchain
4.5.0	-amd	GCCcore/11.2.0

hipify-clang

Hipify-clang is a clang-based tool for translating CUDA sources into HIP sources. It translates CUDA source into an abstract syntax tree, which is traversed by transformation matchers. After applying all the matchers, the output HIP source is produced.

homepage: https://github.com/ROCm-Developer-Tools/HIPIFY

version	toolchain
4.2.0	gcccuda/2020b

HIPS

HIPS (Hierarchical Iterative Parallel Solver) is a scientific library that provides an efficient parallel iterative solver for very large sparse linear systems.

homepage: http://hips.gforge.inria.fr/

version	toolchain
1.2b-rc5	foss/2017b

hipSYCL

hipSYCL is a modern SYCL implementation targeting CPUs and GPUs, with a focus on leveraging existing toolchains such as CUDA or HIP

homepage: https://github.com/illuhad/hipSYCL

version	toolchain
0.9.1	GCC/10.2.0, gcccuda/2020b

hiredis

Hiredis is a minimalistic C client library for the Redis database. It is minimalistic because it just adds minimal support for the protocol, but at the same time it uses a high level printf-alike API in order to make it much higher level than otherwise suggested by its minimal code base and the lack of explicit bindings for every Redis command.

homepage: https://github.com/redis/hiredis

version	toolchain
1.0.2	GCCcore/11.2.0, GCCcore/11.3.0
1.2.0	GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

HISAT2

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome).

homepage: https://daehwankimlab.github.io/hisat2

version	toolchain
2.0.3-beta	intel/2016a
2.0.4	foss/2016b
2.0.5	intel/2017a
2.1.0	foss/2017b, foss/2018b, intel/2017a, intel/2017b, intel/2018a
2.2.0	foss/2018b
2.2.1	foss/2019b, foss/2020a, gompi/2020b, gompi/2021a, gompi/2021b, gompi/2022a

histolab

Library for Digital Pathology Image Processing

homepage: https://github.com/histolab/histolab

version	toolchain
0.4.1	foss/2021a, foss/2021b

hivtrace

HIV-TRACE is an application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.

homepage: https://github.com/veg/hivtrace

version	toolchain
0.6.2	foss/2021a

hl7apy

Python library to parse, create and handle HL7 v2 messages.

homepage: https://github.com/crs4/hl7apy

version	versionsuffix	toolchain
1.3.3	-Python-3.7.4	GCCcore/8.3.0

HLAminer

HLAminer is a software for HLA predictions from next-generation shotgun (NGS) sequence read data and supports direct read alignment and targeted de novo assembly of sequence reads.

homepage: http://www.bcgsc.ca/platform/bioinfo/software/hlaminer

version	versionsuffix	toolchain
1.4	-Perl-5.28.0	foss/2018b

HMMER

HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.

homepage: http://hmmer.org/

version	toolchain
3.1b2	GCC/6.4.0-2.28, foss/2016a, foss/2016b, foss/2018a, iccifort/2017.4.196-GCC-6.4.0-2.28, intel/2017a, intel/2018a
3.2.1	GCC/8.2.0-2.31.1, foss/2018b, gompi/2019b, iccifort/2019.1.144-GCC-8.2.0-2.31.1, iimpi/2019b, intel/2018b
3.3.1	gompi/2020a, iimpi/2020a
3.3.2	gompi/2019b, gompi/2020a, gompi/2020b, gompi/2021a, gompi/2021b, gompi/2022a, gompi/2022b, gompic/2020b, iimpi/2020b, iimpi/2021b
3.4	gompi/2023a

HMMER2

HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments.

homepage: http://hmmer.org

version	toolchain
2.3.2	GCC/10.2.0, GCC/10.3.0, GCC/8.3.0

hmmlearn

hmmlearn is a set of algorithms for unsupervised learning and inference of Hidden Markov Models

homepage: https://github.com/hmmlearn/hmmlearn

version	versionsuffix	toolchain
0.2.0	-Python-2.7.14	intel/2017b
0.2.0	-Python-3.6.4	intel/2018a
0.3.0		foss/2022b, gfbf/2023a

HOME

HOME (histogram of methylation) is a python package for differential methylation region (DMR) identification. The method uses histogram of methylation features and the linear Support Vector Machine (SVM) to identify DMRs from whole genome bisulfite sequencing (WGBS) data.

homepage: https://github.com/ListerLab/HOME

version	versionsuffix	toolchain
0.9	-Python-2.7.13	foss/2017a

HOOMD-blue

HOOMD-blue is a general-purpose particle simulation toolkit, implementing molecular dynamics and hard particle Monte Carlo optimized for fast execution on both GPUs and CPUs.

homepage: https://bitbucket.org/glotzer/hoomd-blue

version	versionsuffix	toolchain
4.0.1		foss/2022a
4.0.1	-CUDA-11.7.0	foss/2022a

Horovod

Horovod is a distributed training framework for TensorFlow.

homepage: https://github.com/uber/horovod

version	versionsuffix	toolchain
0.9.10	-Python-3.6.3	intel/2017b
0.18.1	-Python-3.7.2	foss/2019a
0.18.2	-TensorFlow-1.15.0-Python-3.7.4	fosscuda/2019b
0.18.2	-TensorFlow-1.15.2-Python-3.7.4	fosscuda/2019b
0.18.2	-TensorFlow-2.0.0-Python-3.7.4	fosscuda/2019b
0.19.1	-TensorFlow-2.1.0-Python-3.7.4	fosscuda/2019b
0.19.5	-TensorFlow-2.2.0-Python-3.7.4	fosscuda/2019b
0.20.3	-TensorFlow-2.3.1-Python-3.7.4	fosscuda/2019b
0.21.1	-PyTorch-1.7.1-Python-3.7.4	fosscuda/2019b
0.21.1	-TensorFlow-2.4.1	fosscuda/2020b
0.21.1	-TensorFlow-2.4.1-Python-3.7.4	fosscuda/2019b
0.21.3	-PyTorch-1.7.1	fosscuda/2020b
0.21.3	-TensorFlow-2.3.1-Python-3.8.2	foss/2020a, fosscuda/2020a
0.22.0	-PyTorch-1.8.1	fosscuda/2020b
0.22.1	-CUDA-11.3.1-TensorFlow-2.5.3	foss/2021a
0.22.1	-CUDA-11.3.1-TensorFlow-2.6.0	foss/2021a
0.22.1	-TensorFlow-2.5.0	fosscuda/2020b
0.22.1	-TensorFlow-2.5.0-Python-3.7.4	fosscuda/2019b
0.23.0	-CUDA-11.3.1-PyTorch-1.10.0	foss/2021a
0.23.0	-TensorFlow-2.5.0	fosscuda/2020b
0.25.0	-CUDA-11.3.1-PyTorch-1.10.0	foss/2021a
0.28.1	-CUDA-11.3.1-PyTorch-1.11.0	foss/2021a
0.28.1	-CUDA-11.3.1-PyTorch-1.12.1	foss/2021a
0.28.1	-CUDA-11.4.1-TensorFlow-2.7.1	foss/2021b
0.28.1	-CUDA-11.4.1-TensorFlow-2.8.4	foss/2021b
0.28.1	-CUDA-11.5.2-PyTorch-1.12.1	foss/2021b
0.28.1	-CUDA-11.7.0-PyTorch-1.12.0	foss/2022a
0.28.1	-CUDA-11.7.0-PyTorch-1.12.1	foss/2022a
0.28.1	-CUDA-11.7.0-PyTorch-1.13.1	foss/2022a
0.28.1	-CUDA-11.7.0-TensorFlow-2.11.0	foss/2022a
0.28.1	-CUDA-11.7.0-TensorFlow-2.9.1	foss/2022a
0.28.1	-PyTorch-1.12.0	foss/2022a
0.28.1	-PyTorch-1.9.0	fosscuda/2020b

horton

HORTON is a Helpful Open-source Research TOol for N-fermion systems, written primarily in the Python programming language. (HORTON is named after the helpful pachyderm, not the Canadian caffeine supply store.) The ultimate goal of HORTON is to provide a platform for testing new ideas on the quantum many-body problem at a reasonable computational cost. Although HORTON is primarily designed to be a quantum-chemistry program, it can perform computations involving model Hamiltonians, and could be extended for computations in nuclear physics.

homepage: https://theochem.github.io/horton

version	versionsuffix	toolchain
2.1.1	-Python-2.7.15	foss/2018b, intel/2018b
2.1.1	-Python-2.7.18	intel/2020a

how_are_we_stranded_here

Python package for testing strandedness of RNA-Seq fastq files

homepage: https://github.com/signalbash/how_are_we_stranded_here

version	toolchain
1.0.1	foss/2021b

HPCC

HPC Challenge is a benchmark suite that measures a range memory access patterns. The HPC Challenge benchmark consists of basically 7 tests: HPL, DGEMM, STREAM, PTRANS, RandomAccess, FFT, Communication bandwidth and latency

homepage: https://hpcchallenge.org/

version	toolchain
1.5.0	foss/2022a

HPCG

The HPCG Benchmark project is an effort to create a more relevant metric for ranking HPC systems than the High Performance LINPACK (HPL) benchmark, that is currently used by the TOP500 benchmark.

homepage: https://software.sandia.gov/hpcg

version	toolchain
3.0	foss/2016b, foss/2018b, intel/2018b
3.1	foss/2018b, foss/2021a, foss/2021b, foss/2022a, foss/2022b, foss/2023a, intel/2018b, intel/2021a, intel/2021b, intel/2022a, intel/2022b, intel/2023a

HPCX

The Mellanox HPC-X Toolkit is a comprehensive MPI and SHMEM/PGAS software suite for high performance computing environments

homepage: http://www.mellanox.com/page/products_dyn?product_family=189&mtag=hpc-x

version	toolchain
2.3.0	GCC/8.2.0-2.31.1

HPDBSCAN

Highly parallel density based spatial clustering for application with noise

homepage: https://github.com/Markus-Goetz/hpdbscan

version	toolchain
20171110	foss/2017b
20210826	foss/2020b

HPL

HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.

homepage: https://www.netlib.org/benchmark/hpl/

version	versionsuffix	toolchain
2.0.15	-CUDA-11.7.0	intel/2022a
2.1		foss/2016.04, foss/2016.06, foss/2016a, foss/2016b, gimkl/2.11.5, gmpolf/2016a, gmvolf/1.7.20, gmvolf/2016a, intel/2016.00, intel/2016.01, intel/2016.02-GCC-4.9, intel/2016.02-GCC-5.3, intel/2016.03-GCC-4.9, intel/2016.03-GCC-5.3, intel/2016.03-GCC-5.4, intel/2016a, intel/2016b, iomkl/2016.07, pomkl/2016.03, pomkl/2016.04, pomkl/2016.09
2.2		foss/2016.07, foss/2016.09, foss/2017a, foss/2017b, foss/2018.08, foss/2018a, foss/2018b, fosscuda/2017b, fosscuda/2018a, fosscuda/2018b, gimkl/2018b, giolf/2017b, giolf/2018a, giolfc/2017b, gmpolf/2017.10, goblf/2018b, gomkl/2018b, intel/2017.00, intel/2017.01, intel/2017.02, intel/2017.09, intel/2017a, intel/2017b, intel/2018.00, intel/2018.01, intel/2018.02, intel/2018.04, intel/2018a, intel/2018b, intel/2019.00, intel/2019.01, intelcuda/2016.10, intelcuda/2017b, iomkl/2016.09-GCC-4.9.3-2.25, iomkl/2016.09-GCC-5.4.0-2.26, iomkl/2017.01, iomkl/2017a, iomkl/2017b, iomkl/2018.02, iomkl/2018a, iomkl/2018b, pomkl/2016.09
2.3		CrayCCE/19.06, CrayGNU/19.06, CrayIntel/19.06, Fujitsu/21.05, foss/2019a, foss/2019b, foss/2020a, foss/2020b, foss/2021a, foss/2021b, foss/2022.05, foss/2022.10, foss/2022a, foss/2022b, foss/2023.09, foss/2023a, foss/2023b, fosscuda/2019b, fosscuda/2020a, gobff/2020.06-amd, gobff/2020.11, gobff/2020b, gobff/2021a, goblf/2020b, gomkl/2019a, gomkl/2020b, gomkl/2021a, gomkl/2022a, iibff/2020b, intel/2019.02, intel/2019.03, intel/2019a, intel/2019b, intel/2020.00, intel/2020.06-impi-18.5, intel/2020.12, intel/2020a, intel/2020b, intel/2021a, intel/2021b, intel/2022.00, intel/2022.09, intel/2022.11, intel/2022.12, intel/2022a, intel/2022b, intel/2023.03, intel/2023.07, intel/2023a, intel/2023b, intelcuda/2019b, intelcuda/2020a, iomkl/2019.01, iomkl/2021a, iomkl/2021b

htop

An interactive process viewer for Unix

homepage: https://htop.dev

version	toolchain
2.0.0	system
2.0.1	system
3.2.1	system
3.2.2	GCCcore/11.3.0

HTSeq

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.

homepage: https://github.com/simon-anders/htseq

version	versionsuffix	toolchain
0.6.1p1	-Python-2.7.11	foss/2016a
0.6.1p1	-Python-2.7.12	foss/2016b, intel/2016b
0.9.1	-Python-2.7.12	foss/2016b
0.9.1	-Python-2.7.13	intel/2017a
0.9.1	-Python-2.7.14	foss/2017b, intel/2017b, intel/2018a
0.9.1	-Python-3.6.3	foss/2017b, intel/2017b
0.10.0	-Python-2.7.14	foss/2018a
0.11.0	-Python-2.7.15	foss/2018b, intel/2018b
0.11.2	-Python-3.6.6	foss/2018b
0.11.2	-Python-3.7.2	foss/2019a
0.11.2	-Python-3.7.4	foss/2019b
0.11.3		foss/2020b, foss/2021b
2.0.2		foss/2022a

HTSlib

PacBio fork of C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix

homepage: https://github.com/PacificBiosciences/htslib

version	versionsuffix	toolchain
1.2.1		foss/2016b
1.3		foss/2016a, intel/2016a
1.3.1		foss/2016a, foss/2016b, intel/2016b
1.3.2		intel/2016b
1.4		foss/2016b, intel/2016b
1.4.1		foss/2016a, intel/2017a
1.6		foss/2016b, foss/2017b, intel/2017b
1.7		intel/2018a
1.8		GCC/6.4.0-2.28, foss/2018a, intel/2018a
1.9		GCC/6.4.0-2.28, GCC/8.2.0-2.31.1, foss/2018b, iccifort/2017.4.196-GCC-6.4.0-2.28, iccifort/2019.1.144-GCC-8.2.0-2.31.1, intel/2018b
1.10.2		GCC/8.3.0, GCC/9.3.0, iccifort/2019.5.281
1.11		GCC/10.2.0, iccifort/2020.4.304
1.12		GCC/10.2.0, GCC/10.3.0, GCC/9.3.0
1.14		GCC/11.2.0
1.15.1		GCC/11.3.0
1.17		GCC/12.2.0
1.18		GCC/12.3.0
20160107	-PacBio	intel/2017a

HTSplotter

HTSplotter allows an end-to-end data processing and analysis of chemical and genetic in vitro perturbation screens.

homepage: https://github.com/CBIGR/HTSplotter

version	toolchain
0.15	foss/2022a
2.11	foss/2022b

hub

hub is a command-line wrapper for git that makes you better at GitHub.

homepage: https://hub.github.com/

version	versionsuffix	toolchain
2.2.2	-linux-amd64	system

humann

HUMAnN v3 is a pipeline for efficiently and accurately determining the coverage and abundance of microbial pathways in a community from metagenomic data. Sequencing a metagenome typically produces millions of short DNA/RNA reads. This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question: What are the microbes in my community-of-interest doing (or capable of doing)?

homepage: http://huttenhower.sph.harvard.edu/humann

version	toolchain
3.6	foss/2022a

hunspell

Hunspell is a spell checker and morphological analyzer library and program designed for languages with rich morphology and complex word compounding or character encoding.

homepage: https://hunspell.github.io/

version	toolchain
1.6.1	intel/2017a
1.7.0	GCCcore/8.2.0
1.7.1	GCCcore/11.2.0, GCCcore/11.3.0
1.7.2	GCCcore/12.3.0

hwloc

The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.

homepage: https://www.open-mpi.org/projects/hwloc/

version	toolchain
1.7.2	GCC/4.8.2
1.8.1	GCC/4.8.2, GCC/4.8.3
1.9	GCC/4.8.3
1.10.0	GCC/4.9.2
1.10.1	GCC/4.8.4, GNU/4.9.2-2.25
1.11.0	GNU/4.9.3-2.25
1.11.1	GCC/4.9.3
1.11.2	GCC/4.9.3-2.25, GNU/4.9.3-2.25
1.11.3	GCC/5.2.0, GCC/5.3.0-2.26, GCC/5.4.0-2.26, GCC/6.1.0-2.27, PGI/16.3-GCC-4.9.3-2.25, PGI/16.4-GCC-5.3.0-2.26, iccifort/2016.3.210-GCC-4.9.3-2.25, iccifort/2016.3.210-GCC-5.4.0-2.26, intel/2016a, intel/2016b
1.11.4	GCC/6.2.0-2.27, PGI/16.7-GCC-5.4.0-2.26, iccifort/2017.1.132-GCC-5.4.0-2.26
1.11.5	GCC/5.4.0-2.26, GCC/6.3.0-2.27, iccifort/2017.1.132-GCC-6.3.0-2.27
1.11.6	GCC/6.3.0-2.28
1.11.7	GCCcore/5.4.0, GCCcore/6.4.0
1.11.8	GCCcore/6.4.0, GCCcore/7.2.0, intel/2017a
1.11.10	GCCcore/7.3.0
1.11.11	GCCcore/8.2.0
1.11.12	GCCcore/8.3.0
2.0.2	GCCcore/8.2.0
2.0.3	GCCcore/8.3.0
2.1.0	GCCcore/9.2.0
2.2.0	GCCcore/10.2.0, GCCcore/9.3.0
2.4.1	GCCcore/10.3.0
2.5.0	GCCcore/11.2.0
2.7.1	GCCcore/11.3.0
2.8.0	GCCcore/12.2.0
2.9.1	GCCcore/12.3.0
2.9.2	GCCcore/13.2.0

Hybpiper

HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts/modules that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.

homepage: https://github.com/mossmatters/HybPiper

version	toolchain
2.1.6	foss/2022b

Hydra

Hydra is an open-source Python framework that simplifies the development of research and other complex applications. The key feature is the ability to dynamically create a hierarchical configuration by composition and override it through config files and the command line. The name Hydra comes from its ability to run multiple similar jobs - much like a Hydra with multiple heads.

homepage: https://hydra.cc/

version	toolchain
1.1.1	GCCcore/10.3.0
1.3.2	GCCcore/11.3.0, GCCcore/12.3.0

Hyperopt

hyperopt is a Python library for optimizing over awkward search spaces with real-valued, discrete, and conditional dimensions.

homepage: http://hyperopt.github.io/hyperopt/

version	versionsuffix	toolchain
0.1	-Python-2.7.14	intel/2017b
0.1.1	-Python-3.6.6	intel/2018b
0.2.4	-Python-3.7.4-Java-1.8	intel/2019b
0.2.5		fosscuda/2020b
0.2.7		foss/2021a, foss/2022a

HyperQueue

HyperQueue lets you build a computation plan consisting of a large amount of tasks and then execute it transparently over a system like SLURM/PBS. It dynamically groups jobs into SLURM/PBS jobs and distributes them to fully utilize allocated nodes. You thus do not have to manually aggregate your tasks into SLURM/PBS jobs.

homepage: https://it4innovations.github.io/hyperqueue/

version	toolchain
0.13.0	system

hyperspy

HyperSpy is an open source Python library which provides tools to facilitate the interactive data analysis of multi-dimensional datasets that can be described as multi-dimensional arrays of a given signal (e.g. a 2D array of spectra a.k.a spectrum image)

homepage: https://hyperspy.org/

version	versionsuffix	toolchain
1.1.1	-Python-3.5.2	intel/2016b

HyPhy

HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning

homepage: https://veg.github.io/hyphy-site/

version	toolchain
2.3.13	foss/2016b
2.5.1	gompi/2019a
2.5.33	gompi/2021a

HyPo

HyPo: Super Fast & Accurate Polisher for Long Read Genome Assemblies

homepage: https://github.com/kensung-lab/hypo

version	versionsuffix	toolchain
1.0.3	-Python-3.7.4	GCC/8.3.0

hypothesis

Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets you find more bugs in your code with less work.

homepage: https://github.com/HypothesisWorks/hypothesis

version	versionsuffix	toolchain
4.5.0	-Python-3.6.6	foss/2018b, fosscuda/2018b
4.23.4		GCCcore/8.2.0
4.39.3	-Python-3.6.4	intel/2018a
4.44.2	-Python-3.7.4	GCCcore/8.3.0
4.53.1		GCCcore/10.2.0
4.57.1	-Python-2.7.18	GCCcore/11.2.0
5.6.0	-Python-3.8.2	GCCcore/9.3.0
5.41.2		GCCcore/10.2.0
5.41.5		GCCcore/10.2.0
6.7.0		GCCcore/10.2.0
6.13.1		GCCcore/10.3.0
6.14.6		GCCcore/11.2.0
6.46.7		GCCcore/11.3.0
6.68.2		GCCcore/12.2.0
6.82.0		GCCcore/12.3.0
6.90.0		GCCcore/13.2.0

Hypre

Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.

homepage: https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods

version	toolchain
2.11.1	foss/2016a, intel/2016a
2.14.0	foss/2018a, intel/2018a
2.15.1	foss/2019a, intel/2019a
2.18.2	foss/2019b, foss/2020a, intel/2019b, intel/2020a
2.20.0	foss/2020b, intel/2020b
2.21.0	foss/2021a, fosscuda/2020b, intel/2021a
2.24.0	intel/2021b
2.25.0	foss/2022a
2.27.0	foss/2022b
2.29.0	foss/2023a

I

i-cisTarget - i-PI - I-TASSER - i7z - ICA-AROMA - icc - iccifort - iccifortcuda - iced - ichorCNA - icmake - iCount - ICU - IDBA-UD - idemux - IDG - ieeg-cli - ifort - IgBLAST - IGMPlot - igraph - IGV - igv-reports - igvShiny - IGVTools - iibff - iimkl - iimpi - iimpic - IJulia - ILAMB - IMa2 - IMa2p - imagecodecs - imageio - ImageJ - ImageMagick - imake - Imath - IMB - imbalanced-learn - imgaug - imkl - imkl-FFTW - IML - Imlib2 - immunedeconv - IMOD - impi - IMPUTE2 - imutils - InChI - indicators - Inelastica - inferCNV - infercnvpy - Inferelator - Infernal - inflection - Infomap - inih - inline - InParanoid - inputproto - Inspector - IntaRNA - INTEGRATE - INTEGRATE-Neo - intel - intel-compilers - IntelClusterChecker - intelcuda - IntelDAAL - IntelPython - InterOp - InterProScan - InterProScan_data - intervaltree - intervaltree-python - intltool - io_lib - ioapi - iodata - iomkl - iompi - IonQuant - IOR - IOzone - iperf - IPM - Ipopt - ipp - IPy - ipympl - ipyparallel - ipyrad - IPython - IQ-TREE - Iris - IRkernel - irodsfs - IronPython - ISA-L - ISL - isoCirc - IsoformSwitchAnalyzeR - IsoNet - IsoQuant - IsoSeq - ispc - itac - ITK - itpp - ITSTool - ITSx - iVar

i-cisTarget

An integrative genomics method for the prediction of regulatory features and cis-regulatory modules in Human, Mouse, and Fly

homepage: https://gbiomed.kuleuven.be/apps/lcb/i-cisTarget

version	versionsuffix	toolchain
20160602	-Python-2.7.11	intel/2016a

i-PI

A Python wrapper for (ab initio) (path integrals) molecular dynamics

homepage: https://github.com/i-pi/i-pi

version	versionsuffix	toolchain
1.0-20160213	-Python-2.7.11	intel/2016a

I-TASSER

I-TASSER is a set of pre-compiled binaries and scripts for protein structure and function modelling and comparison.

homepage: http://zhanglab.ccmb.med.umich.edu/I-TASSER/

version	toolchain
4.0	system
4.2	system
5.1	system

i7z

A better i7 (and now i3, i5) reporting tool for Linux

homepage: https://github.com/ajaiantilal/i7z

version	toolchain
20131012	GCCcore/11.2.0

ICA-AROMA

ICA-AROMA (i.e. 'ICA-based Automatic Removal Of Motion Artifacts') concerns a data-driven method to identify and remove motion-related independent components from fMRI data.

homepage: https://github.com/maartenmennes/ICA-AROMA

version	versionsuffix	toolchain
0.4.4-beta	-Python-3.6.6	foss/2018b

icc

C and C++ compiler from Intel

homepage: http://software.intel.com/en-us/intel-compilers/

version	versionsuffix	toolchain
2016.0.109		system
2016.0.109	-GCC-4.9.3-2.25	system
2016.1.150	-GCC-4.9.3-2.25	system
2016.2.181	-GCC-4.9.3-2.25	system
2016.2.181	-GCC-5.3.0-2.26	system
2016.3.210	-GCC-4.9.3-2.25	system
2016.3.210	-GCC-5.3.0-2.26	system
2016.3.210	-GCC-5.4.0-2.26	system
2017.0.098	-GCC-5.4.0-2.26	system
2017.1.132	-GCC-5.4.0-2.26	system
2017.1.132	-GCC-6.3.0-2.27	system
2017.2.174	-GCC-6.3.0-2.27	system
2017.4.196	-GCC-6.4.0-2.28	system
2017.5.239	-GCC-6.4.0-2.28	system
2017.6.256	-GCC-6.4.0-2.28	system
2017.7.259	-GCC-6.4.0-2.28	system
2018.0.128	-GCC-6.4.0-2.28	system
2018.1.163	-GCC-6.4.0-2.28	system
2018.2.199	-GCC-6.4.0-2.28	system
2018.3.222	-GCC-7.3.0-2.30	system
2018.5.274	-GCC-7.3.0-2.30	system
2019.0.117	-GCC-8.2.0-2.31.1	system
2019.1.144	-GCC-8.2.0-2.31.1	system
2019.2.187	-GCC-8.2.0-2.31.1	system
2019.3.199	-GCC-8.3.0-2.32	system
system	-GCC-system-2.29	system

iccifort

Intel C, C++ & Fortran compilers

homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/

version	versionsuffix	toolchain
2016.0.109		system
2016.0.109	-GCC-4.9.3-2.25	system
2016.1.150	-GCC-4.9.3-2.25	system
2016.2.181	-GCC-4.9.3-2.25	system
2016.2.181	-GCC-5.3.0-2.26	system
2016.3.210	-GCC-4.9.3-2.25	system
2016.3.210	-GCC-5.3.0-2.26	system
2016.3.210	-GCC-5.4.0-2.26	system
2017.0.098	-GCC-5.4.0-2.26	system
2017.1.132	-GCC-5.4.0-2.26	system
2017.1.132	-GCC-6.3.0-2.27	system
2017.2.174	-GCC-6.3.0-2.27	system
2017.4.196	-GCC-6.4.0-2.28	system
2017.5.239	-GCC-6.4.0-2.28	system
2018.0.128	-GCC-6.4.0-2.28	system
2018.1.163	-GCC-6.4.0-2.28	system
2018.2.199	-GCC-6.4.0-2.28	system
2018.3.222	-GCC-7.3.0-2.30	system
2018.5.274	-GCC-7.3.0-2.30	system
2019.0.117	-GCC-8.2.0-2.31.1	system
2019.1.144	-GCC-8.2.0-2.31.1	system
2019.2.187	-GCC-8.2.0-2.31.1	system
2019.3.199	-GCC-8.3.0-2.32	system
2019.4.243		system
2019.5.281		system
2020.0.166		system
2020.0.166	-GCC-9.2.0	system
2020.1.217		system
2020.4.304		system
system	-GCC-system-2.29	system

iccifortcuda

Intel C, C++ & Fortran compilers with CUDA toolkit

homepage: <(none)>

version	versionsuffix	toolchain
2016.10		system
2017.4.196	-GCC-6.4.0-2.28	system
2019a		system
2019b		system
2020a		system
2020b		system

iced

Implements the ICE normalization of hic data.

homepage: https://github.com/hiclib/iced

version	toolchain
0.5.10	foss/2022a

ichorCNA

ichorCNA is a tool for estimating the fraction of tumor in cell-free DNA from ultra-low-pass whole genome sequencing

homepage: https://github.com/broadinstitute/ichorCNA/wiki

version	toolchain
0.2.0	foss/2019b
0.3.2-20191219	foss/2020a

icmake

Icmake is a hybrid between a 'make' utility and a 'shell script' language. Originally, it was written to provide a useful tool for automatic program maintenance and system administrative tasks on old MS-DOS platforms.

homepage: http://icmake.sourceforge.net/

version	toolchain
7.23.02	foss/2016a

iCount

iCount: protein-RNA interaction analysis is a Python module and associated command-line interface (CLI), which provides all the commands needed to process iCLIP data on protein-RNA interactions.

homepage: https://github.com/tomazc/iCount

version	versionsuffix	toolchain
20180820	-Python-3.6.6	foss/2018b

ICU

ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications.

homepage: https://icu.unicode.org

version	toolchain
61.1	GCCcore/6.4.0, GCCcore/7.3.0
64.2	GCCcore/8.2.0, GCCcore/8.3.0
65.1	GCCcore/8.3.0
66.1	GCCcore/9.3.0
67.1	GCCcore/10.2.0
69.1	GCCcore/10.3.0, GCCcore/11.2.0
71.1	GCCcore/11.3.0
72.1	GCCcore/12.2.0
73.2	GCCcore/12.3.0
74.1	GCCcore/13.2.0

IDBA-UD

IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions.

homepage: http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/

version	toolchain
1.1.3	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/8.2.0-2.31.1, GCC/8.3.0, GCC/9.3.0, foss/2018a, foss/2018b

idemux

idemux - inline barcode demultiplexing Idemux is a command line tool designed to demultiplex paired-end FASTQ files from QuantSeq-Pool.

homepage: https://github.com/Lexogen-Tools/idemux

version	toolchain
0.1.6	GCCcore/10.2.0

IDG

Image Domain Gridding (IDG) is a fast method for convolutional resampling (gridding/degridding) of radio astronomical data (visibilities). Direction dependent effects (DDEs) or A-tems can be applied in the gridding process. The algorithm is described in "Image Domain Gridding: a fast method for convolutional resampling of visibilities", Van der Tol (2018). The implementation is described in "Radio-astronomical imaging on graphics processors", Veenboer (2020). Please cite these papers in publications using IDG.

homepage: https://idg.readthedocs.io/

version	toolchain
1.2.0	foss/2023b

ieeg-cli

IEEG.ORG is a collaborative initiative funded by the National Institutes of Neurological Disorders and Stroke. This initiative seeks to advance research towards the understanding of epilepsy by providing a platform for sharing data, tools and expertise between researchers.

homepage: https://www.ieeg.org/

version	toolchain
1.14.56	system

ifort

Fortran compiler from Intel

homepage: http://software.intel.com/en-us/intel-compilers/

version	versionsuffix	toolchain
2016.0.109		system
2016.0.109	-GCC-4.9.3-2.25	system
2016.1.150	-GCC-4.9.3-2.25	system
2016.2.181	-GCC-4.9.3-2.25	system
2016.2.181	-GCC-5.3.0-2.26	system
2016.3.210	-GCC-4.9.3-2.25	system
2016.3.210	-GCC-5.3.0-2.26	system
2016.3.210	-GCC-5.4.0-2.26	system
2017.0.098	-GCC-5.4.0-2.26	system
2017.1.132	-GCC-5.4.0-2.26	system
2017.1.132	-GCC-6.3.0-2.27	system
2017.2.174	-GCC-6.3.0-2.27	system
2017.4.196	-GCC-6.4.0-2.28	system
2017.5.239	-GCC-6.4.0-2.28	system
2017.6.256	-GCC-6.4.0-2.28	system
2017.7.259	-GCC-6.4.0-2.28	system
2018.0.128	-GCC-6.4.0-2.28	system
2018.1.163	-GCC-6.4.0-2.28	system
2018.2.199	-GCC-6.4.0-2.28	system
2018.3.222	-GCC-7.3.0-2.30	system
2018.5.274	-GCC-7.3.0-2.30	system
2019.0.117	-GCC-8.2.0-2.31.1	system
2019.1.144	-GCC-8.2.0-2.31.1	system
2019.2.187	-GCC-8.2.0-2.31.1	system
2019.3.199	-GCC-8.3.0-2.32	system
system	-GCC-system-2.29	system

IgBLAST

IgBLAST faclilitates the analysis of immunoglobulin and T cell receptor variable domain sequences.

homepage: https://ncbi.github.io/igblast

version	versionsuffix	toolchain
1.15.0	-x64-linux	system
1.18.0	-x64-linux	system
1.21.0	-x64-linux	system

IGMPlot

IGMPlot is a free open-source program developed to identify molecular interactions and prepare data to build 2D and 3D representations of them in the molecular environment.

homepage: http://igmplot.univ-reims.fr

version	toolchain
2.4.2	GCC/8.3.0, iccifort/2019.5.281
2.6.9b	GCC/11.2.0

igraph

igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++.

homepage: https://igraph.org

version	toolchain
0.7.1	foss/2018b, intel/2016b, intel/2017b
0.8.0	foss/2019b
0.8.2	foss/2020a
0.8.5	foss/2020b
0.9.1	foss/2020b, fosscuda/2020b
0.9.4	foss/2021a
0.9.5	foss/2021b
0.10.3	foss/2022a
0.10.6	foss/2022b
0.10.10	foss/2023a

IGV

This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files.

homepage: https://www.broadinstitute.org/software/igv/

version	versionsuffix	toolchain
2.3.68	-Java-1.7.0_80	system
2.3.80	-Java-1.7.0_80	system
2.5.0	-Java-11	system
2.8.0	-Java-11	system
2.9.4	-Java-11	system
2.12.3	-Java-11	system
2.16.0	-Java-11	system

igv-reports

Python application to generate self-contained igv.js pages that can be opened within a browser with "file" protocol.

homepage: https://github.com/igvteam/igv-reports

version	versionsuffix	toolchain
0.9.8	-Python-3.7.4	GCC/8.3.0

igvShiny

An htmlwidget version of igv, for RStudio and Shiny apps

homepage: https://github.com/gladkia/igvShiny

version	versionsuffix	toolchain
20240112	-R-4.2.1	foss/2022a

IGVTools

This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files. See also http://www.broadinstitute.org/software/igv/igvtools_commandline.

homepage: https://software.broadinstitute.org/software/igv/igvtools

version	versionsuffix	toolchain
2.3.68	-Java-1.7.0_80	system
2.3.72	-Java-1.7.0_80	system
2.3.75	-Java-1.7.0_80	system
2.4.18	-Java-1.8	system

iibff

GCC and GFortran based compiler toolchain with OpenMPI, BLIS, libFLAME, ScaLAPACK and FFTW.

homepage: <(none)>

version	toolchain
2020b	system

iimkl

Intel C/C++ and Fortran compilers, alongside Intel Math Kernel Library (MKL).

homepage: https://software.intel.com/en-us/intel-cluster-toolkit-compiler/

version	toolchain
2018a	system
2022a	system
2022b	system
2023a	system
2023b	system

iimpi

Intel C/C++ and Fortran compilers, alongside Intel MPI.

homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/

version	versionsuffix	toolchain
8.1.5	-GCC-4.9.3-2.25	system
2016.00	-GCC-4.9.3-2.25	system
2016.01	-GCC-4.9.3-2.25	system
2016.02	-GCC-4.9.3-2.25	system
2016.02	-GCC-5.3.0-2.26	system
2016.03	-GCC-4.9.3-2.25	system
2016.03	-GCC-5.3.0-2.26	system
2016.03	-GCC-5.4.0-2.26	system
2016b		system
2017.00	-GCC-5.4.0-2.26	system
2017.01	-GCC-5.4.0-2.26	system
2017.02	-GCC-6.3.0-2.27	system
2017.09		system
2017a		system
2017b		system
2018.00		system
2018.01		system
2018.02		system
2018.04		system
2018a		system
2018b		system
2019.00		system
2019.01		system
2019.02		system
2019.03		system
2019a		system
2019b		system
2020.00		system
2020.06-impi-18.5		system
2020.12		system
2020a		system
2020b		system
2021a		system
2021b		system
2022.00		system
2022.05		system
2022.09		system
2022.11		system
2022.12		system
2022a		system
2022b		system
2023.03		system
2023.07		system
2023.11		system
2023a		system
2023b		system
system	-GCC-system-2.29	system

iimpic

Intel C/C++ and Fortran compilers, alongside Intel MPI and CUDA.

homepage: <(none)>

version	toolchain
2016.10	system
2017b	system
2019a	system
2019b	system
2020a	system
2020b	system

IJulia

Julia kernel for Jupyter

homepage: https://github.com/JuliaLang/IJulia.jl

version	versionsuffix	toolchain
1.23.3	-Julia-1.6.7	system
1.24.0	-Julia-1.8.5	system

ILAMB

The International Land Model Benchmarking (ILAMB) project is a model-data intercomparison and integration project designed to improve the performance of land models and, in parallel, improve the design of new measurement campaigns to reduce uncertainties associated with key land surface processes.

homepage: https://www.ilamb.org/

version	versionsuffix	toolchain
2.5	-Python-3.8.2	foss/2020a

IMa2

IMa2 is a progam for population genetic analysis that can handle two or more populations.

homepage: https://bio.cst.temple.edu/~hey/software/software.htm#IMa2

version	toolchain
8.27.12	foss/2016a

IMa2p

IMa2p is a parallel implementation of IMa2, using OpenMPI-C++ - a Bayesian MCMC based method for inferring population demography under the IM (Isolation with Migration) model. http://dx.doi.org/10.1111/1755-0998.12437

homepage: https://github.com/arunsethuraman/ima2p

version	toolchain
20151123	foss/2016a
20160804	intel/2016b

imagecodecs

Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation, compression, and decompression functions for use in the tifffile, czifile, zarr, and other scientific image input/output modules.

homepage: https://github.com/cgohlke/imagecodecs

version	toolchain
2021.8.26	foss/2020b
2022.9.26	foss/2021a, foss/2022a

imageio

Imageio is a Python library that provides an easy interface to read and write a wide range of image data, including animated images, video, volumetric data, and scientific formats.

homepage: https://imageio.github.io

version	versionsuffix	toolchain
2.3.0	-Python-3.6.4	intel/2018a
2.5.0		foss/2019a
2.9.0		foss/2020b, fosscuda/2020b
2.9.0	-Python-3.7.4	foss/2019b, intel/2019b
2.10.5		foss/2021a
2.13.5		foss/2021b
2.22.2		foss/2022a
2.31.1		foss/2022b
2.33.1		gfbf/2023a

ImageJ

Image Processing and Analysis in Java

homepage: https://imagej.nih.gov/ij

version	versionsuffix	toolchain
1.51a		system
1.51i		system
1.51k		system
1.52q	-Java-1.8	system

ImageMagick

ImageMagick is a software suite to create, edit, compose, or convert bitmap images

homepage: https://www.imagemagick.org/

version	versionsuffix	toolchain
6.9.4-8		intel/2016a
7.0.1-6		intel/2016a
7.0.1-9		intel/2016a
7.0.2-9		intel/2016a
7.0.3-1		intel/2016b
7.0.5-4		intel/2017a
7.0.5-10		foss/2016b
7.0.7-8	-JasPer-1.900.1	intel/2017a
7.0.7-14		foss/2017b, intel/2017b
7.0.7-15		GCCcore/6.4.0
7.0.7-26		foss/2018a
7.0.7-30		GCCcore/6.4.0
7.0.7-30	-Ghostscript-9.22-cairo-1.14.12	GCCcore/6.4.0
7.0.7-39	-Ghostscript-9.23-cairo-1.14.12	GCCcore/6.4.0
7.0.8-11		GCCcore/7.3.0
7.0.8-46		GCCcore/8.2.0
7.0.9-5		GCCcore/8.3.0
7.0.10-1		GCCcore/9.3.0
7.0.10-35		GCCcore/10.2.0
7.0.11-14		GCCcore/10.3.0
7.1.0-4		GCCcore/11.2.0
7.1.0-37		GCCcore/11.3.0
7.1.0-53		GCCcore/12.2.0
7.1.1-15		GCCcore/12.3.0

imake

imake is a Makefile-generator that is intended to make it easier to develop software portably for multiple systems.

homepage: https://www.x.org/

version	toolchain
1.0.7	intel/2016a
1.0.8	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0

Imath

Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics

homepage: https://imath.readthedocs.io/en/latest/

version	toolchain
3.1.5	GCCcore/11.3.0
3.1.6	GCCcore/12.2.0
3.1.7	GCCcore/12.3.0
3.1.9	GCCcore/13.2.0

IMB

The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and global communication operations for a range of message sizes

homepage: https://software.intel.com/en-us/articles/intel-mpi-benchmarks

version	toolchain
4.1	foss/2016a, foss/2017a, intel/2017.02, intel/2017a
2018.1	intel/2017a
2019.3	gompi/2019a, iimpi/2019a
2021.3	gompi/2020b, gompi/2021b, gompi/2022a, gompi/2022b, iimpi/2022a, iimpi/2022b

imbalanced-learn

imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in datasets showing strong between-class imbalance.

homepage: https://github.com/scikit-learn-contrib/imbalanced-learn

version	versionsuffix	toolchain
0.2.1	-Python-2.7.12	intel/2016b
0.2.1	-Python-3.5.2	intel/2016b
0.3.3	-Python-3.6.4	foss/2018a
0.4.3	-Python-3.6.6	foss/2018b
0.7.0		foss/2020b
0.9.0		foss/2021b
0.10.1		foss/2022a

imgaug

This python library helps you with augmenting images for your machine learning projects. It converts a set of input images into a new, much larger set of slightly altered images.

homepage: https://imgaug.readthedocs.io/en/latest/

version	versionsuffix	toolchain
0.2.8	-Python-3.6.6	foss/2018b
0.4.0		foss/2021a, foss/2021b, foss/2022a
0.4.0	-CUDA-11.3.1	foss/2021a
0.4.0	-CUDA-11.4.1	foss/2021b
0.4.0	-CUDA-11.7.0	foss/2022a
0.4.0	-Python-3.7.4	foss/2019b

imkl

Intel oneAPI Math Kernel Library

homepage: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html

version	versionsuffix	toolchain
11.2.3.187		gimpi/2.11.5
11.3.0.109		iimpi/2016.00-GCC-4.9.3-2.25
11.3.1.150		iimpi/2016.01-GCC-4.9.3-2.25, iimpi/8.1.5-GCC-4.9.3-2.25
11.3.2.181		iimpi/2016.02-GCC-4.9.3-2.25, iimpi/2016.02-GCC-5.3.0-2.26, pompi/2016.03
11.3.3.210		iimpi/2016.03-GCC-4.9.3-2.25, iimpi/2016.03-GCC-5.3.0-2.26, iimpi/2016.03-GCC-5.4.0-2.26, iimpi/2016b, iimpic/2016.10, iompi/2016.07, iompi/2016.09-GCC-4.9.3-2.25, iompi/2016.09-GCC-5.4.0-2.26, pompi/2016.04, pompi/2016.09
2017.0.098		iimpi/2017.00-GCC-5.4.0-2.26
2017.1.132		gimpi/2017a, iimpi/2017.01-GCC-5.4.0-2.26, iimpi/2017a, iompi/2017.01, iompi/2017a
2017.2.174		iimpi/2017.02-GCC-6.3.0-2.27
2017.3.196		gompi/2017b, iimpi/2017b, iimpic/2017b, iompi/2017b
2017.4.239		iimpi/2017.09
2018.0.128		iimpi/2018.00
2018.1.163		iimpi/2018.01, iimpi/2018a, iompi/2018a
2018.1.163	-serial	iccifort/2018.1.163-GCC-6.4.0-2.28
2018.2.199		iimpi/2018.02, iompi/2018.02
2018.3.222		gimpi/2018b, gompi/2018b, iimpi/2018b, iompi/2018b
2018.4.274		iimpi/2018.04
2019.0.117		iimpi/2019.00
2019.1.144		gompi/2019a, iimpi/2019.01, iimpi/2019a, iimpic/2019a, iompi/2019.01
2019.2.187		iimpi/2019.02
2019.3.199		iimpi/2019.03
2019.5.281		gompi/2019b, gompic/2019b, iimpi/2019b, iimpic/2019b, iompi/2019b
2020.0.166		iimpi/2020.00
2020.1.217		gompi/2020a, iimpi/2020.06-impi-18.5, iimpi/2020a, iimpic/2020a, iompi/2020a
2020.4.304		NVHPC/21.2, gompi/2020b, gompic/2020b, iimpi/2020b, iimpic/2020b, iompi/2020b
2021.1.1		iimpi/2020.12
2021.2.0		gompi/2021a, iimpi/2021a, iompi/2021a
2021.3.0		gompi/2021a
2021.4.0		iompi/2021b, system
2022.0.1		system
2022.1.0		gompi/2022a, system
2022.2.0		system
2022.2.1		system
2023.0.0		system
2023.1.0		gompi/2023a, system
2023.2.0		system
2024.0.0		system

imkl-FFTW

FFTW interfaces using Intel oneAPI Math Kernel Library

homepage: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html

version	toolchain
2021.4.0	gompi/2021b, iimpi/2021b
2022.0.1	iimpi/2022.00
2022.1.0	iimpi/2022.05, iimpi/2022a
2022.2.0	iimpi/2022.09
2022.2.1	iimpi/2022.11, iimpi/2022b
2023.0.0	iimpi/2022.12
2023.1.0	iimpi/2023.03, iimpi/2023a
2023.2.0	iimpi/2023.07, iimpi/2023b
2024.0.0	iimpi/2023.11

IML

IML is a free library of C source code which implements algorithms for computing exact solutions to dense systems of linear equations over the integers.

homepage: https://cs.uwaterloo.ca/~astorjoh/iml.html

version	toolchain
1.0.5	gfbf/2022a

Imlib2

This is the Imlib 2 library - a library that does image file loading and saving as well as rendering, manipulation, arbitrary polygon support, etc. It does ALL of these operations FAST. Imlib2 also tries to be highly intelligent about doing them, so writing naive programs can be done easily, without sacrificing speed.

homepage: https://docs.enlightenment.org/api/imlib2/html/

version	toolchain
1.5.1	GCCcore/6.4.0

immunedeconv

immunedeconv is an R package for unified access to computational methods for estimating immune cell fractions from bulk RNA sequencing data.

homepage: https://github.com/icbi-lab/immunedeconv

version	versionsuffix	toolchain
2.0.2	-R-4.0.0	foss/2020a

IMOD

IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim Kremer, Quanren Xiong, and John Heumann at the University of Colorado.

homepage: http://bio3d.colorado.edu/imod/

version	versionsuffix	toolchain
4.7.15	_RHEL6-64_CUDA6.0	system
4.11.5		foss/2020b, fosscuda/2020b

impi

The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.

homepage: http://software.intel.com/en-us/intel-mpi-library/

version	versionsuffix	toolchain
3.2.2.006		system
4.0.0.028		system
4.0.0.028	-32bit	system
4.0.2.003		system
4.1.0.027		system
4.1.0.030		system
4.1.1.036		system
4.1.2.040		system
4.1.3.045		system
4.1.3.049		GCC/4.8.3, system
5.0.3.048		GCC/4.9.3
5.1.1.109		iccifort/2016.0.109-GCC-4.9.3-2.25
5.1.2.150		iccifort/2016.1.150-GCC-4.9.3-2.25
5.1.3.181		iccifort/2016.2.181-GCC-4.9.3-2.25, iccifort/2016.2.181-GCC-5.3.0-2.26, iccifort/2016.3.210-GCC-4.9.3-2.25, iccifort/2016.3.210-GCC-5.3.0-2.26, iccifort/2016.3.210-GCC-5.4.0-2.26, iccifortcuda/2016.10
2017.0.098		iccifort/2017.0.098-GCC-5.4.0-2.26
2017.1.132		GCC/5.4.0-2.26, iccifort/2017.1.132-GCC-5.4.0-2.26, iccifort/2017.1.132-GCC-6.3.0-2.27
2017.2.174		iccifort/2017.2.174-GCC-6.3.0-2.27
2017.3.196		GCC/6.4.0-2.28, gcccuda/2017b, iccifort/2017.4.196-GCC-6.4.0-2.28, iccifortcuda/2017.4.196-GCC-6.4.0-2.28
2017.4.239		iccifort/2017.5.239-GCC-6.4.0-2.28
2018.0.128		iccifort/2018.0.128-GCC-6.4.0-2.28
2018.1.163		GCC/6.4.0-2.28, iccifort/2018.1.163-GCC-6.4.0-2.28
2018.2.199		iccifort/2018.2.199-GCC-6.4.0-2.28
2018.3.222		GCC/7.3.0-2.30, iccifort/2018.3.222-GCC-7.3.0-2.30
2018.4.274		iccifort/2018.5.274-GCC-7.3.0-2.30, iccifort/2019.1.144-GCC-8.2.0-2.31.1, iccifortcuda/2019a
2018.5.288		iccifort/2019.5.281, iccifort/2020.1.217, iccifortcuda/2019b
2019.0.117		iccifort/2019.0.117-GCC-8.2.0-2.31.1
2019.1.144		iccifort/2019.1.144-GCC-8.2.0-2.31.1
2019.2.187		iccifort/2019.2.187-GCC-8.2.0-2.31.1
2019.3.199		iccifort/2019.3.199-GCC-8.3.0-2.32
2019.6.166		iccifort/2020.0.166-GCC-9.2.0
2019.7.217		iccifort/2020.1.217, iccifortcuda/2020a
2019.9.304		iccifort/2020.4.304, iccifortcuda/2020b
2019.12.320		iccifort/2020.4.304
2021.1.1		intel-compilers/2021.1.2
2021.2.0		intel-compilers/2021.2.0
2021.3.0		intel-compilers/2021.3.0
2021.4.0		intel-compilers/2021.4.0
2021.5.0		intel-compilers/2022.0.1
2021.6.0		intel-compilers/2022.1.0
2021.7.0		intel-compilers/2022.2.0
2021.7.1		intel-compilers/2022.2.1
2021.8.0		intel-compilers/2023.0.0
2021.9.0		intel-compilers/2023.1.0
2021.10.0		intel-compilers/2023.2.1
2021.11.0		intel-compilers/2024.0.0
system		iccifort/system-GCC-system-2.29

IMPUTE2

IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009

homepage: http://mathgen.stats.ox.ac.uk/impute/impute_v2.html

version	versionsuffix	toolchain
2.3.0	_x86_64_dynamic	system
2.3.0	_x86_64_static	system
2.3.2	_x86_64_dynamic	system
2.3.2	_x86_64_static	system

imutils

A series of convenience functions to make basic image processing operations such as translation, rotation, resizing, skeletonization, and displaying Matplotlib images easier with OpenCV and Python.

homepage: https://github.com/jrosebr1/imutils

version	versionsuffix	toolchain
0.5.4		fosscuda/2020b
0.5.4	-CUDA-11.7.0	foss/2022a

InChI

The IUPAC International Chemical Identifier (InChI TM) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources thus enabling easier linking of diverse data compilations.

homepage: https://www.inchi-trust.org/

version	toolchain
1.06	GCC/10.3.0

indicators

• Thread-safe progress bars and spinners - Header-only library. Grab a copy of include/indicators. - Single-header version in single_include/indicators.

homepage: https://github.com/p-ranav/indicators

version	toolchain
2.2	GCCcore/11.2.0, GCCcore/11.3.0

Inelastica

Python package for eigenchannels, vibrations and inelastic electron transport based on SIESTA/TranSIESTA DFT.

homepage: https://github.com/tfrederiksen/inelastica

version	versionsuffix	toolchain
1.3.5	-Python-2.7.15	intel/2018b

inferCNV

InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence for somatic large-scale chromosomal copy number alterations, such as gains or deletions of entire chromosomes or large segments of chromosomes.

homepage: https://github.com/broadinstitute/inferCNV/wiki

version	versionsuffix	toolchain
1.0.4	-Python-3.7.2-R-3.6.0	foss/2019a
1.2.1	-Python-3.7.4	foss/2019b
1.3.3		foss/2020b, foss/2021a
1.3.3	-Python-3.8.2	foss/2020a
1.10.1	-R-4.1.2	foss/2021b
1.12.0	-R-4.2.1	foss/2022a
1.14.2	-R-4.2.2	foss/2022b

infercnvpy

Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.

homepage: https://github.com/icbi-lab/infercnvpy

version	toolchain
0.4.0	foss/2021b
0.4.2	foss/2022a
0.4.3	foss/2023a

Inferelator

Inferelator 3.0 is a package for gene regulatory network inference that is based on regularized regression.

homepage: https://github.com/flatironinstitute/inferelator

version	toolchain
0.6.1	foss/2022a

Infernal

Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities.

homepage: http://eddylab.org/infernal/

version	toolchain
1.1.2	foss/2016b, foss/2018b, intel/2017a, intel/2018b
1.1.4	foss/2020b, foss/2021a, foss/2021b, foss/2022a, foss/2022b

inflection

inflection is a package that finds the inflection point of a planar curve which is given as a data frame of discrete (xi,yi) points

homepage: https://github.com/dchristop/inflection

version	versionsuffix	toolchain
1.3.5	-R-4.3.2	foss/2023a

Infomap

Multi-level network clustering based on the Map equation.

homepage: https://www.mapequation.org/code.html#Linux

version	toolchain
20190308	GCC/8.2.0-2.31.1

inih

Direct Rendering Manager runtime library.

homepage: https://dri.freedesktop.org

version	toolchain
57	GCCcore/12.3.0

inline

Functionality to dynamically define R functions and S4 methods with 'inlined' C, C++ or Fortran code supporting the .C and .Call calling conventions.

homepage: https://cran.r-project.org/web/packages/inline

version	versionsuffix	toolchain
0.3.19	-R-4.0.4	foss/2020b

InParanoid

InParanoid: ortholog groups with inparalogs.

homepage: https://inparanoid.sbc.su.se

version	toolchain
5.0-20220607	GCC/10.3.0

inputproto

X.org InputProto protocol headers.

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
2.3.1	foss/2016a, gimkl/2.11.5, intel/2016a
2.3.2	intel/2016a

Inspector

Intel Inspector is a dynamic memory and threading error checking tool for users developing serial and parallel applications

homepage: https://software.intel.com/en-us/inspector

version	toolchain
2013_update6	system
2013_update7	system
2016_update3	system
2017_update1	system
2017_update2	system
2018_update1	system
2018_update2	system
2018_update3	system
2019_update2	system
2019_update5	system
2021.4.0	system
2022.0.0	system
2022.1.0	system
2023.2.0	system

IntaRNA

Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites

homepage: https://github.com/BackofenLab/IntaRNA

version	versionsuffix	toolchain
2.3.1	-Python-2.7.15	foss/2018b

INTEGRATE

INTEGRATE is a tool calling gene fusions with exact fusion junctions and genomic breakpoints by combining RNA-Seq and WGS data. It is highly sensitive and accurate by applying a fast split-read mapping algorithm based on Burrow-Wheeler transform.

homepage: https://sourceforge.net/p/integrate-fusion/wiki/Home/

version	toolchain
0.2.6	GCCcore/8.2.0

INTEGRATE-Neo

INTEGRATE-Neo is a gene fusion neoantigen discovering tool using next-generation sequencing data. It is written in C++ and Python.

homepage: <>

version	versionsuffix	toolchain
1.2.1	-Python-3.6.6	foss/2018b

intel

Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL).

homepage: https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain

version	versionsuffix	toolchain
2016.00		system
2016.01		system
2016.02	-GCC-4.9	system
2016.02	-GCC-5.3	system
2016.03	-GCC-4.9	system
2016.03	-GCC-5.3	system
2016.03	-GCC-5.4	system
2016a		system
2016b		system
2017.00		system
2017.01		system
2017.02		system
2017.09		system
2017a		system
2017b		system
2018.00		system
2018.01		system
2018.02		system
2018.04		system
2018a		system
2018b		system
2019.00		system
2019.01		system
2019.02		system
2019.03		system
2019a		system
2019b		system
2020.00		system
2020.06-impi-18.5		system
2020.12		system
2020a		system
2020b		system
2021a		system
2021b		system
2022.00		system
2022.05		system
2022.09		system
2022.11		system
2022.12		system
2022a		system
2022b		system
2023.03		system
2023.07		system
2023.11		system
2023a		system
2023b		system

intel-compilers

Intel C, C++ & Fortran compilers (classic and oneAPI)

homepage: https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html

version	toolchain
2021.1.2	system
2021.2.0	system
2021.3.0	system
2021.4.0	system
2022.0.1	system
2022.0.2	system
2022.1.0	system
2022.2.0	system
2022.2.1	system
2023.0.0	system
2023.1.0	system
2023.2.1	system
2024.0.0	system

IntelClusterChecker

Intel Cluster Checker verifies the configuration and performance of Linux OS-based clusters. Anomalies and performance differences can be identified and practical resolutions provided.

homepage: https://software.intel.com/en-us/cluster-checker

version	toolchain
2017.1.016	system
2021.5.0	system

intelcuda

Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit

homepage: <(none)>

version	toolchain
2016.10	system
2017b	system
2019a	system
2019b	system
2020a	system
2020b	system

IntelDAAL

Intel® Data Analytics Acceleration Library (Intel® DAAL) is the library of Intel® architecture optimized building blocks covering all stages of data analytics: data acquisition from a data source, preprocessing, transformation, data mining, modeling, validation, and decision making.

homepage: https://software.intel.com/en-us/daal

version	toolchain
2019.4.007	system

IntelPython

Intel® Distribution for Python. Powered by Anaconda. Accelerating Python* performance on modern architectures from Intel.

homepage: https://software.intel.com/en-us/intel-distribution-for-python

version	versionsuffix	toolchain
2.7.15	-2019.2.066	system
3.6.8	-2019.2.066	system

InterOp

The Illumina InterOp libraries are a set of common routines used for reading InterOp metric files produced by Illumina sequencers including NextSeq 1k/2k and NovaSeqX. These libraries are backwards compatible and capable of supporting prior releases of the software, with one exception: GA systems have been excluded.

homepage: https://illumina.github.io/interop/

version	toolchain
1.2.4	foss/2021a

InterProScan

InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource [code only: libraries and external binaries but no data].

homepage: https://www.ebi.ac.uk/interpro/

version	toolchain
5.26-65.0	intel/2017b
5.27-66.0	intel/2017b
5.28-67.0	intel/2018a
5.52-86.0	GCCcore/10.3.0
5.55-88.0	foss/2021a
5.62-94.0	foss/2022b

InterProScan_data

InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource [data only].

homepage: https://www.ebi.ac.uk/interpro/

version	toolchain
5.55-88.0	foss/2021a

intervaltree

An interval tree can be used to efficiently find a set of numeric intervals overlapping or containing another interval. This library provides a basic implementation of an interval tree using C++ templates, allowing the insertion of arbitrary types into the tree.

homepage: https://github.com/ekg/intervaltree

version	toolchain
0.1	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.3.0, GCCcore/9.3.0

intervaltree-python

A mutable, self-balancing interval tree. Queries may be by point, by range overlap, or by range containment.

homepage: https://github.com/chaimleib/intervaltree

version	versionsuffix	toolchain
3.0.2	-Python-3.6.6	foss/2018b
3.1.0		GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0

intltool

intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.

homepage: http://freedesktop.org/wiki/Software/intltool/

version	versionsuffix	toolchain
0.51.0		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
0.51.0	-Perl-5.20.3	intel/2016a
0.51.0	-Perl-5.22.1	foss/2016a, intel/2016a
0.51.0	-Perl-5.24.0	GCCcore/4.9.3, GCCcore/5.4.0, foss/2016b, gimkl/2017a, intel/2016b
0.51.0	-Perl-5.24.1	GCCcore/6.3.0, intel/2017a
0.51.0	-Perl-5.26.0	GCCcore/6.4.0
0.51.0	-Perl-5.26.1	GCCcore/6.4.0
0.51.0	-Perl-5.28.0	GCCcore/7.3.0

io_lib

Io_lib is a library of file reading and writing code to provide a general purpose trace file (and Experiment File) reading interface. The programmer simply calls the (eg) read_reading to create a "Read" C structure with the data loaded into memory. It has been compiled and tested on a variety of unix systems, MacOS X and MS Windows.

homepage: http://sourceforge.net/projects/staden/files/io_lib/

version	toolchain
1.14.8	foss/2016a

ioapi

The Models-3/EDSS Input/Output Applications Programming Interface (I/O API) provides the environmental model developer with an easy-to-learn, easy-to-use programming library for data storage and access, available from both Fortran and C. The same routines can be used for both file storage (using netCDF files) and model coupling (using PVM mailboxes). It is the standard data access library for both the NCSC/CMAS's EDSS project and EPA's Models-3, CMAQ, and SMOKE, as well as various other atmospheric and hydrological modeling systems.

homepage: https://www.cmascenter.org/ioapi/

version	versionsuffix	toolchain
3.2-2020111	-nocpl	gompi/2019b

iodata

Python library for reading, writing, and converting computational chemistry file formats and generating input files.

homepage: https://github.com/theochem/iodata

version	toolchain
1.0.0a2	intel/2022a

iomkl

Compiler toolchain including Intel compilers, Open MPI and Intel Math Kernel Library (MKL).

homepage: https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html

version	toolchain
2016.07	system
2016.09-GCC-4.9.3-2.25	system
2016.09-GCC-5.4.0-2.26	system
2017.01	system
2017a	system
2017b	system
2018.02	system
2018a	system
2018b	system
2019.01	system
2019b	system
2020a	system
2020b	system
2021a	system
2021b	system

iompi

Intel C/C++ and Fortran compilers, alongside Open MPI.

homepage: https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html

version	toolchain
2016.07	system
2016.09-GCC-4.9.3-2.25	system
2016.09-GCC-5.4.0-2.26	system
2017.01	system
2017a	system
2017b	system
2018.02	system
2018a	system
2018b	system
2019.01	system
2019b	system
2020a	system
2020b	system
2021a	system
2021b	system

IonQuant

IonQuant is a fast and comprehensive tool for MS1 precursor intensity-based quantification for timsTOF PASEF DDA and non-timsTOF (e.g., Orbitrap) data. It enables label-free quantification with false discovery (FDR) controlled match-between-runs (MBR). It can also be used for quantification in labelling-based experiments such as those involving SILAC, dimethyl, or similar labelling strategies. IonQuant is available as part of FragPipe.

homepage: https://ionquant.nesvilab.org/

version	versionsuffix	toolchain
1.10.12	-Java-11	system

IOR

The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, or HDF5 interfaces.

homepage: https://github.com/hpc/ior

version	versionsuffix	toolchain
3.0.1	-mpiio	foss/2016a
3.2.1		gompi/2019b
3.3.0		gompi/2020b, gompi/2021a, gompi/2022a

IOzone

IOzone is a filesystem benchmark tool. The benchmark generates and measures a variety of file operations. Iozone has been ported to many machines and runs under many operating systems.

homepage: http://www.iozone.org/

version	toolchain
3.434	foss/2016a

iperf

iperf is a tool for active measurements of the maximum achievable bandwidth on IP networks.

homepage: https://software.es.net/iperf

version	toolchain
2.1.9	GCCcore/10.2.0
3.15	system
3.16	system

IPM

IPM is a portable profiling infrastructure for parallel codes. It provides a low-overhead profile of application performance and resource utilization in a parallel program. Communication, computation, and IO are the primary focus.

homepage: https://github.com/nerscadmin/IPM

version	toolchain
2.0.6	gompi/2019b, gompi/2020a, iimpi/2019b, iimpi/2020a, iompi/2020a

Ipopt

IPOPT (Interior Point Optimizer, pronounced Eye-Pea-Opt) is an open source software package for large-scale nonlinear optimization.

homepage: https://projects.coin-or.org/Ipopt

version	toolchain
3.12.9	foss/2017b
3.12.13	intel/2019a

ipp

Intel Integrated Performance Primitives (Intel IPP) is an extensive library of multicore-ready, highly optimized software functions for multimedia, data processing, and communications applications. Intel IPP offers thousands of optimized functions covering frequently used fundamental algorithms.

homepage: https://software.intel.com/en-us/articles/intel-ipp/

version	toolchain
7.0.5.233	system
8.1.0.144	system
9.0.1.150	system
2017.1.132	system

IPy

Class and tools for handling of IPv4 and IPv6 addresses and networks

homepage: https://pypi.python.org/pypi/IPy

version	toolchain
0.83	system

ipympl

Leveraging the Jupyter interactive widgets framework, ipympl enables the interactive features of matplotlib in the Jupyter notebook and in JupyterLab. Besides, the figure canvas element is a proper Jupyter interactive widget which can be positioned in interactive widget layouts.

homepage: https://matplotlib.org/ipympl

version	toolchain
0.9.3	foss/2022a, foss/2023a

ipyparallel

ipyparallel is a Python package and collection of CLI scripts for controlling clusters for Jupyter

homepage: https://ipyparallel.readthedocs.io

version	versionsuffix	toolchain
6.2.2	-Python-3.6.4	foss/2018a

ipyrad

ipyrad is an interactive toolkit for assembly and analysis of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies.

homepage: https://ipyrad.readthedocs.io

version	versionsuffix	toolchain
0.6.15	-Python-2.7.13	intel/2017a

IPython

IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. Support for interactive data visualization and use of GUI toolkits. Flexible, embeddable interpreters to load into your own projects. Easy to use, high performance tools for parallel computing.

homepage: https://ipython.org/index.html

version	versionsuffix	toolchain
3.2.3	-Python-2.7.11	foss/2016a, intel/2016a
4.2.0	-Python-2.7.11	intel/2016a
5.0.0	-Python-2.7.11	foss/2016a
5.0.0	-Python-3.5.1	foss/2016a
5.1.0	-Python-2.7.12	foss/2016b, intel/2016b
5.1.0	-Python-3.5.2	intel/2016b
5.2.2	-Python-2.7.12	intel/2016b
5.3.0	-Python-2.7.13	intel/2017a
5.7.0	-Python-2.7.14	foss/2018a, intel/2018a
5.8.0	-Python-2.7.14	foss/2017b, fosscuda/2017b, intel/2017b, intelcuda/2017b
5.8.0	-Python-2.7.15	foss/2018b, foss/2019a, fosscuda/2018b, fosscuda/2019a, intel/2018b
5.8.0	-Python-3.6.3	foss/2017b, fosscuda/2017b, intel/2017b, intelcuda/2017b
5.10.0	-Python-2.7.18	foss/2021b
6.2.1	-Python-3.6.4	foss/2017a
6.3.1	-Python-3.6.4	intel/2018a
6.4.0	-Python-3.6.4	foss/2018a
7.2.0	-Python-3.6.6	foss/2018b, fosscuda/2018b, intel/2018b
7.7.0	-Python-3.7.2	foss/2019a, fosscuda/2019a, intel/2019a
7.9.0	-Python-3.7.4	foss/2019b, fosscuda/2019b, intel/2019b
7.13.0	-Python-3.8.2	foss/2020a, intel/2020a
7.15.0	-Python-3.8.2	foss/2020a, intel/2020a
7.18.1		GCCcore/10.2.0
7.25.0		GCCcore/10.3.0
7.26.0		GCCcore/11.2.0
8.5.0		GCCcore/11.3.0
8.14.0		GCCcore/12.2.0, GCCcore/12.3.0
8.17.2		GCCcore/13.2.0

IQ-TREE

Efficient phylogenomic software by maximum likelihood

homepage: http://www.iqtree.org/

version	versionsuffix	toolchain
1.5.5	-omp-mpi	foss/2016a
1.6.6		intel/2018a
1.6.12		foss/2018b, foss/2020a, intel/2019b
2.1.2		foss/2020a, gompi/2020b
2.1.3		gompi/2021a
2.2.1		gompi/2021b
2.2.2.3		gompi/2022a
2.2.2.6		gompi/2022a, gompi/2022b
2.2.2.7		gompi/2023a

Iris

A module for improving the insertion sequences of structural variant calls

homepage: https://github.com/mkirsche/Iris

version	versionsuffix	toolchain
1.0.5	-Java-15	GCC/11.2.0

IRkernel

The R kernel for the 'Jupyter' environment executes R code which the front-end (Jupyter Notebook or other front-ends) submits to the kernel via the network.

homepage: https://irkernel.github.io

version	versionsuffix	toolchain
0.8.15	-R-3.4.3-Python-2.7.14	foss/2017b, intel/2017b
1.1	-R-3.6.2-Python-3.7.4	foss/2019b, fosscuda/2019b
1.1	-R-3.6.3-Python-3.8.2	foss/2020a
1.2	-R-4.0.0-Python-3.8.2	foss/2020a
1.2	-R-4.1.0	foss/2021a
1.3	-R-4.2.0	foss/2021b
1.3.2	-R-4.2.1	foss/2022a

irodsfs

FUSE implementation of iRODS Client written in Golang.

homepage: https://github.com/cyverse/irodsfs

version	versionsuffix	toolchain
0.8.9	-linux-amd64	system
0.8.11	-linux-amd64	system
0.8.12	-linux-amd64	system

IronPython

IronPython is an open-source implementation of the Python programming language which is tightly integrated with the .NET Framework. IronPython can use the .NET Framework and Python libraries, and other .NET languages can use Python code just as easily.

homepage: http://ironpython.net/

version	toolchain
2.7	intel/2016b

ISA-L

Intelligent Storage Acceleration Library

homepage: https://github.com/intel/isa-l

version	toolchain
2.30.0	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0
2.31.0	GCCcore/13.2.0

ISL

isl is a library for manipulating sets and relations of integer points bounded by linear constraints.

homepage: https://libisl.sourceforge.io

version	toolchain
0.14	GCC/4.9.2
0.15	GCC/4.9.3-2.25, GNU/4.9.3-2.25, foss/2016a
0.16	GCC/4.9.3-2.25
0.17	foss/2016a
0.23	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/9.3.0
0.24	GCCcore/11.2.0, GCCcore/11.3.0
0.26	GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

isoCirc

isoCirc: computational pipeline to identify high-confidence BSJs and full-length circRNA isoforms from isoCirc long-read data

homepage: https://github.com/Xinglab/isoCirc

version	toolchain
1.0.4	foss/2020b

IsoformSwitchAnalyzeR

Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.

homepage: https://bioconductor.org/packages/release/bioc/html/IsoformSwitchAnalyzeR.html

version	versionsuffix	toolchain
1.18.0	-R-4.2.1	foss/2022a

IsoNet

IsoNet stands for for ISOtropic reconstructioN of Electron Tomography. It trains deep convolutional neural networks to reconstruct meaningful contents in the mis sing wedge for electron tomography, and to increase signal-to-noise ratio, using the information learned from the original tomogram. The software requires tomograms as input. Observing at about 30A resolution, the IsoNet generated tomograms are largely isotropic.

homepage: https://github.com/Heng-Z/IsoNet

version	toolchain
0.1_20210822_04_674f67f	fosscuda/2020b

IsoQuant

IsoQuant is a tool for the genome-based analysis of long RNA reads, such as PacBio or Oxford Nanopores. IsoQuant allows to reconstruct and quantify transcript models with high precision and decent recall. If the reference annotation is given, IsoQuant also assigns reads to the annotated isoforms based on their intron and exon structure. IsoQuant further performs annotated gene, isoform, exon and intron quantification. If reads are grouped (e.g. according to cell type), counts are reported according to the provided grouping.

homepage: https://github.com/ablab/IsoQuant

version	toolchain
3.3.0	foss/2022b

IsoSeq

IsoSeq v3 contains the newest tools to identify transcripts in PacBio single-molecule sequencing data. Starting in SMRT Link v6.0.0, those tools power the IsoSeq GUI-based analysis application. A composable workflow of existing tools and algorithms, combined with a new clustering technique, allows to process the ever-increasing yield of PacBio machines with similar performance to IsoSeq versions 1 and 2. Starting with version 3.4, support for UMI and cell barcode based deduplication has been added.

homepage: https://github.com/PacificBiosciences/ioseq3

version	versionsuffix	toolchain
3.8.2	-linux-x86_64	system
4.0.0	-linux-x86_64	system

ispc

Intel SPMD Program Compilers; An open-source compiler for high-performance SIMD programming on the CPU. ispc is a compiler for a variant of the C programming language, with extensions for 'single program, multiple data' (SPMD) programming. Under the SPMD model, the programmer writes a program that generally appears to be a regular serial program, though the execution model is actually that a number of program instances execute in parallel on the hardware.

homepage: http://ispc.github.io/ , https://github.com/ispc/ispc/

version	toolchain
1.6.0	system
1.10.0	system
1.12.0	system
1.16.0	system

itac

The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays.

homepage: https://software.intel.com/en-us/intel-trace-analyzer/

version	toolchain
8.0.0.011	system
8.1.4.045	system
9.0.3.051	system
2017.1.024	system
2018.1.017	system
2018.3.022	system
2019.2.026	system
2019.4.036	system
2021.2.0	system
2021.5.0	system
2021.6.0	system
2021.10.0	system

ITK

Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data.

homepage: https://itk.org

version	versionsuffix	toolchain
4.12.2	-Python-2.7.12	foss/2016b
4.13.0	-Python-2.7.14	foss/2018a
4.13.0	-Python-3.6.4	foss/2018a
4.13.1	-Python-2.7.14	foss/2018a
4.13.1	-Python-2.7.15	foss/2018b
4.13.1	-Python-3.6.4	foss/2018a
4.13.1	-Python-3.6.6	foss/2018b
4.13.1	-Python-3.7.4	foss/2019b
5.0.1	-Python-3.7.2	foss/2019a
5.0.1	-Python-3.7.4	foss/2019b
5.0b01	-Python-3.6.6	foss/2018b
5.1.2		foss/2020a, fosscuda/2020a
5.1.2	-Python-3.8.2	foss/2020a, fosscuda/2020a
5.2.1		foss/2020b, foss/2021a, foss/2021b, foss/2022a, fosscuda/2020b
5.3.0		foss/2023a

itpp

IT++ is a C++ library of mathematical, signal processing and communication classes and functions. Its main use is in simulation of communication systems and for performing research in the area of communications.

homepage: https://sourceforge.net/projects/itpp/

version	toolchain
4.3.1	foss/2019b

ITSTool

ITS Tool allows you to translate your XML documents with PO files

homepage: http://itstool.org/

version	versionsuffix	toolchain
2.0.5	-Python-2.7.14	intel/2018a
2.0.5	-Python-2.7.15	foss/2018b
2.0.6	-Python-3.7.2	GCCcore/8.2.0
2.0.7		GCCcore/11.3.0, GCCcore/12.3.0

ITSx

ITSx: Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing.

homepage: https://microbiology.se/software/itsx/

version	toolchain
1.1.2	GCCcore/9.3.0
1.1.3	GCCcore/10.3.0, GCCcore/11.3.0

iVar

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

homepage: https://github.com/andersen-lab/ivar

version	toolchain
1.0.1	foss/2018b
1.3.1	GCC/10.2.0, GCC/9.3.0

J

JAGS - Jansson - Jasmine - JasPer - Java - JavaFX - jax - JAXFrontCE - jbigkit - Jblob - jedi - jedi-language-server - Jellyfish - jemalloc - jhbuild - JiTCODE - jModelTest - Jmol - Jorg - joypy - jq - json-c - json-fortran - JSON-GLib - JsonCpp - JUBE - Judy - Julia - JUnit - Jupyter-bundle - jupyter-contrib-nbextensions - jupyter-matlab-proxy - jupyter-resource-usage - jupyter-rsession-proxy - jupyter-server - jupyter-server-proxy - JupyterHub - JupyterLab - jupyterlab-lmod - jupyterlmod - JupyterNotebook - JWM - jxrlib

JAGS

JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation

homepage: http://mcmc-jags.sourceforge.net/

version	toolchain
4.2.0	foss/2016a, intel/2016a, intel/2017a
4.3.0	foss/2017b, foss/2018b, foss/2019a, foss/2019b, foss/2020a, foss/2020b, foss/2021a, foss/2021b, fosscuda/2020b, intel/2017b
4.3.1	foss/2022a
4.3.2	foss/2022b

Jansson

Jansson is a C library for encoding, decoding and manipulating JSON data. Its main features and design principles are: * Simple and intuitive API and data model * Comprehensive documentation * No dependencies on other libraries * Full Unicode support (UTF-8) * Extensive test suite

homepage: http://www.digip.org/jansson/

version	toolchain
2.6	GCC/4.8.3
2.13.1	GCC/10.2.0, GCC/11.2.0
2.14	GCC/11.3.0

Jasmine

SV Merging Across Samples

homepage: https://github.com/mkirsche/Jasmine

version	versionsuffix	toolchain
1.1.4	-Java-15	GCC/11.2.0

JasPer

The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.

homepage: https://www.ece.uvic.ca/~frodo/jasper/

version	toolchain
1.900.1	GCCcore/5.4.0, GCCcore/6.4.0, GCCcore/8.2.0, foss/2016a, foss/2016b, foss/2017a, intel/2016a, intel/2016b, intel/2017a
2.0.10	intel/2016b
2.0.12	GCCcore/6.4.0, foss/2016b, intel/2017a
2.0.14	GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
2.0.16	GCCcore/9.3.0
2.0.24	GCCcore/10.2.0
2.0.28	GCCcore/10.3.0
2.0.33	GCCcore/11.2.0, GCCcore/11.3.0
4.0.0	GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

Java

Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.

homepage: https://java.com/

version	versionsuffix	toolchain
1.6.0_24		system
1.7.0_10		system
1.7.0_15		system
1.7.0_21		system
1.7.0_40		system
1.7.0_45		system
1.7.0_60		system
1.7.0_75		system
1.7.0_76		system
1.7.0_79		system
1.7.0_80		system
1.8		system
1.8.0_20		system
1.8.0_25		system
1.8.0_31		system
1.8.0_40		system
1.8.0_45		system
1.8.0_60		system
1.8.0_65		system
1.8.0_66		system
1.8.0_72		system
1.8.0_74		system
1.8.0_77		system
1.8.0_92		system
1.8.0_112		system
1.8.0_121		system
1.8.0_131		system
1.8.0_141		system
1.8.0_144		system
1.8.0_152		system
1.8.0_162		system
1.8.0_172		system
1.8.0_181		system
1.8.0_192		system
1.8.0_202		system
1.8.0_212		system
1.8.0_221		system
1.8.0_231		system
1.8.0_241		system
1.8.0_271		system
1.8.0_281		system
1.8.0_292	-OpenJDK	system
1.8.0_311		system
1.8_191	-b26-OpenJDK	system
1.8_265	-b01-OpenJDK-aarch64	system
1.9.0.4		system
8		system
8.345		system
8.362		system
8.402		system
11		system
11.0.2		system
11.0.6	-ppc64le	system
11.0.8	-aarch64	system
11.0.16		system
11.0.18		system
11.0.20		system
13		system
13.0.2		system
15		system
15.0.1		system
16		system
16.0.1		system
17		system
17.0.1		system
17.0.2		system
17.0.4		system
17.0.6		system
19		system
19.0.2		system
21		system
21.0.2		system

JavaFX

OpenJFX is an open source, next generation client application platform for desktop, mobile and embedded systems built on Java

homepage: https://openjfx.io/

version	versionsuffix	toolchain
11.0.2	_linux-x64_bin-sdk	system

jax

Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more

homepage: https://pypi.python.org/pypi/jax

version	versionsuffix	toolchain
0.2.19		foss/2020b, fosscuda/2020b
0.2.20		foss/2021a
0.2.24		foss/2021a
0.2.24	-CUDA-11.3.1	foss/2021a
0.3.9		foss/2021a
0.3.9	-CUDA-11.3.1	foss/2021a
0.3.14	-CUDA-11.7.0	foss/2022a
0.3.23		foss/2022a
0.3.23	-CUDA-11.4.1	foss/2021b
0.3.25		foss/2022a
0.3.25	-CUDA-11.7.0	foss/2022a
0.4.4		foss/2022a
0.4.4	-CUDA-11.7.0	foss/2022a

JAXFrontCE

JAXFront is a technology to generate graphical user interfaces on multiple channels (Java Swing, HTML, PDF) on the basis of an XML schema.

homepage: http://www.jaxfront.org/pages/free_community_edition.html

version	toolchain
2.75	system

jbigkit

JBIG-KIT is a software implementation of the JBIG1 data compression standard (ITU-T T.82), which was designed for bi-level image data, such as scanned documents.

homepage: https://www.cl.cam.ac.uk/~mgk25/jbigkit/

version	toolchain
2.1	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0

Jblob

Jblob - WDC Climate dataset download

homepage: https://www.wdc-climate.de/ui/info?site=jblob

version	toolchain
3.0	system

jedi

Jedi - an awesome autocompletion, static analysis and refactoring library for Python.

homepage: https://github.com/davidhalter/jedi

version	toolchain
0.18.1	GCCcore/11.3.0
0.19.1	GCCcore/13.2.0

jedi-language-server

A Python Language Server powered by Jedi.

homepage: https://github.com/pappasam/jedi-language-server

version	toolchain
0.39.0	GCCcore/11.3.0

Jellyfish

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.

homepage: http://www.genome.umd.edu/jellyfish.html

version	toolchain
1.1.11	foss/2016a, foss/2016b
1.1.12	foss/2018b, intel/2018a
2.2.6	foss/2016b, intel/2017a
2.2.10	foss/2018b, intel/2018a
2.3.0	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/11.3.0, GCC/8.2.0-2.31.1, GCC/8.3.0

jemalloc

jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.

homepage: http://jemalloc.net

version	toolchain
4.1.0	intel/2016a
4.2.0	foss/2016a, intel/2016a
4.2.1	intel/2016b
4.5.0	intel/2017a
5.0.1	GCCcore/6.4.0
5.1.0	GCCcore/7.3.0
5.2.0	GCCcore/8.2.0
5.2.1	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/8.3.0, GCCcore/9.3.0
5.3.0	GCCcore/11.3.0, GCCcore/12.2.0

jhbuild

JHBuild allows you to automatically download and compile “modules” (i.e. source code packages). Modules are listed in “module set” files, which also include dependency information so that JHBuild can discover what modules need to be built and in what order.

homepage: https://wiki.gnome.org/action/show/Projects/Jhbuild

version	toolchain
3.15.92	GCCcore/4.9.3

JiTCODE

Just-in-time compilation for ordinary/delay/stochastic differential equations (DDEs)

homepage: https://jitcde-common.readthedocs.io

version	versionsuffix	toolchain
1.3.2	-Python-3.6.4	intel/2018a
1.4.0	-Python-3.7.2	foss/2019a

jModelTest

jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution.

homepage: https://github.com/ddarriba/jmodeltest2

version	versionsuffix	toolchain
2.1.10r20160303	-Java-1.8.0_92	system

Jmol

Jmol: an open-source Java viewer for chemical structures in 3D

homepage: http://jmol.sourceforge.net/

version	versionsuffix	toolchain
16.1.41	-Java-11	system

Jorg

A MAG Circularization Method By Lauren Lui, Torben Nielsen, and Adam Arkin

homepage: https://github.com/lmlui/Jorg

version	toolchain
1.0.1	foss/2020b

joypy

Joyplots in Python with matplotlib & pandas

homepage: https://github.com/sbebo/joypy

version	versionsuffix	toolchain
0.2.2	-Python-3.7.4	intel/2019b
0.2.4		intel/2020b

jq

jq is a lightweight and flexible command-line JSON processor.

homepage: https://stedolan.github.io/jq/

version	toolchain
1.5	GCCcore/10.2.0, GCCcore/6.4.0
1.6	GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0

json-c

JSON-C implements a reference counting object model that allows you to easily construct JSON objects in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON objects.

homepage: https://github.com/json-c/json-c

version	toolchain
0.15	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0
0.16	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0
0.17	GCCcore/13.2.0

json-fortran

JSON-Fortran: A Modern Fortran JSON API

homepage: https://github.com/jacobwilliams/json-fortran

version	toolchain
8.3.0	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/11.3.0, GCC/12.2.0, iccifort/2020.4.304, intel-compilers/2022.0.1, intel-compilers/2022.1.0, intel-compilers/2022.2.1

JSON-GLib

JSON-GLib implements a full JSON parser and generator using GLib and GObject, and integrates JSON with GLib data types.

homepage: https://wiki.gnome.org/Projects/JsonGlib

version	toolchain
1.6.2	GCCcore/10.3.0

JsonCpp

JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files.

homepage: https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html

version	toolchain
0.10.7	GCCcore/8.2.0
1.9.3	GCCcore/8.3.0
1.9.4	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/9.3.0
1.9.5	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0

JUBE

The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, run those sets on different computer systems and evaluate the results.

homepage: https://www.fz-juelich.de/jsc/jube

version	toolchain
2.0.3	system
2.0.4	system
2.0.5	system
2.4.0	system
2.4.1	system
2.4.2	system

Judy

A C library that implements a dynamic array.

homepage: http://judy.sourceforge.net/

version	toolchain
1.0.5	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/8.2.0, GCCcore/8.3.0

Julia

Julia is a high-level, high-performance dynamic programming language for numerical computing

homepage: https://julialang.org

version	versionsuffix	toolchain
1.1.1	-linux-x86_64	system
1.2.0	-linux-x86_64	system
1.3.1	-linux-x86_64	system
1.4.0	-linux-x86_64	system
1.4.1	-linux-x86_64	system
1.4.2	-linux-x86_64	system
1.5.1	-linux-x86_64	system
1.5.3	-linux-x86_64	system
1.6.0	-linux-aarch64	system
1.6.1	-linux-x86_64	system
1.6.2	-linux-x86_64	system
1.6.4	-linux-x86_64	system
1.6.5	-linux-x86_64	system
1.6.6	-linux-x86_64	system
1.6.7	-linux-x86_64	system
1.7.0	-linux-x86_64	system
1.7.1	-linux-x86_64	system
1.7.2	-linux-x86_64	system
1.7.3	-linux-x86_64	system
1.8.0	-linux-x86_64	system
1.8.2	-linux-x86_64	system
1.8.5	-linux-x86_64	system
1.9.0	-linux-x86_64	system
1.9.2	-linux-x86_64	system
1.9.3	-linux-x86_64	system
1.10.0	-linux-x86_64	system

JUnit

A programmer-oriented testing framework for Java.

homepage: http://sourceforge.net/projects/junit

version	versionsuffix	toolchain
4.10	-Java-1.7.0_10	system
4.10	-Java-1.7.0_21	system
4.11	-Java-1.7.0_15	system
4.11	-Java-1.7.0_21	system
4.11	-Java-1.7.0_60	system
4.11	-Java-1.7.0_75	system
4.11	-Java-1.7.0_79	system
4.12	-Java-1.7.0_80	system
4.12	-Java-1.8	system
4.12	-Java-1.8.0_112	system
4.12	-Java-1.8.0_121	system
4.12	-Java-1.8.0_144	system
4.12	-Java-1.8.0_152	system
4.12	-Java-1.8.0_162	system
4.12	-Java-1.8.0_66	system
4.12	-Java-1.8.0_72	system
4.12	-Java-1.8.0_77	system
4.12	-Java-1.8.0_92	system

Jupyter-bundle

This bundle collects a range of Jupyter interfaces (Lab, Notebook and nbclassic), extensions (Jupyter Server Proxy, Jupyter Resource Monitor, Jupyter Lmod) and the JupyterHub.

homepage: https://jupyter.org/

version	toolchain
20230823	GCCcore/12.3.0

jupyter-contrib-nbextensions

A collection of various notebook extensions for Jupyter

homepage: https://github.com/ipython-contrib/jupyter_contrib_nbextensions

version	toolchain
0.7.0	GCCcore/11.3.0

jupyter-matlab-proxy

MATLAB Integration for Jupyter

homepage: https://github.com/mathworks/jupyter-matlab-proxy

version	toolchain
0.3.4	GCCcore/10.3.0
0.5.0	GCCcore/11.3.0

jupyter-resource-usage

Jupyter Notebook Extension for monitoring your own Resource Usage (memory and/or CPU)

homepage: https://github.com/jupyter-server/jupyter-resource-usage

version	toolchain
0.6.1	GCCcore/10.3.0
0.6.2	GCCcore/10.3.0
0.6.3	GCCcore/11.3.0
1.0.0	GCCcore/12.3.0

jupyter-rsession-proxy

Jupyter extensions for running an RStudio rsession proxy

homepage: https://github.com/jupyterhub/jupyter-rsession-proxy

version	toolchain
2.1.0	GCCcore/11.3.0

jupyter-server

The Jupyter Server provides the backend (i.e. the core services, APIs, and REST endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and Voila.

homepage: https://jupyter.org/

version	toolchain
1.21.0	GCCcore/11.3.0
2.7.0	GCCcore/12.2.0
2.7.2	GCCcore/12.3.0

jupyter-server-proxy

Jupyter Server Proxy lets you run arbitrary external processes (such as RStudio, Shiny Server, Syncthing, PostgreSQL, Code Server, etc) alongside your notebook server and provide authenticated web access to them using a path like /rstudio next to others like /lab. Alongside the python package that provides the main functionality, the JupyterLab extension (@jupyterlab/server-proxy) provides buttons in the JupyterLab launcher window to get to RStudio for example.

homepage: https://github.com/jupyterhub/jupyter-server-proxy

version	toolchain
3.2.1	GCCcore/10.3.0
3.2.2	GCCcore/11.3.0, GCCcore/12.2.0
4.0.0	GCCcore/12.3.0

JupyterHub

JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed for centralized deployments in companies, university classrooms and research labs.

homepage: https://jupyter.org

version	versionsuffix	toolchain
0.6.1	-Python-3.5.1	foss/2016a
0.8.1	-Python-3.6.4	foss/2017a
1.1.0		GCCcore/10.2.0
1.4.1		GCCcore/10.3.0
3.0.0		GCCcore/11.3.0
4.0.1		GCCcore/12.2.0
4.0.2		GCCcore/12.3.0

JupyterLab

JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter Notebook.

homepage: https://jupyter.org/

version	versionsuffix	toolchain
1.2.5	-Python-3.7.4	foss/2019b, fosscuda/2019b
2.2.8		GCCcore/10.2.0
3.0.16		GCCcore/10.3.0
3.1.6		GCCcore/11.2.0
3.2.8		GCCcore/10.3.0
3.5.0		GCCcore/11.3.0
4.0.3		GCCcore/12.2.0
4.0.5		GCCcore/12.3.0

jupyterlab-lmod

JupyterLab extension that allows user to interact with environment modules before launching kernels. The extension use Lmod's Python interface to accomplish module related task like loading, unloading, saving collection, etc.

homepage: https://github.com/cmd-ntrf/jupyter-lmod

version	toolchain
1.0.2	GCCcore/11.3.0

jupyterlmod

Jupyter interactive notebook server extension that allows users to interact with environment modules before launching kernels. The extension uses Lmod's Python interface to accomplish module-related tasks like loading, unloading, saving collections, etc.

homepage: https://github.com/cmd-ntrf/jupyter-lmod

version	toolchain
3.0.0	GCCcore/11.3.0
4.0.3	GCCcore/11.3.0, GCCcore/12.3.0

JupyterNotebook

The Jupyter Notebook is the original web application for creating and sharing computational documents. It offers a simple, streamlined, document-centric experience.

homepage: https://jupyter.org/

version	toolchain
7.0.2	GCCcore/12.3.0
7.0.3	GCCcore/12.2.0

JWM

JWM is a light-weight window manager for the X11 Window System.

homepage: https://joewing.net/projects/jwm/

version	toolchain
2.3.5	intel/2016a

jxrlib

Open source implementation of jpegxr

homepage: https://github.com/4creators/jxrlib

version	toolchain
1.1	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.3.0

K

KaHIP - Kaiju - Kaleido - Kalign - kallisto - KAT - kb-python - kbproto - kedro - Kent_tools - Keras - KerasTuner - khmer - kim-api - kineto - king - KITE - kma - KMC - KMCP - KmerGenie - kneaddata - KNIME - kpcalg - Kraken - Kraken2 - KrakenUniq - Kratos - krbalancing - KronaTools - kwant - KWIML - kWIP - KyotoCabinet

KaHIP

The graph partitioning framework KaHIP -- Karlsruhe High Quality Partitioning.

homepage: https://kahip.github.io/

version	toolchain
3.14	gompi/2022a, gompi/2022b
3.16	gompi/2023a

Kaiju

Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing experiments

homepage: http://kaiju.binf.ku.dk/

version	versionsuffix	toolchain
1.5.0		intel/2016b
1.7.2	-Python-3.7.2	iimpi/2019a
1.7.3	-Python-3.7.4	gompi/2019b

Kaleido

Fast static image export for web-based visualization libraries with zero dependencies

homepage: https://github.com/plotly/Kaleido

version	toolchain
0.1.0	GCCcore/10.2.0
0.2.1	GCCcore/10.3.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/13.2.0

Kalign

Kalign is a fast multiple sequence alignment program for biological sequences.

homepage: https://github.com/TimoLassmann/kalign

version	toolchain
2.0.4	GCCcore/10.2.0
3.3.1	GCCcore/10.2.0, GCCcore/10.3.0
3.3.2	GCCcore/11.2.0
3.3.5	GCCcore/11.3.0

kallisto

kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.

homepage: https://pachterlab.github.io/kallisto/

version	toolchain
0.42.5	foss/2016a
0.43.0	intel/2016b
0.43.1	foss/2016b, intel/2017a, intel/2017b
0.44.0	foss/2016b, intel/2018a
0.45.0	foss/2018b
0.45.1	foss/2019a
0.46.0	intel/2019a
0.46.1	foss/2019b, iimpi/2020a, iimpi/2020b
0.46.2	foss/2020b
0.48.0	gompi/2021a, gompi/2021b, gompi/2022a

KAT

The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.

homepage: https://www.earlham.ac.uk/kat-tools

version	versionsuffix	toolchain
2.4.2	-Python-3.6.4	foss/2018a
2.4.2	-Python-3.7.2	foss/2019a

kb-python

kallisto | bustools is a workflow for pre-processing single-cell RNA-seq data. Pre-processing single-cell RNA-seq involves: (1) association of reads with their cells of origin, (2) collapsing of reads according to unique molecular identifiers (UMIs), and (3) generation of gene or feature counts from the reads to generate a cell x gene matrix.

homepage: https://www.kallistobus.tools/

version	toolchain
0.27.3	foss/2021b, foss/2022a

kbproto

X.org KBProto protocol headers.

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.0.7	foss/2016a, gimkl/2.11.5, intel/2016a, intel/2017b

kedro

Kedro is an open-source Python framework that applies software engineering best-practice to data and machine-learning pipelines.

homepage: https://github.com/quantumblacklabs/kedro

version	versionsuffix	toolchain
0.16.5	-Python-3.8.2	foss/2020a

Kent_tools

Kent utilities: collection of tools used by the UCSC genome browser.

homepage: https://genome.cse.ucsc.edu/

version	versionsuffix	toolchain
401		gompi/2019b
411		GCC/10.2.0
418		GCC/10.3.0
422		GCC/11.2.0
442		GCC/11.3.0
457		GCC/12.2.0
20130806	-linux.x86_64	system
20171107	-linux.x86_64	system
20180716	-linux.x86_64	system
20190326	-linux.x86_64	system

Keras

Keras is a deep learning API written in Python, running on top of the machine learning platform TensorFlow.

homepage: https://keras.io/

version	versionsuffix	toolchain
1.0.8	-Python-3.5.2	intel/2016b
1.1.0	-Python-3.5.2	intel/2016b
2.0.4	-Python-2.7.13	intel/2017a
2.0.4	-Python-3.6.1	intel/2017a
2.0.5	-Python-3.6.1	intel/2017a
2.0.8	-Python-3.6.1	intel/2017a
2.1.1	-Python-2.7.14	intel/2017b
2.1.1	-Python-3.6.3	intel/2017b
2.1.2	-Python-2.7.14	intel/2017b
2.1.2	-Python-3.6.3	foss/2017b
2.1.3	-Python-3.6.3	foss/2017b, intel/2017b
2.2.0	-Python-2.7.14	fosscuda/2017b
2.2.0	-Python-3.6.3	fosscuda/2017b
2.2.0	-Python-3.6.4	foss/2018a
2.2.2	-Python-2.7.15	fosscuda/2018b
2.2.4	-Python-3.6.4	intel/2018a
2.2.4	-Python-3.6.6	foss/2018b, fosscuda/2018b
2.2.4	-Python-3.7.2	foss/2019a, fosscuda/2019a
2.3.1	-Python-3.7.4	foss/2019b, fosscuda/2019b
2.3.1	-Python-3.8.2	foss/2020a
2.4.3		foss/2020b, fosscuda/2020b
2.4.3	-TensorFlow-2.5.0	fosscuda/2020b

KerasTuner

KerasTuner is an easy-to-use, scalable hyperparameter optimization framework that solves the pain points of hyperparameter search.

homepage: https://keras.io/keras_tuner

version	toolchain
1.3.5	foss/2022a

khmer

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

homepage: https://github.com/ged-lab/khmer/

version	versionsuffix	toolchain
1.4.1	-Python-2.7.12	foss/2016b
2.1.1	-Python-2.7.13	intel/2017a

kim-api

Open Knowledgebase of Interatomic Models. KIM is an API and OpenKIM is a collection of interatomic models (potentials) for atomistic simulations. This is a library that can be used by simulation programs to get access to the models in the OpenKIM database. This EasyBuild only installs the API, the models can be installed with the package openkim-models, or the user can install them manually by running kim-api-collections-management install user MODELNAME or kim-api-collections-management install user OpenKIM to install them all.

homepage: https://openkim.org/

version	toolchain
2.1.2	foss/2019a, intel/2019a
2.1.3	foss/2019b, foss/2020a, intel/2019b, intel/2020a
2.2.1	GCC/10.2.0, GCC/10.3.0, iccifort/2020.4.304
2.3.0	GCC/11.2.0, GCC/11.3.0, GCC/12.2.0, GCC/12.3.0, intel-compilers/2023.1.0

kineto

A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters

homepage: https://github.com/pytorch/kineto

version	toolchain
0.4.0	GCC/11.3.0

king

KING is a toolset that makes use of high-throughput SNP data typically seen in a genome-wide association study (GWAS) or a sequencing project. Applications of KING include family relationship inference and pedigree error checking, quality control, population substructure identification, forensics, gene mapping, etc.

homepage: https://kingrelatedness.com/

version	toolchain
2.2.4	system
2.2.7	system

KITE

KITE is an open-source Python/C++ software suite for efficient real-space tight-binding (TB) simulations of electronic structure and bulk quantum transport properties of disordered systems scalable to multi billions of atomic orbitals.

homepage: https://github.com/quantum-kite/kite

version	toolchain
1.1	gompi/2022a

kma

KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.

homepage: https://bitbucket.org/genomicepidemiology/kma

version	toolchain
1.2.22	intel/2019b
1.4.12a	GCC/12.2.0

KMC

KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files.

homepage: http://sun.aei.polsl.pl/kmc

version	versionsuffix	toolchain
3.1.0		foss/2018a, foss/2018b
3.1.1	-Python-3.7.2	GCC/8.2.0-2.31.1
3.1.2rc1	-Python-3.7.4	GCC/8.3.0
3.2.1		GCC/11.2.0
3.2.1	-Python-2.7.18	GCC/11.2.0
3.2.2		GCC/12.2.0

KMCP

KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping

homepage: https://bioinf.shenwei.me/kmcp

version	toolchain
0.9.1	system

KmerGenie

KmerGenie estimates the best k-mer length for genome de novo assembly.

homepage: http://kmergenie.bx.psu.edu/

version	toolchain
1.7044	intel/2017a
1.7048	intel/2018a

kneaddata

KneadData is a tool designed to perform quality control on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.

homepage: http://huttenhower.sph.harvard.edu/kneaddata

version	toolchain
0.12.0	foss/2022a

KNIME

KNIME Analytics Platform is the open source software for creating data science applications and services. KNIME stands for KoNstanz Information MinEr.

homepage: https://www.knime.com/

version	toolchain
3.6.2	system

kpcalg

Kernel PC (kPC) algorithm for causal structure learning and causal inference using graphical models. kPC is a version of PC algorithm that uses kernel based independence criteria in order to be able to deal with non-linear relationships and non-Gaussian noise. Includes pcalg: Functions for causal structure learning and causal inference using graphical models.

homepage: https://cran.r-project.org/package=kpcalg

version	versionsuffix	toolchain
1.0.1	-R-3.5.1	foss/2018b

Kraken

Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.

homepage: https://ccb.jhu.edu/software/kraken/

version	versionsuffix	toolchain
0.10.5-beta	-Perl-5.22.1	foss/2016a
0.10.5-beta	-Perl-5.24.0	foss/2016b
1.0	-Perl-5.26.1	intel/2018a
1.1	-Perl-5.28.0	foss/2018b
1.1.1		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.3.0, GCCcore/9.3.0
1.1.1	-Perl-5.28.1	GCCcore/8.2.0

Kraken2

Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.

homepage: https://github.com/DerrickWood/kraken2/wiki

version	versionsuffix	toolchain
2.0.6-beta	-Perl-5.26.1	foss/2018a
2.0.7-beta	-Perl-5.28.0	foss/2018b
2.0.8-beta	-Perl-5.30.0	gompi/2019b
2.0.9-beta	-Perl-5.28.0	foss/2018b
2.0.9-beta	-Perl-5.30.2	gompi/2020a
2.1.1		gompi/2020b
2.1.2		gompi/2021a, gompi/2021b, gompi/2022a

KrakenUniq

KrakenUniq: confident and fast metagenomics classification using unique k-mer counts

homepage: https://github.com/fbreitwieser/krakenuniq/

version	toolchain
1.0.3	GCC/11.3.0

Kratos

Kratos Multiphysics (A.K.A Kratos) is a framework for building parallel multi-disciplinary simulation software.

homepage: https://www.cimne.com/kratos

version	versionsuffix	toolchain
6.0	-Python-3.6.4	foss/2018a, intel/2018a

krbalancing

A C++ extension for Python which computes K.R. balanced matrices.

homepage: https://github.com/deeptools/Knight-Ruiz-Matrix-balancing-algorithm

version	toolchain
0.5.0b0	GCCcore/11.3.0

KronaTools

Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.

homepage: https://github.com/marbl/Krona/wiki/KronaTools

version	toolchain
2.7	GCCcore/7.3.0
2.7.1	GCCcore/8.2.0
2.8	GCC/10.3.0, GCCcore/10.2.0
2.8.1	GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0

kwant

Kwant is a free (open source), powerful, and easy to use Python package for numerical calculations on tight-binding models with a strong focus on quantum transport.

homepage: https://kwant-project.org/

version	versionsuffix	toolchain
1.4.1	-Python-3.7.2	foss/2019a, intel/2019a

KWIML

The Kitware Information Macro Library

homepage: https://gitlab.kitware.com/utils/kwiml

version	toolchain
20180201	GCCcore/6.4.0

kWIP

This software implements a de novo, alignment free measure of sample genetic dissimilarity which operates upon raw sequencing reads. It is able to calculate the genetic dissimilarity between samples without any reference genome, and without assembling one.

homepage: https://github.com/kdmurray91/kWIP

version	toolchain
0.2.0	GCCcore/6.4.0

KyotoCabinet

Kyoto Cabinet is a library of routines for managing a database.

homepage: https://dbmx.net/kyotocabinet/

version	toolchain
1.2.77	GCCcore/7.3.0, GCCcore/8.2.0
1.2.80	GCCcore/11.3.0

L

L_RNA_scaffolder - Lab-Streaming-Layer - Lace - LADR - lagrangian-filtering - LAME - LAMMPS - lancet - LAPACK - LASSO-Python - LAST - LASTZ - lavaan - LayoutParser - LBFGS++ - lcalc - LCov - LDC - lDDT - LeadIT - leafcutter - leidenalg - LEMON - Leptonica - LERC - less - LevelDB - Levenshtein - lftp - LHAPDF - LIANA - libaec - libaed2 - libaio - libarchive - libav - libavif - libbaseencode - libBigWig - libbitmask - libcdms - libcerf - libcint - libcircle - libcmaes - libconfig - libcotp - libcpuset - libcroco - libctl - libdap - libde265 - libdeflate - libdivsufsort - libdrm - libdrs - libdwarf - libedit - libelf - libemf - libepoxy - libev - libevent - libexif - libfabric - libfdf - libffcall - libffi - libFLAME - libfontenc - libfyaml - libgcrypt - libgd - libgdiplus - libGDSII - libgeotiff - libgit2 - libglade - libGLU - libglvnd - libgpg-error - libgpuarray - libGridXC - libgtextutils - libgxps - libhandy - libharu - libheif - libibmad - libibumad - libICE - libiconv - libidn - libidn2 - Libint - LiBis - libjpeg-turbo - libjxl - libleidenalg - LibLZF - libmad - libmatheval - libmaus2 - libmbd - libMemcached - libmicrohttpd - libmo_unpack - libmypaint - libnsl - libobjcryst - libogg - libopus - libosmium - libpci - libpciaccess - libplinkio - libpng - libpsl - libPSML - libpsortb - libpspio - libpthread-stubs - libQGLViewer - libreadline - libRmath - librosa - librsb - librsvg - librttopo - libsamplerate - libSBML - libsigc++ - libsigsegv - libSM - libsndfile - libsodium - LibSoup - libspatialindex - libspatialite - libspectre - libssh - libStatGen - LIBSVM - LIBSVM-Python - libtar - libtasn1 - libtecla - LibTIFF - libtirpc - libtool - libtree - libunistring - libunwind - libutempter - LibUUID - libuv - libvdwxc - libvorbis - libvori - libWallModelledLES - libwebp - libwpe - libX11 - libXau - libxc - libxcb - libXcursor - libXdamage - libXdmcp - libXext - libXfixes - libXfont - libXft - libXi - libXinerama - libxkbcommon - libxml++ - libxml2 - libxml2-python - libXmu - libXp - libXpm - libXrandr - libXrender - libxslt - libxsmm - libXt - libXxf86vm - libyaml - libzeep - libzip - lie_learn - lifelines - Lighter - liknorm - likwid - limix - LinBox - line_profiler - Lingeling - LISFLOOD-FP - lit - LittleCMS - LLDB - LLVM - LMDB - LMfit - Lmod - lmoments3 - LncLOOM - LocARNA - LoFreq - Log-Log4perl - logaddexp - LOHHLA - Loki - longestrunsubsequence - longread_umi - Longshot - loompy - loomR - LoopTools - LoRDEC - LPeg - LPJmL - lpsolve - lrslib - LS-PrePost - LSD2 - LSMS - LTR_retriever - LtrDetector - Lua - LuaJIT - LuaJIT2-OpenResty - LuaRocks - Lucene-Geo-Gazetteer - LUMPY - LUSCUS - lwgrp - lxml - lynx - lz4 - LZO

L_RNA_scaffolder

L_RNA_scaffolder is a genome scaffolding tool with long trancriptome reads

homepage: https://github.com/CAFS-bioinformatics/L_RNA_scaffolder

version	versionsuffix	toolchain
20141124	-Perl-5.24.0	intel/2016b
20190530		GCC/11.3.0

Lab-Streaming-Layer

The lab streaming layer (LSL) is a system for the unified collection of measurement time series in research experiments that handles both the networking, time-synchronization, (near-) real-time access as well as optionally the centralized collection, viewing and disk recording of the data.

homepage: https://labstreaminglayer.readthedocs.io

version	toolchain
1.16.2	GCCcore/12.3.0

Lace

Building SuperTranscripts: A linear representation of transcriptome data

homepage: https://github.com/Oshlack/Lace

version	toolchain
1.14.1	foss/2022a

LADR

Prover9, Mace4, and several related programs come packaged in a system called LADR (Library for Automated Deduction Research).

homepage: https://www.cs.unm.edu/~mccune/mace4/download

version	toolchain
2009-11A	GCCcore/10.2.0

lagrangian-filtering

Temporal filtering of data in a Lagrangian frame of reference.

homepage: https://github.com/angus-g/lagrangian-filtering

version	toolchain
0.8.3	foss/2022a

LAME

LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.

homepage: http://lame.sourceforge.net/

version	toolchain
3.99.5	foss/2016b, intel/2017a
3.100	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0, intel/2017b

LAMMPS

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.

homepage: https://lammps.sandia.gov/

version	versionsuffix	toolchain
2Aug2023_update2	-kokkos	foss/2023a
2Aug2023_update2	-kokkos-CUDA-12.1.1	foss/2023a
3Mar2020	-Python-3.7.4-kokkos	foss/2019b, intel/2019b
3Mar2020	-Python-3.8.2-kokkos	foss/2020a, intel/2020a
7Aug2019	-Python-3.7.4-kokkos	foss/2019b, intel/2019b
7Aug2019	-Python-3.7.4-kokkos-OCTP	intel/2019b
23Jun2022	-kokkos	foss/2021a, foss/2021b, foss/2022a
23Jun2022	-kokkos-CUDA-11.3.1	foss/2021a
23Jun2022	-kokkos-CUDA-11.4.1	foss/2021b

lancet

Lancet is a somatic variant caller (SNVs and indels) for short read data.

homepage: https://github.com/nygenome/lancet

version	toolchain
1.1.0	iccifort/2019.5.281

LAPACK

LAPACK is written in Fortran90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems.

homepage: https://www.netlib.org/lapack/

version	toolchain
3.8.0	GCC/7.3.0-2.30
3.9.1	GCC/10.2.0
3.10.1	GCC/11.2.0, GCC/11.3.0

LASSO-Python

This python library is designed for general purpose usage in the field of Computer Aided Engineering (CAE). It's name originates from the original initiator and donator of the project Lasso GmbH. The library is now maintained by an open-source community.

homepage: https://open-lasso-python.github.io/lasso-python/

version	toolchain
2.0.0	foss/2022b

LAST

LAST finds similar regions between sequences.

homepage: http://last.cbrc.jp/

version	toolchain
869	intel/2017a
914	intel/2017b
1045	intel/2019b
1179	GCC/10.2.0

LASTZ

LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.

homepage: https://github.com/lastz/lastz

version	toolchain
1.02.00	GCCcore/8.2.0, foss/2016a
1.04.03	foss/2019b
1.04.22	GCC/12.3.0

lavaan

Fit a variety of latent variable models, including confirmatory factor analysis, structural equation modeling and latent growth curve models.

homepage: https://cran.r-project.org/web/packages/lavaan

version	versionsuffix	toolchain
0.6-2	-R-3.4.4	intel/2018a
0.6-4.1433	-R-3.6.0	foss/2019a
0.6-9	-R-4.1.0	foss/2021a

LayoutParser

A Unified Toolkit for Deep Learning Based Document Image Analysis

homepage: https://layout-parser.github.io/

version	versionsuffix	toolchain
0.3.4		foss/2022a
0.3.4	-CUDA-11.7.0	foss/2022a

LBFGS++

A header-only C++ library for L-BFGS and L-BFGS-B algorithms

homepage: https://lbfgspp.statr.me

version	toolchain
0.1.0	system

lcalc

Lcalc is a package for working with L-functions.

homepage: https://gitlab.com/sagemath/lcalc

version	toolchain
2.0.5	GCCcore/11.3.0

LCov

LCOV - the LTP GCOV extension

homepage: http://ltp.sourceforge.net/coverage/lcov.php

version	toolchain
1.13	GCCcore/7.2.0

LDC

The LLVM-based D Compiler

homepage: https://wiki.dlang.org/LDC

version	versionsuffix	toolchain
0.17.6	-x86_64	system
1.24.0	-x86_64	system
1.25.1		GCCcore/10.2.0
1.26.0		GCCcore/10.3.0
1.30.0		GCCcore/11.3.0
1.36.0		GCCcore/12.3.0

lDDT

The local Distance Difference Test (lDDT) is a superposition-free score which evaluates local distance differences in a model compared to a reference structure.

homepage: https://openstructure.org

version	toolchain
1.2	system

LeadIT

Visually Informed LeadOpt

homepage: http://www.biosolveit.de/LeadIT/index.html

version	toolchain
2.1.9	system

leafcutter

Leafcutter quantifies RNA splicing variation using short-read RNA-seq data. The core idea is to leverage spliced reads (reads that span an intron) to quantify (differential) intron usage across samples. The advantages of this approach include: easy detection of novel introns, modeling of more complex splicing events than exonic PSI, avoiding the challenge of isoform abundance estimation, simple, computationally efficient algorithms scaling to 100s or even 1000s of samples. For details please see our bioRxiv preprint and corresponding Nature Genetics publication.

homepage: http://davidaknowles.github.io/leafcutter/index.html

version	versionsuffix	toolchain
0.2.9	-R-4.2.2	foss/2022b

leidenalg

Implementation of the Leiden algorithm for various quality functions to be used with igraph in Python.

homepage: https://github.com/vtraag/leidenalg

version	versionsuffix	toolchain
0.8.2	-Python-3.8.2	foss/2020a
0.8.3		foss/2020b, fosscuda/2020b
0.8.7		foss/2021a
0.8.8		foss/2021b
0.9.1		foss/2022a
0.10.1		foss/2022b
0.10.2		foss/2023a

LEMON

LEMON stands for Library for Efficient Modeling and Optimization in Networks. It is a C++ template library providing efficient implementations of common data structures and algorithms with focus on combinatorial optimization tasks connected mainly with graphs and networks.

homepage: https://lemon.cs.elte.hu

version	toolchain
1.3.1	GCC/8.2.0-2.31.1

Leptonica

Leptonica is a collection of pedagogically-oriented open source software that is broadly useful for image processing and image analysis applications.

homepage: http://www.leptonica.org

version	toolchain
1.77.0	GCCcore/7.3.0
1.78.0	GCCcore/8.2.0
1.82.0	GCCcore/10.3.0
1.83.0	GCCcore/11.3.0

LERC

LERC is an open-source image or raster format which supports rapid encoding and decoding for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, so the precision of the original input image is preserved (within user defined error bounds).

homepage: https://github.com/Esri/lerc

version	toolchain
3.0	GCCcore/10.2.0, GCCcore/10.3.0
4.0.0	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

less

Less is a free, open-source file pager. It can be found on most versions of Linux, Unix and Mac OS, as well as on many other operating systems.

homepage: http://www.greenwoodsoftware.com/less/

version	toolchain
458	GCC/4.8.2

LevelDB

LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values.

homepage: https://github.com/google/leveldb

version	toolchain
1.18	foss/2016a, intel/2017a, intel/2017b
1.20	GCCcore/7.3.0
1.22	GCCcore/11.3.0, GCCcore/8.2.0, GCCcore/9.3.0

Levenshtein

Python extension for computing string edit distances and similarities.

homepage: https://pypi.org/project/python-Levenshtein/

version	toolchain
0.24.0	GCCcore/12.2.0

lftp

LFTP is a sophisticated ftp/http client, and a file transfer program supporting a number of network protocols. Like BASH, it has job control and uses the readline library for input. It has bookmarks, a built-in mirror command, and can transfer several files in parallel. It was designed with reliability in mind.

homepage: https://lftp.yar.ru

version	toolchain
4.6.4	GNU/4.9.3-2.25
4.8.4	GCCcore/6.4.0
4.9.2	GCCcore/11.2.0

LHAPDF

Les Houches Parton Density Function LHAPDF is the standard tool for evaluating parton distribution functions (PDFs) in high-energy physics.

homepage: http://lhapdf.hepforge.org/

version	toolchain
6.5.3	GCC/11.3.0
6.5.4	GCC/12.3.0

LIANA

LIANA: a LIgand-receptor ANalysis frAmework. LIANA enables the use of any combination of ligand-receptor methods and resources, and their consensus.

homepage: https://saezlab.github.io/liana/

version	versionsuffix	toolchain
0.1.11	-R-4.2.1	foss/2022a

libaec

Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers (samples). The library achieves best results for low entropy data as often encountered in space imaging instrument data or numerical model output from weather or climate simulations. While floating point representations are not directly supported, they can also be efficiently coded by grouping exponents and mantissa.

homepage: https://gitlab.dkrz.de/k202009/libaec

version	toolchain
1.0.6	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

libaed2

libaed2 is a library of modules and algorithms for simulation of "aquatic ecodynamics" - water quality, aquatic biogeochemsitry, biotic habitat and aquatic ecosystem dynamics.

homepage: https://aquatic.science.uwa.edu.au/research/models/AED

version	toolchain
1.3.0	GCC/10.3.0

libaio

Asynchronous input/output library that uses the kernels native interface.

homepage: https://pagure.io/libaio

version	toolchain
0.3.111	GCCcore/8.2.0, GCCcore/8.3.0
0.3.112	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0
0.3.113	GCCcore/12.2.0, GCCcore/12.3.0

libarchive

Multi-format archive and compression library

homepage: https://www.libarchive.org/

version	toolchain
3.4.0	GCCcore/8.2.0
3.4.2	GCCcore/9.3.0
3.4.3	GCCcore/10.2.0
3.5.1	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/8.3.0
3.6.1	GCCcore/11.3.0, GCCcore/12.2.0
3.6.2	GCCcore/12.3.0, GCCcore/13.1.0
3.7.2	GCCcore/13.2.0

libav

Libav is a friendly and community-driven effort to provide its users with a set of portable, functional and high-performance libraries for dealing with multimedia formats of all sorts.

homepage: https://libav.org/

version	toolchain
11.10	GCCcore/6.4.0

libavif

This library aims to be a friendly, portable C implementation of the AV1 Image File Format, as described here: https://aomediacodec.github.io/av1-avif/

homepage: https://github.com/AOMediaCodec/libavif

version	toolchain
0.9.0	foss/2020b
0.11.1	GCCcore/11.3.0, foss/2021a, foss/2022a

libbaseencode

Library written in C for encoding and decoding data using base32 or base64 according to RFC-4648

homepage: https://github.com/paolostivanin/libbaseencode

version	toolchain
1.0.11	GCCcore/10.2.0

libBigWig

A C library for handling bigWig files

homepage: https://github.com/dpryan79/libBigWig

version	toolchain
0.4.4	GCCcore/8.3.0
0.4.6	GCCcore/11.2.0

libbitmask

libbitmask provides a convenient, powerful bitmask data type

homepage: http://oss.sgi.com/projects/cpusets/

version	toolchain
2.0	system

libcdms

Climate Data Management System Library.

homepage: https://github.com/CDAT/libcdms/

version	versionsuffix	toolchain
3.1.2	-Python-3.8.2	foss/2020a

libcerf

libcerf is a self-contained numeric library that provides an efficient and accurate implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions.

homepage: https://jugit.fz-juelich.de/mlz/libcerf

version	toolchain
1.4	foss/2016a, foss/2016b, intel/2016a
1.5	GCCcore/5.4.0, GCCcore/6.3.0, GCCcore/6.4.0, foss/2016b, intel/2016b, intel/2017a
1.7	GCCcore/7.3.0
1.11	GCCcore/7.3.0, GCCcore/8.2.0
1.13	GCCcore/8.3.0, GCCcore/9.3.0
1.14	GCCcore/10.2.0
1.15	GCCcore/10.3.0
1.17	GCCcore/10.3.0, GCCcore/11.2.0
2.1	GCCcore/11.3.0
2.3	GCCcore/12.2.0, GCCcore/12.3.0

libcint

libcint is an open source library for analytical Gaussian integrals.

homepage: https://github.com/sunqm/libcint

version	toolchain
4.4.0	foss/2020b, foss/2021a, gomkl/2021a
5.1.6	foss/2022a
5.4.0	gfbf/2023a
5.5.0	gfbf/2022b

libcircle

An API to provide an efficient distributed queue on a cluster. libcircle is an API for distributing embarrassingly parallel workloads using self-stabilization.

homepage: https://github.com/hpc/libcircle/

version	toolchain
0.2.1-rc.1	gompi/2019a, iimpi/2019a
0.3	gompi/2020a, gompi/2020b, gompi/2022a, gompi/2023a, iimpi/2020a

libcmaes

libcmaes is a multithreaded C++11 library for high performance blackbox stochastic optimization using the CMA-ES algorithm for Covariance Matrix Adaptation Evolution Strategy.

homepage: http://beniz.github.io/libcmaes/

version	toolchain
0.9.5	foss/2016a

libconfig

Libconfig is a simple library for processing structured configuration files

homepage: https://hyperrealm.github.io/libconfig

version	toolchain
1.5	intel/2016b
1.7.1	GCCcore/6.4.0
1.7.2	GCCcore/7.3.0
1.7.3	GCCcore/10.3.0, GCCcore/11.2.0

libcotp

C library that generates TOTP and HOTP according to RFC-6238

homepage: https://github.com/paolostivanin/libcotp

version	toolchain
1.2.3	GCCcore/10.2.0

libcpuset

libcpuset provides full access to cpuset capabilities

homepage: http://oss.sgi.com/projects/cpusets/

version	toolchain
1.0	system

libcroco

Libcroco is a standalone css2 parsing and manipulation library.

homepage: https://github.com/GNOME/libcroco

version	toolchain
0.6.11	intel/2016a
0.6.13	GCC/10.2.0, foss/2019a

libctl

libctl is a free Guile-based library implementing flexible control files for scientific simulations.

homepage: https://libctl.readthedocs.io/en/latest/

version	toolchain
3.2.2	foss/2016a
4.0.0	intel/2020a
4.1.3	GCCcore/6.4.0
4.5.1	GCCcore/10.2.0

libdap

A C++ SDK which contains an implementation of DAP 2.0 and DAP4.0. This includes both Client- and Server-side support classes.

homepage: https://www.opendap.org/software/libdap

version	versionsuffix	toolchain
3.18.1		intel/2017a
3.18.1	-Python-2.7.11	foss/2016a
3.19.1		GCCcore/6.4.0, foss/2017b, intel/2017b
3.20.3		GCCcore/7.3.0
3.20.4		GCCcore/8.2.0
3.20.6		GCCcore/8.3.0
3.20.7		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/9.3.0
3.20.8		GCCcore/11.2.0
3.20.11		GCCcore/11.3.0

libde265

libde265 is an open source implementation of the h.265 video codec

homepage: https://github.com/strukturag/libde265

version	toolchain
1.0.8	GCC/10.3.0, GCC/11.2.0
1.0.11	GCC/11.3.0

libdeflate

Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.

homepage: https://github.com/ebiggers/libdeflate

version	toolchain
1.5	GCCcore/7.3.0
1.7	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/9.3.0
1.8	GCCcore/10.3.0, GCCcore/11.2.0
1.10	GCCcore/11.3.0
1.15	GCCcore/12.2.0
1.18	GCCcore/12.3.0
1.19	GCCcore/13.2.0

libdivsufsort

libdivsufsort is a software library that implements a lightweight suffix array construction algorithm.

homepage: https://github.com/y-256/libdivsufsort

version	toolchain
2.0.1	foss/2018b

libdrm

Direct Rendering Manager runtime library.

homepage: https://dri.freedesktop.org

version	toolchain
2.4.67	foss/2016a, gimkl/2.11.5, intel/2016a
2.4.68	foss/2016a, intel/2016a
2.4.70	GCCcore/5.4.0, foss/2016b, intel/2016b
2.4.76	GCCcore/6.3.0, intel/2017a
2.4.88	GCCcore/6.4.0
2.4.91	GCCcore/6.4.0
2.4.92	GCCcore/7.3.0
2.4.97	GCCcore/8.2.0
2.4.99	GCCcore/8.3.0
2.4.100	GCCcore/9.3.0
2.4.102	GCCcore/10.2.0
2.4.106	GCCcore/10.3.0
2.4.107	GCCcore/11.2.0
2.4.110	GCCcore/11.3.0
2.4.114	GCCcore/12.2.0
2.4.115	GCCcore/12.3.0
2.4.117	GCCcore/13.2.0

libdrs

PCMDI's old DRS format implementation

homepage: https://github.com/CDAT/libdrs/

version	toolchain
3.1.2	foss/2020a

libdwarf

The DWARF Debugging Information Format is of interest to programmers working on compilers and debuggers (and anyone interested in reading or writing DWARF information))

homepage: https://www.prevanders.net/dwarf.html

version	toolchain
0.4.1	GCCcore/11.3.0
0.7.0	GCCcore/12.3.0
20140805	GCC/4.9.2
20150310	GCC/4.9.2, GCCcore/5.4.0, GCCcore/6.3.0
20190529	GCCcore/8.2.0
20201201	GCCcore/10.2.0
20210305	GCCcore/10.3.0
20210528	GCCcore/11.2.0

libedit

This BSD-style licensed command line editor library provides generic line editing, history, and tokenization functions, similar to those found in GNU Readline.

homepage: https://thrysoee.dk/editline/

version	toolchain
20150325	GNU/4.9.3-2.25
20180525	GCCcore/6.4.0
20191231	GCCcore/9.3.0
20210910	GCCcore/10.3.0, GCCcore/11.2.0

libelf

libelf is a free ELF object file access library

homepage: https://directory.fsf.org/wiki/Libelf

version	toolchain
0.8.13	GCC/4.8.3, GCC/4.9.2, GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/5.4.0, GCCcore/6.3.0, GCCcore/8.2.0, GCCcore/9.3.0

libemf

Library implementation of ECMA-234 API for the generation of enhanced metafiles.

homepage: https://sourceforge.net/projects/libemf/

version	toolchain
1.0.13	GCCcore/11.3.0

libepoxy

Epoxy is a library for handling OpenGL function pointer management for you

homepage: https://github.com/anholt/libepoxy

version	toolchain
1.5.2	foss/2018a
1.5.3	GCCcore/8.2.0, fosscuda/2018b
1.5.4	GCCcore/10.2.0, GCCcore/8.3.0, GCCcore/9.3.0
1.5.8	GCCcore/10.3.0, GCCcore/11.2.0
1.5.10	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

libev

A full-featured and high-performance (see benchmark) event loop that is loosely modelled after libevent, but without its limitations and bugs. It is used in GNU Virtual Private Ethernet, rxvt-unicode, auditd, the Deliantra MORPG Server and Client, and many other programs.

homepage: http://software.schmorp.de/pkg/libev.html

version	toolchain
4.33	GCC/11.2.0, GCC/11.3.0

libevent

The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts.

homepage: http://libevent.org/

version	toolchain
2.0.22	GCC/4.9.2, GCC/5.4.0-2.26, GCCcore/4.9.3, GNU/4.9.3-2.25
2.1.8	GCCcore/6.4.0, GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, system
2.1.11	GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/8.3.0, GCCcore/9.3.0
2.1.12	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0, system

libexif

A library for parsing, editing, and saving EXIF data.

homepage: https://libexif.github.io/

version	toolchain
0.6.24	GCCcore/11.2.0

libfabric

Libfabric is a core component of OFI. It is the library that defines and exports the user-space API of OFI, and is typically the only software that applications deal with directly. It works in conjunction with provider libraries, which are often integrated directly into libfabric.

homepage: https://ofiwg.github.io/libfabric/

version	toolchain
1.9.1	GCCcore/9.3.0
1.10.1	GCCcore/9.3.0
1.11.0	GCCcore/10.2.0, GCCcore/9.3.0
1.12.1	GCCcore/10.3.0
1.13.0	GCCcore/11.2.0
1.13.1	GCCcore/11.2.0
1.13.2	GCCcore/11.2.0
1.15.1	GCCcore/11.3.0
1.16.1	GCCcore/12.2.0
1.18.0	GCCcore/12.3.0
1.19.0	GCCcore/13.2.0

libfdf

LibFDF is the official implementation of the FDF specifications for use in client codes.

homepage: https://gitlab.com/siesta-project/libraries/libfdf

version	versionsuffix	toolchain
0.2.2	-serial	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, iccifort/2020.4.304, intel-compilers/2021.2.0, intel-compilers/2021.4.0
0.5.0		GCC/11.3.0

libffcall

GNU Libffcall is a collection of four libraries which can be used to build foreign function call interfaces in embedded interpreters

homepage: https://www.gnu.org/software/libffcall/

version	toolchain
1.13	GCCcore/6.4.0
2.2	GCCcore/8.3.0, GCCcore/9.3.0
2.4	GCCcore/10.2.0

libffi

The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time.

homepage: https://sourceware.org/libffi/

version	toolchain
3.2.1	GCC/4.9.2, GCC/4.9.3-2.25, GCC/5.4.0-2.26, GCCcore/5.4.0, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GNU/4.9.3-2.25, foss/2016.04, foss/2016a, foss/2016b, gimkl/2.11.5, intel/2016a, intel/2016b, system
3.3	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/9.3.0
3.4.2	GCCcore/11.2.0, GCCcore/11.3.0
3.4.4	GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.1.0, GCCcore/13.2.0

libFLAME

libFLAME is a portable library for dense matrix computations, providing much of the functionality present in LAPACK.

homepage: https://developer.amd.com/amd-cpu-libraries/blas-library/#libflame

version	versionsuffix	toolchain
1.0	-amd	GCC/7.3.0-2.30
2.2	-amd	GCCcore/9.3.0
5.2.0		GCC/10.3.0, GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/9.3.0

libfontenc

X11 font encoding library

homepage: http://www.freedesktop.org/wiki/Software/xlibs/

version	toolchain
1.1.3	foss/2016a, gimkl/2.11.5, intel/2016a

libfyaml

Fully feature complete YAML parser and emitter, supporting the latest YAML spec and passing the full YAML testsuite.

homepage: https://github.com/pantoniou/libfyaml

version	toolchain
0.9	GCCcore/12.2.0

libgcrypt

Libgcrypt is a general purpose cryptographic library originally based on code from GnuPG

homepage: https://gnupg.org/related_software/libgcrypt/index.html

version	toolchain
1.6.5	intel/2016a
1.8.4	GCCcore/7.3.0, GCCcore/8.2.0
1.8.5	GCCcore/8.3.0
1.9.2	GCCcore/10.2.0, GCCcore/10.3.0
1.9.3	GCCcore/11.2.0
1.10.1	GCCcore/11.3.0

libgd

GD is an open source code library for the dynamic creation of images by programmers.

homepage: https://libgd.github.io

version	toolchain
2.1.1	foss/2016a, intel/2016a
2.2.3	foss/2016b, intel/2016b
2.2.4	GCCcore/6.4.0, foss/2016b, intel/2017a
2.2.5	GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, intel/2017b, intel/2018a
2.3.0	GCCcore/10.2.0, GCCcore/9.3.0
2.3.1	GCCcore/10.3.0
2.3.3	GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0

libgdiplus

Libgdiplus is the Mono library that provides a GDI+-compatible API on non-Windows operating systems.

homepage: https://www.mono-project.com/docs/gui/libgdiplus

version	toolchain
6.1	GCCcore/11.2.0

libGDSII

libGDSII is a C++ library for working with GDSII binary data files, intended primarily for use with the computational electromagnetism codes scuff-em and meep but sufficiently general-purpose to allow other uses as well.

homepage: https://github.com/HomerReid/libGDSII

version	toolchain
0.21	GCCcore/10.2.0, GCCcore/6.4.0

libgeotiff

Library for reading and writing coordinate system information from/to GeoTIFF files

homepage: https://directory.fsf.org/wiki/Libgeotiff

version	toolchain
1.4.2	foss/2018a, foss/2018b, intel/2018b
1.5.1	GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
1.6.0	GCCcore/10.2.0, GCCcore/10.3.0
1.7.0	GCCcore/11.2.0
1.7.1	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0

libgit2

libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant linkable library with a solid API, allowing you to write native speed custom Git applications in any language which supports C bindings.

homepage: https://libgit2.org/

version	toolchain
1.0.0	GCCcore/8.3.0
1.1.0	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/9.3.0
1.1.1	GCCcore/11.2.0
1.4.3	GCCcore/11.3.0
1.5.0	GCCcore/12.2.0
1.7.1	GCCcore/12.3.0
1.7.2	GCCcore/13.2.0

libglade

Libglade is a library for constructing user interfaces dynamically from XML descriptions.

homepage: https://developer.gnome.org/libglade/

version	toolchain
2.6.4	foss/2018b, intel/2016a, intel/2017b, intel/2018a

libGLU

The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.

homepage: https://mesa.freedesktop.org/archive/glu/

version	versionsuffix	toolchain
9.0.0		GCCcore/8.2.0, foss/2016a, foss/2016b, foss/2017a, foss/2017b, foss/2018a, foss/2018b, fosscuda/2017b, fosscuda/2018a, fosscuda/2018b, gimkl/2.11.5, intel/2016a, intel/2016b, intel/2017a, intel/2017b, intel/2018a, intel/2018b, intelcuda/2017b, iomkl/2018a
9.0.0	-Mesa-11.2.1	foss/2016a, intel/2016a
9.0.1		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/8.3.0, GCCcore/9.3.0
9.0.2		GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0
9.0.3		GCCcore/12.3.0, GCCcore/13.2.0

libglvnd

libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors.

homepage: https://gitlab.freedesktop.org/glvnd/libglvnd

version	toolchain
1.2.0	GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
1.3.2	GCCcore/10.2.0
1.3.3	GCCcore/10.3.0, GCCcore/11.2.0
1.4.0	GCCcore/11.3.0
1.6.0	GCCcore/12.2.0, GCCcore/12.3.0
1.7.0	GCCcore/13.2.0

libgpg-error

Libgpg-error is a small library that defines common error values for all GnuPG components.

homepage: https://gnupg.org/related_software/libgpg-error/index.html

version	toolchain
1.21	intel/2016a
1.35	GCCcore/7.3.0
1.36	GCCcore/8.2.0
1.38	GCCcore/8.3.0
1.41	GCCcore/10.2.0
1.42	GCCcore/10.3.0, GCCcore/11.2.0
1.46	GCCcore/11.3.0

libgpuarray

Library to manipulate tensors on the GPU.

homepage: http://deeplearning.net/software/libgpuarray/

version	versionsuffix	toolchain
0.7.5	-Python-2.7.14	fosscuda/2017b, intelcuda/2017b
0.7.5	-Python-3.6.3	fosscuda/2017b, intel/2017b, intelcuda/2017b
0.7.6		fosscuda/2019a, fosscuda/2020b
0.7.6	-Python-2.7.15	fosscuda/2018b
0.7.6	-Python-3.6.6	fosscuda/2018b
0.7.6	-Python-3.7.4	fosscuda/2019b

libGridXC

A library to compute the exchange and correlation energy and potential in spherical (i.e. atoms) or periodic systems.

homepage: https://gitlab.com/siesta-project/libraries/libgridxc

version	toolchain
0.8.5	iimpi/2019b
0.9.6	gompi/2020b, gompi/2021a, gompi/2021b, iimpi/2020b, iimpi/2021a, iimpi/2021b
1.1.0	gompi/2022a

libgtextutils

ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream

homepage: http://hannonlab.cshl.edu/fastx_toolkit/

version	toolchain
0.7	GCCcore/7.3.0, foss/2016a, foss/2016b, intel/2018a

libgxps

libgxps is a GObject based library for handling and rendering XPS documents.

homepage: https://wiki.gnome.org/Projects/libgxps

version	toolchain
0.3.2	GCCcore/12.3.0

libhandy

Building blocks for modern adaptive GNOME apps

homepage: https://gnome.pages.gitlab.gnome.org/libhandy/

version	toolchain
1.8.2	GCCcore/12.3.0

libharu

libHaru is a free, cross platform, open source library for generating PDF files.

homepage: http://libharu.org/

version	toolchain
2.3.0	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, foss/2016a, foss/2016b, foss/2021a, foss/2021b, intel/2017a, intel/2018b

libheif

libheif is an HEIF and AVIF file format decoder and encoder

homepage: https://github.com/strukturag/libheif

version	toolchain
1.12.0	GCC/10.3.0, GCC/11.2.0
1.16.2	GCC/11.3.0

libibmad

libibmad is a convenience library to encode, decode, and dump IB MAD packets. It is implemented on top of and in conjunction with libibumad (the umad kernel interface library.)

homepage: http://www.openfabrics.org

version	toolchain
1.3.12	GCC/4.9.3-2.25

libibumad

libibumad is the umad kernel interface library.

homepage: http://www.openfabrics.org

version	toolchain
1.3.10.2	GCC/4.9.3-2.25

libICE

X Inter-Client Exchange library for freedesktop.org

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.0.9	foss/2016a, gimkl/2.11.5, intel/2016a

libiconv

Libiconv converts from one character encoding to another through Unicode conversion

homepage: https://www.gnu.org/software/libiconv

version	toolchain
1.15	GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.2.0, GCCcore/7.3.0
1.16	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
1.17	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

libidn

GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. Libidn's purpose is to encode and decode internationalized domain names.

homepage: http://www.gnu.org/software/libidn

version	toolchain
1.32	GCCcore/5.4.0, GNU/4.9.3-2.25, foss/2016a, foss/2016b, intel/2016a
1.34	GCCcore/6.4.0
1.35	GCCcore/7.3.0, GCCcore/8.3.0, GCCcore/9.3.0
1.36	GCCcore/10.2.0, GCCcore/10.3.0
1.38	GCCcore/11.2.0
1.41	GCCcore/11.3.0

libidn2

Libidn2 implements the revised algorithm for internationalized domain names called IDNA2008/TR46.

homepage: http://www.gnu.org/software/libidn2

version	toolchain
2.3.0	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/5.4.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.3.0, GCCcore/9.3.0
2.3.2	GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/13.2.0

Libint

Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.

homepage: https://github.com/evaleev/libint

version	versionsuffix	toolchain
1.1.4		intel/2016a
1.1.6		GCC/8.2.0-2.31.1, foss/2016b, foss/2018a, foss/2020a, foss/2020b, iccifort/2019.1.144-GCC-8.2.0-2.31.1, intel/2016b, intel/2017b, intel/2018a, intel/2018b, intel/2020a
2.0.3		foss/2018b, gompi/2019a, intel/2018b
2.1.0		intel/2016b
2.4.2		intel/2018a
2.5.0		gompi/2019a, iimpi/2019a
2.6.0	-lmax-6-cp2k	GCC/10.2.0, GCC/10.3.0, gompi/2020a, iccifort/2020.4.304, iimpi/2020a, iimpi/2021a
2.7.2	-lmax-6-cp2k	GCC/11.3.0, GCC/12.2.0, GCC/12.3.0

LiBis

An ultrasensitive alignment method for low input bisulfite sequencing

homepage: https://github.com/Dangertrip/LiBis

version	versionsuffix	toolchain
20200428	-Python-3.7.4	foss/2019b

libjpeg-turbo

libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.

homepage: https://sourceforge.net/projects/libjpeg-turbo/

version	versionsuffix	toolchain
1.4.2		foss/2016a, foss/2016b, intel/2016a
1.4.2	-NASM-2.12.01	foss/2016a, intel/2016a
1.5.0		GCCcore/5.4.0, foss/2016a, foss/2016b, intel/2016b
1.5.1		foss/2016b, intel/2016b, intel/2017a
1.5.2		GCCcore/6.3.0, GCCcore/6.4.0
1.5.3		GCCcore/6.4.0
2.0.0		GCCcore/7.3.0
2.0.2		GCCcore/7.3.0, GCCcore/8.2.0
2.0.3		GCCcore/8.3.0
2.0.4		GCCcore/9.3.0
2.0.5		GCCcore/10.2.0
2.0.6		GCCcore/10.3.0, GCCcore/11.2.0
2.1.3		GCCcore/11.3.0
2.1.4		GCCcore/12.2.0
2.1.5.1		GCCcore/12.3.0
3.0.1		GCCcore/13.2.0

libjxl

JPEG XL image format reference implementation

homepage: https://github.com/libjxl/libjxl

version	toolchain
0.5	GCCcore/10.3.0
0.6.1	GCCcore/10.2.0
0.8.1	foss/2022a
0.8.2	GCCcore/13.2.0

libleidenalg

Implements the Leiden algorithm in C++

homepage: https://github.com/vtraag/libleidenalg

version	toolchain
0.11.1	foss/2022b, foss/2023a

LibLZF

LibLZF is a very small data compression library. It consists of only two .c and two .h files and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still written in portable C.

homepage: http://oldhome.schmorp.de/marc/liblzf.html

version	toolchain
3.4	GCCcore/10.2.0
3.6	GCCcore/10.3.0, GCCcore/11.3.0

libmad

MAD is a high-quality MPEG audio decoder.

homepage: https://www.underbit.com/products/mad/

version	toolchain
0.15.1b	GCCcore/11.3.0

libmatheval

GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.

homepage: http://www.gnu.org/software/libmatheval/

version	toolchain
1.1.11	GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0, foss/2016b, foss/2017a, intel/2016a, intel/2016b

libmaus2

libmaus2 is a collection of data structures and algorithms.

homepage: https://github.com/gt1/libmaus2

version	toolchain
2.0.453	intel/2018a
2.0.499	GCC/11.3.0
2.0.813	GCC/12.3.0

libmbd

Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: - The Fortran implementation is the reference, most advanced implementation, with support for analytical gradients and distributed parallelism, and additional functionality beyond the MBD method itself. It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings to the C API are provided. - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine learning applications with MBD. The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the Python package called Pymbd.

homepage: https://libmbd.github.io/index.html

version	toolchain
0.10.4	foss/2020b, foss/2021a, intel/2020b, intel/2021a

libMemcached

libMemcached is an open source C/C++ client library and tools for the memcached server (http://danga.com/memcached). It has been designed to be light on memory usage, thread safe, and provide full access to server side methods.

homepage: https://memcached.org

version	toolchain
1.0.18	GCCcore/13.2.0, GCCcore/6.4.0, GCCcore/9.3.0

libmicrohttpd

GNU libmicrohttpd is a small C library that is supposed to make it easy to run an HTTP server as part of another application.

homepage: https://www.gnu.org/software/libmicrohttpd/

version	toolchain
0.9.71	GCCcore/9.3.0
0.9.73	GCCcore/10.2.0, GCCcore/8.2.0, GCCcore/8.3.0

libmo_unpack

A library for handling the WGDOS and RLE compression schemes used in UM files.

homepage: https://github.com/SciTools/libmo_unpack

version	toolchain
3.1.2	GCCcore/6.4.0

libmypaint

libmypaint, a.k.a. "brushlib", is a library for making brushstrokes which is used by MyPaint and other projects

homepage: https://github.com/mypaint/libmypaint

version	toolchain
1.6.1	GCCcore/10.3.0

libnsl

The libnsl package contains the public client interface for NIS(YP).

homepage: https://github.com/thkukuk/libnsl

version	toolchain
1.3.0	GCCcore/10.3.0
2.0.0	GCCcore/11.3.0, GCCcore/12.2.0

libobjcryst

ObjCryst++ is Object-Oriented Crystallographic Library for C++

homepage: https://github.com/diffpy/libobjcryst

version	toolchain
2017.2.3	intel/2020a
2021.1.2	foss/2021b

libogg

Ogg is a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs.

homepage: https://xiph.org/ogg/

version	toolchain
1.3.4	GCCcore/10.2.0, GCCcore/10.3.0
1.3.5	GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0

libopus

Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unmatched for interactive speech and music transmission over the Internet, but is also intended for storage and streaming applications. It is standardized by the Internet Engineering Task Force (IETF) as RFC 6716 which incorporated technology from Skype’s SILK codec and Xiph.Org’s CELT codec.

homepage: https://www.opus-codec.org/

version	toolchain
1.3.1	GCCcore/11.3.0, GCCcore/12.2.0
1.4	GCCcore/12.3.0

libosmium

A fast and flexible C++ library for working with OpenStreetMap data. The Osmium Library has extensive support for all types of OSM entities: nodes, ways, relations, and changesets. It allows reading from and writing to OSM files in XML and PBF formats, including change files and full history files. Osmium can store OSM data in memory and on disk in various formats and using various indexes. Its easy to use handler interface allows you to quickly write data filtering and conversion functions. Osmium can create WKT, WKB, OGR, GEOS and GeoJSON geometries for easy conversion into many GIS formats and it can assemble multipolygons from ways and relations.

homepage: https://osmcode.org/libosmium/

version	versionsuffix	toolchain
2.15.4	-Python-3.6.6	foss/2018b
2.15.6	-Python-3.7.4	foss/2019b

libpci

Library for portable access to PCI bus configuration registers from PCI Utils.

homepage: https://github.com/pciutils/pciutils

version	toolchain
3.7.0	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/6.4.0

libpciaccess

Generic PCI access library.

homepage: https://cgit.freedesktop.org/xorg/lib/libpciaccess/

version	toolchain
0.13.4	foss/2016a, foss/2016b, gimkl/2.11.5, intel/2016a, intel/2016b
0.14	GCCcore/6.4.0, GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0
0.16	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/9.2.0, GCCcore/9.3.0
0.17	GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

libplinkio

A small C and Python library for reading PLINK genotype files.

homepage: https://github.com/mfranberg/libplinkio

version	toolchain
0.9.8	GCCcore/9.3.0

libpng

libpng is the official PNG reference library

homepage: http://www.libpng.org/pub/png/libpng.html

version	toolchain
1.2.58	system
1.2.59	system
1.5.30	system
1.6.21	foss/2016a, gimkl/2.11.5, intel/2016a
1.6.23	foss/2016a, foss/2016b, intel/2016b
1.6.24	GCCcore/4.9.3, GCCcore/5.4.0, foss/2016b, intel/2016b
1.6.26	foss/2016b, intel/2016b
1.6.27	intel/2016b
1.6.28	GCCcore/5.4.0, GCCcore/6.3.0, gimkl/2017a
1.6.29	GCCcore/6.3.0
1.6.32	GCCcore/6.4.0
1.6.34	GCCcore/6.4.0, GCCcore/7.3.0
1.6.36	GCCcore/8.2.0
1.6.37	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/8.3.0, GCCcore/9.3.0
1.6.38	GCCcore/12.2.0
1.6.39	GCCcore/12.3.0
1.6.40	GCCcore/13.2.0

libpsl

C library for the Public Suffix List

homepage: https://rockdaboot.github.io/libpsl

version	toolchain
0.20.2	GCCcore/7.3.0
0.21.0	GCCcore/8.2.0, GCCcore/8.3.0
0.21.1	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0

libPSML

A library to handle PSML, the pseudopotential markup language.

homepage: https://launchpad.net/libpsml

version	toolchain
1.1.7	foss/2016b, foss/2017a
1.1.8	iccifort/2019.5.281
1.1.10	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, iccifort/2020.4.304, intel-compilers/2021.2.0, intel-compilers/2021.4.0
1.1.12	GCC/11.3.0

libpsortb

PSORT family of programs for subcellular localization prediction as well as other datasets and resources relevant to localization prediction.

homepage: http://psort.org/

version	toolchain
1.0	foss/2016a

libpspio

libpspio is a library to read and write pseudopotentials in multiple formats.

homepage: https://gitlab.com/ElectronicStructureLibrary/libpspio

version	toolchain
0.2.4	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, iccifort/2020.4.304, intel-compilers/2021.2.0, intel-compilers/2021.4.0

libpthread-stubs

The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.

homepage: http://xcb.freedesktop.org/

version	toolchain
0.3	GCCcore/6.4.0, foss/2016a, foss/2016b, gimkl/2.11.5, intel/2016a, intel/2016b
0.4	GCCcore/6.4.0

libQGLViewer

libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers.

homepage: http://libqglviewer.com/

version	versionsuffix	toolchain
2.6.3		foss/2016a, foss/2016b, intel/2016b
2.6.3	-Mesa-11.2.1	foss/2016a, intel/2016a
2.6.4		intel/2016b
2.7.1		intel/2018a
2.8.0		GCCcore/10.3.0

libreadline

The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.

homepage: https://tiswww.case.edu/php/chet/readline/rltop.html

version	toolchain
6.3	GCC/4.8.2, GCC/4.8.4, GCC/4.9.2, GCC/4.9.3-2.25, GCC/5.4.0-2.26, GCCcore/4.9.3, GCCcore/5.4.0, GCCcore/6.3.0, GNU/4.9.3-2.25, foss/2016.04, foss/2016a, foss/2016b, gimkl/2.11.5, gimkl/2017a, intel/2016.02-GCC-4.9, intel/2016a, intel/2016b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25, system
7.0	GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.2.0, GCCcore/7.3.0
8.0	GCCcore/10.2.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0, system
8.1	FCC/4.5.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0
8.1.2	GCCcore/11.3.0, GCCcore/12.1.0
8.2	GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.1.0, GCCcore/13.2.0

libRmath

The routines supporting the distribution and special functions in R and a few others are declared in C header file Rmath.h. These can be compiled into a standalone library for linking to other applications.

homepage: https://cran.r-project.org/doc/manuals/r-release/R-admin.html#The-standalone-Rmath-library

version	toolchain
3.6.0	foss/2018b
4.0.0	GCCcore/9.3.0
4.1.0	GCCcore/10.2.0
4.1.2	GCCcore/11.2.0
4.2.0	GCCcore/10.3.0
4.2.1	GCCcore/11.3.0

librosa

Python module for audio and music processing

homepage: https://librosa.github.io

version	versionsuffix	toolchain
0.7.2	-Python-3.7.4	foss/2019b, fosscuda/2019b
0.10.1		foss/2023a

librsb

A shared memory parallel sparse matrix computations library for the Recursive Sparse Blocks format

homepage: https://sourceforge.net/projects/librsb/

version	toolchain
1.2.0.9	GCC/10.2.0
1.2.0.10	GCC/10.2.0
1.2.0.11	GCC/10.2.0
1.3.0.0	GCC/10.2.0
1.3.0.1	GCC/10.2.0

librsvg

Librsvg is a library to render SVG files using cairo.

homepage: https://wiki.gnome.org/Projects/LibRsvg

version	toolchain
2.40.15	intel/2016a
2.48.4	foss/2019a
2.51.2	GCCcore/10.3.0
2.52.8	GCCcore/11.2.0
2.55.1	GCCcore/11.3.0
2.58.0	GCCcore/13.2.0

librttopo

The RT Topology Library exposes an API to create and manage standard (ISO 13249 aka SQL/MM) topologies using user-provided data stores.

homepage: https://git.osgeo.org/gitea/rttopo/librttopo

version	toolchain
1.1.0	GCC/11.2.0

libsamplerate

Secret Rabbit Code (aka libsamplerate) is a Sample Rate Converter for audio.

homepage: http://www.mega-nerd.com/libsamplerate

version	toolchain
0.1.9	GCCcore/8.2.0

libSBML

libSBML (Systems Biology Markup Language library) is a free, open-source programming library to help you read, write, manipulate, translate, and validate SBML files and data streams. It's not an application itself (though it does come with example programs), but rather a library you embed in your own applications.

homepage: http://sbml.org/Software/libSBML

version	toolchain
5.19.0	GCC/10.2.0, GCC/10.3.0
5.19.7	GCC/11.3.0

libsigc++

The libsigc++ package implements a typesafe callback system for standard C++.

homepage: https://libsigcplusplus.github.io/libsigcplusplus/

version	toolchain
2.10.0	GCCcore/6.4.0
2.10.1	GCCcore/7.3.0
2.10.2	GCCcore/8.2.0, GCCcore/8.3.0
2.10.8	GCCcore/10.3.0
2.12.1	GCCcore/11.3.0
3.4.0	GCCcore/11.3.0

libsigsegv

GNU libsigsegv is a library for handling page faults in user mode.

homepage: https://www.gnu.org/software/libsigsegv/

version	toolchain
2.11	GCCcore/6.4.0
2.12	GCCcore/9.3.0
2.13	GCCcore/10.2.0
2.14	GCCcore/12.2.0

libSM

X11 Session Management library, which allows for applications to both manage sessions, and make use of session managers to save and restore their state for later use.

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.2.2	foss/2016a, gimkl/2.11.5, intel/2016a

libsndfile

Libsndfile is a C library for reading and writing files containing sampled sound (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.

homepage: http://www.mega-nerd.com/libsndfile

version	toolchain
1.0.28	GCCcore/10.2.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0, intel/2017a
1.0.31	GCCcore/10.3.0, GCCcore/11.2.0
1.1.0	GCCcore/11.3.0
1.2.0	GCCcore/12.2.0
1.2.2	GCCcore/12.3.0

libsodium

Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.

homepage: https://doc.libsodium.org/

version	toolchain
1.0.6	intel/2016a
1.0.8	foss/2016a
1.0.11	foss/2016b, intel/2016b
1.0.12	GCCcore/6.4.0, intel/2017a
1.0.13	GCCcore/6.4.0, foss/2017a
1.0.16	GCCcore/6.4.0, GCCcore/7.3.0
1.0.17	GCCcore/8.2.0
1.0.18	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/8.3.0, GCCcore/9.3.0
1.0.19	GCCcore/13.2.0

LibSoup

libsoup is an HTTP client/server library for GNOME. It uses GObjects and the glib main loop, to integrate well with GNOME applications, and also has a synchronous API, for use in threaded applications.

homepage: https://wiki.gnome.org/Projects/libsoup

version	toolchain
2.66.1	GCCcore/8.2.0
2.70.0	GCCcore/8.3.0
2.72.0	GCCcore/10.2.0
2.74.0	GCCcore/10.3.0
3.0.7	GCC/11.2.0
3.0.8	GCC/11.3.0

libspatialindex

C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API

homepage: https://libspatialindex.org

version	toolchain
1.8.5	GCCcore/6.4.0, GCCcore/8.2.0, foss/2016b, intel/2016b, intel/2018a
1.9.3	GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/13.2.0

libspatialite

SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities.

homepage: https://www.gaia-gis.it/fossil/libspatialite/home

version	versionsuffix	toolchain
4.3.0a		foss/2016b, foss/2018b, intel/2016b
4.3.0a	-Python-3.7.2	foss/2019a
4.3.0a	-Python-3.7.4	GCC/8.3.0
5.0.1		GCC/11.2.0

libspectre

libspectre is a small library for rendering Postscript documents. It provides a convenient easy to use API for handling and rendering Postscript documents.

homepage: https://www.freedesktop.org/wiki/Software/libspectre/

version	toolchain
0.2.12	GCCcore/12.3.0

libssh

Multiplatform C library implementing the SSHv2 protocol on client and server side

homepage: https://www.libssh.org

version	toolchain
0.9.0	GCCcore/6.4.0

libStatGen

Useful set of classes for creating statistical genetic programs.

homepage: https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen

version	toolchain
1.0.15	GCCcore/10.2.0
20190330	GCCcore/6.4.0

LIBSVM

LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification.

homepage: https://www.csie.ntu.edu.tw/~cjlin/libsvm/

version	toolchain
3.22	intel/2016b, intel/2017b
3.23	foss/2018b, intel/2018b
3.24	GCCcore/9.3.0
3.25	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0
3.30	GCCcore/11.3.0

LIBSVM-Python

This tool provides a simple Python interface to LIBSVM, a library for support vector machines (http://www.csie.ntu.edu.tw/~cjlin/libsvm). The interface is very easy to use as the usage is the same as that of LIBSVM. The interface is developed with the built-in Python library "ctypes".

homepage: https://pypi.org/project/libsvm-official/

version	toolchain
3.30	foss/2022a

libtar

C library for manipulating POSIX tar files

homepage: https://repo.or.cz/libtar.git

version	toolchain
1.2.20	GCCcore/7.3.0, GCCcore/8.2.0

libtasn1

Libtasn1 is the ASN.1 library used by GnuTLS, GNU Shishi and some other packages. It was written by Fabio Fiorina, and has been shipped as part of GnuTLS for some time but is now a proper GNU package.

homepage: https://www.gnu.org/software/libtasn1/

version	toolchain
4.7	GNU/4.9.3-2.25, foss/2016a, intel/2016a
4.12	GCCcore/5.4.0
4.13	GCCcore/7.3.0, GCCcore/8.2.0
4.16.0	GCCcore/10.2.0, GCCcore/8.3.0
4.17.0	GCCcore/10.3.0
4.18.0	GCCcore/11.2.0
4.19.0	GCCcore/11.3.0

libtecla

The tecla library provides UNIX and LINUX programs with interactive command line editing facilities, similar to those of the UNIX tcsh shell. In addition to simple command-line editing, it supports recall of previously entered command lines, TAB completion of file names or other tokens, and in-line wild-card expansion of filenames. The internal functions which perform file-name completion and wild-card expansion are also available externally for optional use by programs.

homepage: https://sites.astro.caltech.edu/~mcs/tecla/

version	toolchain
1.6.3	GCCcore/10.2.0

LibTIFF

tiff: Library and tools for reading and writing TIFF data files

homepage: https://libtiff.gitlab.io/libtiff/

version	toolchain
4.0.6	GCCcore/5.4.0, foss/2016a, foss/2016b, intel/2016a, intel/2016b
4.0.7	foss/2016b, intel/2017a
4.0.8	intel/2017a, intel/2017b
4.0.9	GCCcore/6.4.0, GCCcore/7.3.0, foss/2017b, intel/2017b, intel/2018.01, intel/2018b
4.0.10	GCCcore/8.2.0, GCCcore/8.3.0
4.1.0	GCCcore/10.2.0, GCCcore/8.3.0, GCCcore/9.3.0
4.2.0	GCCcore/10.3.0
4.3.0	GCCcore/11.2.0, GCCcore/11.3.0
4.4.0	GCCcore/12.2.0
4.5.0	GCCcore/12.3.0
4.6.0	GCCcore/13.2.0

libtirpc

Libtirpc is a port of Suns Transport-Independent RPC library to Linux.

homepage: https://sourceforge.net/projects/libtirpc/

version	toolchain
1.1.4	GCCcore/7.3.0, GCCcore/8.2.0
1.2.6	GCCcore/8.3.0, GCCcore/9.3.0
1.3.1	GCCcore/10.2.0
1.3.2	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0
1.3.3	GCCcore/12.2.0, GCCcore/12.3.0
1.3.4	GCCcore/13.2.0

libtool

GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.

homepage: https://www.gnu.org/software/libtool

version	toolchain
2.4.2	GCC/4.8.2, GCC/4.9.2
2.4.5	GCC/4.8.4, GCC/4.9.2
2.4.6	FCC/4.5.0, GCC/4.8.4, GCC/4.9.2, GCC/4.9.3, GCC/4.9.3-2.25, GCC/5.2.0, GCC/5.4.0-2.26, GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/4.9.2, GCCcore/4.9.3, GCCcore/5.3.0, GCCcore/5.4.0, GCCcore/6.1.0, GCCcore/6.2.0, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.2.0, GCCcore/9.3.0, GNU/4.9.2-2.25, GNU/4.9.3-2.25, GNU/5.1.0-2.25, foss/2016.04, foss/2016a, foss/2016b, gimkl/2.11.5, intel/2016.02-GCC-4.9, intel/2016a, intel/2016b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25, system
2.4.7	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.1.0, GCCcore/13.2.0, system

libtree

libtree is a tool that turns ldd into a tree, explains why shared libraries are found and why not and optionally deploys executables and dependencies into a single directory

homepage: https://github.com/haampie/libtree

version	toolchain
2.0.0	GCCcore/10.3.0
3.0.3	system

libunistring

This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.

homepage: https://www.gnu.org/software/libunistring/

version	toolchain
0.9.3	GCC/4.9.3-2.25, GNU/4.9.3-2.25, foss/2016a, intel/2016a
0.9.6	GCCcore/5.4.0, foss/2016b, foss/2017a, intel/2016b
0.9.7	GCCcore/6.4.0
0.9.10	GCCcore/10.3.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
1.0	GCCcore/11.2.0, GCCcore/11.3.0
1.1	GCCcore/10.2.0, GCCcore/12.3.0

libunwind

The primary goal of libunwind is to define a portable and efficient C programming interface (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain (non-local goto). The API supports both local (same-process) and remote (across-process) operation. As such, the API is useful in a number of applications

homepage: https://www.nongnu.org/libunwind/

version	toolchain
1.1	GCC/4.9.2, foss/2016a, intel/2016b
1.2.1	GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.3.0, foss/2016b
1.3.1	GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
1.4.0	GCCcore/10.2.0, GCCcore/10.3.0
1.5.0	GCCcore/10.3.0, GCCcore/11.2.0
1.6.2	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

libutempter

libutempter is library that provides an interface for terminal emulators such as screen and xterm to record user sessions to utmp and wtmp files.

homepage: http://git.altlinux.org/people/ldv/packages/?p=libutempter.git

version	toolchain
1.1.6.2	GCC/6.4.0-2.28

LibUUID

Portable uuid C library

homepage: http://sourceforge.net/projects/libuuid/

version	toolchain
1.0.3	GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, foss/2016a, intel/2017a, intel/2017b

libuv

libuv is a multi-platform support library with a focus on asynchronous I/O.

homepage: https://libuv.org

version	toolchain
1.37.0	GCCcore/8.3.0

libvdwxc

libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.

homepage: https://libvdwxc.org

version	toolchain
0.3.2	foss/2018b
0.4.0	foss/2019a, foss/2019b, foss/2020a, foss/2020b, foss/2021a, foss/2021b, foss/2022a, foss/2023a, intel/2020b, intel/2021a, intel/2021b

libvorbis

Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed audio format

homepage: https://xiph.org/vorbis/

version	toolchain
1.3.7	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0

libvori

C++ library implementing the Voronoi integration as well as the compressed bqb file format. The present version of libvori is a very early development version, which is hard-coded to work with the CP2k program package.

homepage: https://brehm-research.de/libvori.php

version	toolchain
220621	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0

libWallModelledLES

libWallModelledLES is a library based on OpenFOAM® technology, extending the capabilities of OpenFOAM in the area of wall-modelled LES (WMLES). This is a turbulence modelling methodology, which allows to make LES cheaper by not resolving the inner region of turbulent boundary layers.

homepage: https://bitbucket.org/lesituu/libwallmodelledles/

version	toolchain
0.6.1	foss/2021b

libwebp

WebP is a modern image format that provides superior lossless and lossy compression for images on the web. Using WebP, webmasters and web developers can create smaller, richer images that make the web faster.

homepage: https://developers.google.com/speed/webp/

version	toolchain
1.0.0	foss/2018b
1.0.2	GCCcore/7.3.0, GCCcore/8.2.0
1.1.0	GCCcore/10.2.0, GCCcore/8.3.0, GCCcore/9.3.0
1.2.0	GCCcore/10.3.0, GCCcore/11.2.0
1.2.4	GCCcore/11.3.0
1.3.1	GCCcore/12.2.0, GCCcore/12.3.0
1.3.2	GCCcore/13.2.0

libwpe

WPE is the reference WebKit port for embedded and low-consumption computer devices. It has been designed from the ground-up with performance, small footprint, accelerated content rendering, and simplicity of deployment in mind, bringing the excellence of the WebKit engine to countless platforms and target devices.

homepage: https://webkit.org/wpe

version	toolchain
1.13.3	GCCcore/11.2.0
1.14.1	GCCcore/11.3.0

libX11

X11 client-side library

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.6.3	foss/2016a, gimkl/2.11.5, intel/2016a

libXau

The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display.

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.0.8	GCCcore/6.4.0, foss/2016a, gimkl/2.11.5, intel/2016a

libxc

Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.

homepage: https://libxc.gitlab.io

version	toolchain
2.2.2	GCC/8.2.0-2.31.1, foss/2018b, intel/2018b
2.2.3	foss/2016b, intel/2016a, intel/2016b, intel/2017b, intel/2018a
3.0.0	GCC/5.4.0-2.26, iccifort/2016.3.210-GCC-5.4.0-2.26, intel/2016a, intel/2016b, intel/2017a, intel/2017b
3.0.1	GCC/8.2.0-2.31.1, foss/2016b, foss/2017a, foss/2018a, foss/2018b, foss/2020a, foss/2020b, gimkl/2017a, intel/2018a, intel/2018b, intel/2020a
4.0.1	foss/2017b, intel/2017b
4.0.3	foss/2016b, foss/2017a
4.2.3	foss/2017b, foss/2018a, foss/2018b, gimkl/2017a, intel/2018a, intel/2018b
4.3.4	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/8.2.0-2.31.1, GCC/8.3.0, GCC/9.3.0, iccifort/2019.1.144-GCC-8.2.0-2.31.1, iccifort/2019.5.281, iccifort/2020.1.217, iccifort/2020.4.304, intel-compilers/2021.2.0, intel-compilers/2021.4.0
5.1.2	GCC/10.2.0
5.1.3	GCC/10.2.0
5.1.5	GCC/10.3.0, intel-compilers/2021.2.0
5.1.6	GCC/11.2.0, intel-compilers/2021.4.0
5.2.3	GCC/11.3.0, intel-compilers/2022.1.0
6.1.0	GCC/12.2.0, intel-compilers/2022.2.1
6.2.2	GCC/12.3.0, GCC/13.2.0, intel-compilers/2023.1.0, intel-compilers/2023.2.1

libxcb

The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.

homepage: https://xcb.freedesktop.org/

version	toolchain
1.11.1	foss/2016a, gimkl/2.11.5, intel/2016a
1.13	GCCcore/6.4.0

libXcursor

X Cursor management library

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.1.14	foss/2016a, intel/2016a

libXdamage

X Damage extension library

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.1.4	foss/2016a, gimkl/2.11.5, intel/2016a

libXdmcp

The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is useful for allowing clients to interact with the X Display Manager.

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.1.2	GCCcore/6.4.0, foss/2016a, gimkl/2.11.5, intel/2016a

libXext

Common X Extensions library

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.3.3	foss/2016a, gimkl/2.11.5, intel/2016a

libXfixes

X Fixes extension library

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
5.0.1	foss/2016a, gimkl/2.11.5, intel/2016a
5.0.2	intel/2016a

libXfont

X font libary

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	versionsuffix	toolchain
1.5.1		foss/2016a, gimkl/2.11.5, intel/2016a
1.5.1	-freetype-2.6.3	foss/2016a, intel/2016a

libXft

X11 client-side library

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	versionsuffix	toolchain
2.3.2		foss/2016a, intel/2016a
2.3.2	-fontconfig-2.11.95	intel/2016a
2.3.2	-freetype-2.6.3	foss/2016a

libXi

LibXi provides an X Window System client interface to the XINPUT extension to the X protocol.

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.7.6	foss/2016a, intel/2016a

libXinerama

Xinerama multiple monitor library

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.1.3	foss/2016a, intel/2016a

libxkbcommon

xkbcommon is a library to handle keyboard descriptions, including loading them from disk, parsing them and handling their state. It's mainly meant for client toolkits, window systems, and other system applications.

homepage: http://xkbcommon.org/

version	toolchain
0.6.1	foss/2016a, intel/2016a

libxml++

libxml++ is a C++ wrapper for the libxml XML parser library.

homepage: http://libxmlplusplus.sourceforge.net

version	toolchain
2.40.1	GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0
2.42.1	GCC/10.3.0

libxml2

Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).

homepage: http://xmlsoft.org/

version	versionsuffix	toolchain
2.9.2		GCC/4.8.3, GCC/4.8.4, GCC/4.9.2, GCC/4.9.3-2.25, GNU/4.9.3-2.25
2.9.3		GCC/4.9.3-2.25, foss/2016a, gimkl/2.11.5, intel/2016a
2.9.3	-Python-2.7.11	foss/2016a, intel/2016a
2.9.4		GCC/5.4.0-2.26, GCCcore/4.9.3, GCCcore/5.4.0, GCCcore/6.3.0, GCCcore/6.4.0, foss/2016.04, foss/2016a, foss/2016b, gimkl/2017a, intel/2016b
2.9.4	-Python-2.7.12	foss/2016b, intel/2016b
2.9.4	-Python-2.7.13	intel/2017a
2.9.5		GCCcore/6.3.0
2.9.6		GCCcore/6.4.0
2.9.7		GCCcore/6.4.0
2.9.8		GCCcore/6.4.0, GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/8.2.0
2.9.9		GCCcore/8.3.0
2.9.10		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/9.2.0, GCCcore/9.3.0
2.9.13		GCCcore/11.3.0
2.10.3		GCCcore/12.2.0
2.11.4		GCCcore/12.3.0
2.11.5		GCCcore/13.2.0

libxml2-python

Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). This is the Python binding.

homepage: http://xmlsoft.org/

version	versionsuffix	toolchain
2.9.7	-Python-2.7.14	intel/2018a
2.9.8	-Python-2.7.15	foss/2018b
2.9.8	-Python-3.7.2	GCCcore/8.2.0
2.9.13		GCCcore/11.3.0
2.11.4		GCCcore/12.3.0

libXmu

libXmu provides a set of miscellaneous utility convenience functions for X libraries to use. libXmuu is a lighter-weight version that does not depend on libXt or libXext

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.1.2	foss/2016a, intel/2016a

libXp

libXp provides the X print library.

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.0.3	intel/2016a

libXpm

libXp provides the X print library.

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
3.5.11	foss/2016a, intel/2016a

libXrandr

X Resize, Rotate and Reflection extension library

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.5.0	foss/2016a, intel/2016a

libXrender

X11 client-side library

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
0.9.9	foss/2016a, gimkl/2.11.5, intel/2016a

libxslt

Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform).

homepage: http://xmlsoft.org/

version	versionsuffix	toolchain
1.1.28		foss/2016a, intel/2016a
1.1.28	-Python-2.7.11	intel/2016a
1.1.29		foss/2016b, intel/2016a, intel/2016b, intel/2017a
1.1.30		GCCcore/6.3.0
1.1.32		GCCcore/6.4.0, GCCcore/7.3.0
1.1.33		GCCcore/8.2.0
1.1.34		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/8.3.0, GCCcore/9.3.0
1.1.37		GCCcore/12.2.0
1.1.38		GCCcore/12.3.0, GCCcore/13.2.0

libxsmm

LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).

homepage: https://github.com/hfp/libxsmm

version	toolchain
1.4	intel/2016a
1.4.4	foss/2016b, intel/2016b
1.6.4	foss/2016b, intel/2016b
1.8.2	intel/2017b
1.8.3	foss/2018a, intel/2018a
1.10	GCC/8.2.0-2.31.1, foss/2018b, iccifort/2019.1.144-GCC-8.2.0-2.31.1, intel/2018b
1.16.1	GCC/10.2.0, GCC/9.3.0, iccifort/2020.1.217, iccifort/2020.4.304
1.16.2	GCC/10.3.0, intel-compilers/2021.2.0
1.17	GCC/11.2.0, GCC/11.3.0, GCC/12.2.0, GCC/12.3.0

libXt

libXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation).

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.1.5	foss/2016a, gimkl/2.11.5, intel/2016a

libXxf86vm

X11 XFree86 video mode extension library

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.1.4	foss/2016a, intel/2016a

libyaml

LibYAML is a YAML parser and emitter written in C.

homepage: https://pyyaml.org/wiki/LibYAML

version	toolchain
0.1.6	GCCcore/6.4.0, foss/2016b, intel/2016a, intel/2016b
0.1.7	GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.3.0, system
0.2.1	GCCcore/7.3.0, system
0.2.2	GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
0.2.5	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

libzeep

Libzeep was originally developed to make it easy to create SOAP servers.

homepage: https://github.com/mhekkel/libzeep

version	toolchain
5.0.1	gompi/2019b

libzip

libzip is a C library for reading, creating, and modifying zip archives.

homepage: https://libzip.org/

version	toolchain
1.5.2	GCCcore/8.2.0
1.7.3	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0
1.9.2	GCCcore/11.3.0

lie_learn

lie_learn is a python package that knows how to do various tricky computations related to Lie groups and manifolds (mainly the sphere S2 and rotation group SO3).

homepage: https://github.com/AMLab-Amsterdam/lie_learn

version	versionsuffix	toolchain
0.0.1.post1	-Python-3.7.4	fosscuda/2019b

lifelines

lifelines is a complete survival analysis library, written in pure Python.

homepage: https://lifelines.readthedocs.io/en/latest/

version	versionsuffix	toolchain
0.22.8	-Python-3.7.2	fosscuda/2019a
0.26.3		fosscuda/2020b
0.27.4		foss/2022a

Lighter

Fast and memory-efficient sequencing error corrector

homepage: https://github.com/mourisl/Lighter

version	toolchain
1.1.1	foss/2018a
1.1.2	GCC/11.2.0, foss/2018b

liknorm

Moments of the product of an exponential-family likelihood with a Normal distribution.

homepage: https://github.com/limix/liknorm

version	toolchain
1.5.2	GCCcore/7.3.0

likwid

Likwid stands for Like I knew what I am doing. This project contributes easy to use command line tools for Linux to support programmers in developing high performance multi threaded programs.

homepage: https://github.com/RRZE-HPC/likwid

version	toolchain
4.0.1	GNU/4.9.3-2.25
4.1.0	GCCcore/4.9.3
4.2.0	GCCcore/6.3.0, GCCcore/6.4.0, foss/2017a, intel/2017a
4.3.2	GCCcore/6.4.0, GCCcore/7.3.0
5.0.1	GCCcore/8.3.0
5.1.0	GCCcore/9.3.0
5.2.0	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, iccifort/2020.4.304, intel-compilers/2021.2.0
5.2.1	GCC/11.2.0
5.2.2	GCC/11.3.0
5.3.0	GCC/12.3.0

limix

Limix is a flexible and efficient linear mixed model library with interfaces to Python. Genomic analyses require flexible models that can be adapted to the needs of the user. Limix is smart about how particular models are fitted to save computational cost.

homepage: https://github.com/limix/limix

version	versionsuffix	toolchain
2.0.4	-Python-3.6.6	foss/2018b

LinBox

C++ library for exact, high-performance linear algebra

homepage: https://linalg.org/

version	toolchain
1.4.0	foss/2016a
1.7.0	gfbf/2022a

line_profiler

line_profiler is a module for doing line-by-line profiling of functions. kernprof is a convenient script for running either line_profiler or the Python standard library's cProfile or profile modules, depending on what is available.

homepage: https://github.com/pyutils/line_profiler

version	versionsuffix	toolchain
3.1.0	-Python-3.8.2	foss/2020a
3.5.1		foss/2021b
4.0.0		foss/2022a
4.1.1		GCCcore/12.2.0

Lingeling

One of the design principles of the state-of-the-art SAT solver Lingeling is to use as compact data structures as possible. These reduce memory usage, increase cache efficiency and thus improve runtime, particularly, when using multiple solver instances on multi-core machines, as in our parallel portfolio solver Plingeling and our cube and conquer solver Treengeling.

homepage: http://fmv.jku.at/lingeling/

version	toolchain
bcp	GCC/9.3.0

LISFLOOD-FP

The LISFLOOD-FP is a raster-based hydrodynamic model originally developed by the University of Bristol. It has undergone extensive development since conception and includes a collection of numerical schemes implemented to solve a variety of mathematical approximations of the 2D shallow water equations of different complexity. The local inertia solver, known as the ACC solver, is widely used to simulate floods with gradually-varying, subcritical flow over sufficiently rough surfaces with Manning’s coefficient of at least 0.03. It has a version with CPU-specific optimisations and enhanced with a subgrid channel model. LISFLOOD-FP also includes second-order discontinuous Galerkin (DG2) and first-order finite volume (FV1) solvers of the full shallow water equations for modelling a wide range of flows, including rapidly-propagating, supercritical flows, shock waves, or flows over very smooth surfaces. The DG2/FV1 solvers are parallelised for the multi-core CPU architecture, but do not integrate with the subgrid channel model nor with the CPU-specific optimisations.

homepage: https://www.seamlesswave.com/LISFLOOD8.0.html

version	versionsuffix	toolchain
8.1		gompi/2022a
8.1	-CUDA-11.7.0	gompi/2022a

lit

lit is a portable tool for executing LLVM and Clang style test suites, summarizing their results, and providing indication of failures.

homepage: https://llvm.org/docs/CommandGuide/lit.html

version	toolchain
18.1.2	GCCcore/12.3.0

LittleCMS

Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance.

homepage: http://www.littlecms.com/

version	toolchain
2.7	intel/2016a
2.8	GCCcore/6.4.0, foss/2016b, intel/2016b, intel/2017a
2.9	GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0, foss/2017b, foss/2018a, intel/2017b
2.11	GCCcore/10.2.0
2.12	GCCcore/10.3.0, GCCcore/11.2.0
2.13.1	GCCcore/11.3.0
2.14	GCCcore/12.2.0
2.15	GCCcore/12.3.0, GCCcore/13.2.0

LLDB

The debugger component of the LLVM project

homepage: https://lldb.llvm.org/

version	versionsuffix	toolchain
11.0.0	-Python-3.8.2	GCCcore/9.3.0

LLVM

The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator.

homepage: https://llvm.org/

version	versionsuffix	toolchain
3.7.1		foss/2016a, gimkl/2.11.5, intel/2016a
3.8.0		foss/2016a, intel/2016a
3.8.1		GCCcore/4.9.3, foss/2016b, intel/2016b
3.9.0		foss/2016b, intel/2016b
3.9.1		foss/2017a
4.0.0		foss/2017a, intel/2017a
4.0.1		intel/2017a, intel/2017b
5.0.0		foss/2017b, fosscuda/2017b, intel/2017b, intelcuda/2017b
5.0.1		GCCcore/6.4.0
6.0.0		GCCcore/6.4.0, GCCcore/7.3.0
7.0.0		GCCcore/7.2.0, GCCcore/7.3.0
7.0.1		GCCcore/8.2.0
8.0.1		GCCcore/8.3.0
9.0.0		GCCcore/8.3.0
9.0.1		GCCcore/8.3.0, GCCcore/9.3.0
10.0.0		GCCcore/8.3.0
10.0.1		GCCcore/10.2.0
11.0.0		GCCcore/10.2.0
11.1.0		GCCcore/10.3.0
12.0.1		GCCcore/10.3.0, GCCcore/11.2.0
14.0.3		GCCcore/11.3.0
14.0.6	-llvmlite	GCCcore/12.2.0, GCCcore/12.3.0
15.0.5		GCCcore/12.2.0
16.0.6		GCCcore/12.3.0, GCCcore/13.2.0

LMDB

LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases.

homepage: https://symas.com/lmdb

version	toolchain
0.9.18	foss/2016a
0.9.21	GCCcore/6.4.0, intel/2017a
0.9.22	GCCcore/7.3.0
0.9.23	GCCcore/8.2.0
0.9.24	GCCcore/10.2.0, GCCcore/8.3.0, GCCcore/9.3.0
0.9.28	GCCcore/10.3.0
0.9.29	GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0
0.9.31	GCCcore/12.3.0

LMfit

Lmfit provides a high-level interface to non-linear optimization and curve fitting problems for Python

homepage: https://lmfit.github.io/lmfit-py

version	versionsuffix	toolchain
0.9.9	-Python-3.6.4	intel/2018a
0.9.14	-Python-2.7.15	intel/2018b
1.0.0	-Python-3.7.4	foss/2019b, intel/2019b
1.0.1	-Python-3.8.2	foss/2020a
1.0.2		foss/2020b, intel/2020b
1.0.3		foss/2021a, foss/2022a, intel/2022a
1.2.1		foss/2021b

Lmod

Lmod is a Lua based module system. Modules allow for dynamic modification of a user's environment under Unix systems. See www.tacc.utexas.edu/tacc-projects/lmod for a complete description. Lmod is a new implementation that easily handles the MODULEPATH Hierarchical problem. It is drop-in replacement for TCL/C modules and reads TCL modulefiles directly.

homepage: http://sourceforge.net/projects/lmod/

version	toolchain
5.2	GCC/4.8.2
5.2.5	GCC/4.8.2
5.3	GCC/4.8.2
5.4	GCC/4.8.2
5.4.2	GCC/4.8.2
5.5	GCC/4.8.2
5.5.1	GCC/4.8.2
5.6	GCC/4.8.2
5.7	GCC/4.8.2
5.8	GCC/4.8.2
5.8.5	GCC/4.8.2
5.9	GCC/4.8.2, GCC/4.8.4
6.4.2	system
7.3	system

lmoments3

Estimate linear moments for statistical distribution functions.

homepage: https://github.com/OpenHydrology/lmoments3

version	toolchain
1.0.6	foss/2022a

LncLOOM

LncLOOM is a graph-based framework that uses integer programming to identify combinations of short motifs that are deeply conserved in rapidly evolving sequences.

homepage: https://github.com/lncLOOM/lncLOOMv2/

version	toolchain
2.0	foss/2020b

LocARNA

LocARNA is a collection of alignment tools for the structural analysis of RNA. Given a set of RNA sequences, LocARNA simultaneously aligns and predicts common structures for your RNAs. In this way, LocARNA performs Sankoff-like alignment and is in particular suited for analyzing sets of related RNAs without known common structure.

homepage: http://www.bioinf.uni-freiburg.de/Software/LocARNA/

version	versionsuffix	toolchain
1.9.2		foss/2016b
1.9.2.2	-Python-3.6.6	foss/2018b
1.9.2.3		foss/2021b

LoFreq

Fast and sensitive variant calling from next-gen sequencing data

homepage: http://csb5.github.io/lofreq

version	versionsuffix	toolchain
2.1.2	-Python-2.7.12	intel/2016b
2.1.3.1	-Python-2.7.14	foss/2017b, intel/2017b, intel/2018a

Log-Log4perl

Log4perl

homepage: https://metacpan.org/pod/Log::Log4perl

version	toolchain
1.47	foss/2016a

logaddexp

C library that implements the logarithm of the sum of exponentiations. Inspired by NumPy's logaddexp function.

homepage: https://github.com/horta/logaddexp

version	toolchain
1.0.3	GCCcore/7.3.0

LOHHLA

LOHHLA, Loss Of Heterozygosity in Human Leukocyte Antigen, a computational tool to evaluate HLA loss using next-generation sequencing data.

homepage: https://bitbucket.org/mcgranahanlab/lohhla

version	versionsuffix	toolchain
2018.11.05	-R-3.5.1	foss/2018b

Loki

Loki is a C++ library of designs, containing flexible implementations of common design patterns and idioms.

homepage: http://loki-lib.sourceforge.net/

version	toolchain
0.1.7	foss/2016a, foss/2016b, intel/2016a, intel/2016b, intel/2018a

longestrunsubsequence

Implementation of a solver for the Longest Run Subsequence Problem. Given a sequence as input, compute a longest subsequence such that there is at most one run for every character.

homepage: https://pypi.org/project/longestrunsubsequence/

version	toolchain
1.0.1	GCCcore/10.3.0

longread_umi

A collection of scripts for processing longread UMI data.

homepage: https://github.com/SorenKarst/longread_umi

version	toolchain
0.3.2	foss/2020b

Longshot

Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). It takes as input an aligned BAM file and outputs a phased VCF file with variants and haplotype information. It can also output haplotype-separated BAM files that can be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs).

homepage: https://github.com/pjedge/longshot

version	toolchain
0.3.4	GCCcore/8.2.0
0.4.1	GCC/7.3.0-2.30, GCCcore/8.3.0
0.4.3	GCCcore/10.2.0
0.4.5	GCCcore/11.3.0

loompy

Python implementation of the Loom file format, an efficient file format for large omics datasets

homepage: https://loompy.org/

version	toolchain
3.0.6	intel/2020b
3.0.7	foss/2021a, foss/2021b, foss/2022a, foss/2023a, intel/2021b

loomR

An R interface for loom files

homepage: https://github.com/mojaveazure/loomR

version	versionsuffix	toolchain
0.2.0-20180425	-R-4.2.1	foss/2022a
0.2.0-20180425	-R-4.2.2	foss/2022b
0.2.0-20180425	-R-4.3.2	foss/2023a

LoopTools

LoopTools is a package for evaluation of scalar and tensor one-loop integrals. It is based on the FF package by G.J. van Oldenborgh.

homepage: https://feynarts.de/looptools/

version	toolchain
2.15	GCC/12.3.0

LoRDEC

Program for correcting sequencing errors in long reads (e.g., PacBio, Oxford Nanopore) using highly accurate short reads (e.g., Illumina).

homepage: https://www.lirmm.fr/~rivals/lordec

version	toolchain
0.9	gompi/2022a

LPeg

LPeg is a new pattern-matching library for Lua, based on Parsing Expression Grammars (PEGs).

homepage: http://www.inf.puc-rio.br/~roberto/lpeg/

version	toolchain
1.0.2	GCCcore/10.2.0

LPJmL

Dynamic global vegetation model with managed land and river routing

homepage: https://github.com/PIK-LPJmL/LPJmL

version	toolchain
4.0.003	iimpi/2020b

lpsolve

Mixed Integer Linear Programming (MILP) solver

homepage: https://sourceforge.net/projects/lpsolve/

version	toolchain
5.5.2.5	GCC/6.4.0-2.28, GCC/8.3.0, foss/2018a, iccifort/2017.4.196-GCC-6.4.0-2.28, iccifort/2019.1.144-GCC-8.2.0-2.31.1, iccifort/2019.5.281, intel/2017a, intel/2018b
5.5.2.11	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/11.3.0, GCC/12.2.0, GCC/9.3.0

lrslib

lrslib is a self-contained ANSI C implementation of the reverse search algorithm for vertex enumeration/convex hull problems

homepage: http://cgm.cs.mcgill.ca/~avis/C/lrs.html

version	toolchain
6.2	intel/2018b
7.0a	gompi/2019a
7.2	gompi/2022a

LS-PrePost

LS-PrePost is an advanced pre and post-processor that is delivered free with LS-DYNA.

homepage: http://lstc.com/products/ls-prepost

version	versionsuffix	toolchain
4.6	-centos6	system
4.6	-centos7	system
4.6.24		system
4.7.8		system
4.7.15		system

LSD2

Least-squares methods to estimate rates and dates from phylogenies

homepage: https://github.com/tothuhien/lsd2

version	toolchain
1.9.7	GCCcore/9.3.0
2.2	GCCcore/10.2.0
2.3	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0
2.4.1	GCCcore/12.2.0, GCCcore/12.3.0

LSMS

LSMS benchmark, part of CORAL suite

homepage: https://asc.llnl.gov/CORAL-benchmarks/#lsms

version	toolchain
3_rev237	foss/2016a

LTR_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.

homepage: https://github.com/oushujun/LTR_retriever

version	toolchain
2.9.0	foss/2020b, foss/2022a

LtrDetector

A modern tool-suite for detectinglong terminal repeat retrotransposons de-novo onthe genomic scale

homepage: https://github.com/TulsaBioinformaticsToolsmith/LtrDetector

version	versionsuffix	toolchain
1.0	-Python-3.7.4	intel/2019b

Lua

Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping.

homepage: https://www.lua.org/

version	toolchain
5.1.4-5	GCC/4.8.2
5.1.4-8	GCC/4.8.2, GCC/4.8.4, system
5.1.5	GCCcore/7.3.0, GCCcore/8.3.0
5.2.4	GCCcore/6.4.0, GCCcore/7.3.0
5.3.4	GCCcore/7.2.0, system
5.3.5	GCCcore/10.2.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0, system
5.4.2	GCCcore/10.2.0
5.4.3	GCCcore/10.3.0, GCCcore/11.2.0
5.4.4	GCCcore/11.3.0, GCCcore/12.2.0
5.4.6	GCCcore/12.3.0, GCCcore/13.2.0

LuaJIT

LuaJIT is a Just-In-Time Compiler (JIT) for the Lua programming language. Lua is a powerful, dynamic and light-weight programming language. It may be embedded or used as a general-purpose, stand-alone language.

homepage: https://luajit.org/

version	toolchain
2.0.2	GCC/4.9.2
2.1.0-beta3_20230602	GCC/11.3.0

LuaJIT2-OpenResty

openresty/luajit2 - OpenResty's maintained branch of LuaJIT. LuaJIT is a Just-In-Time Compiler (JIT) for the Lua programming language. Lua is a powerful, dynamic and light-weight programming language. It may be embedded or used as a general-purpose, stand-alone language.

homepage: https://github.com/openresty/luajit2

version	toolchain
2.1-20220411	GCC/9.3.0

LuaRocks

LuaRocks is the package manager for Lua modules. It allows you to create and install Lua modules as self-contained packages called rocks.

homepage: https://luarocks.org

version	toolchain
3.9.2	GCCcore/11.3.0

Lucene-Geo-Gazetteer

A command line gazetteer built around the Geonames.org dataset, that uses the Apache Lucene library to create a searchable gazetteer.

homepage: https://github.com/chrismattmann/lucene-geo-gazetteer

version	toolchain
20170718	system

LUMPY

A probabilistic framework for structural variant discovery.

homepage: https://github.com/arq5x/lumpy-sv

version	toolchain
0.2.13	foss/2016b
0.3.1	foss/2020b

LUSCUS

Luscus is the program for graphical display and editing of molecular systems.

homepage: https://sourceforge.net/projects/luscus/

version	toolchain
0.8.6	foss/2018b, intel/2018a

lwgrp

The light-weight group library defines data structures and collective operations to group MPI processes as an ordered set. Such groups are useful as substitutes for MPI communicators when the overhead of communicator creation is too costly. For example, certain sorting algorithms recursively divide processes into subgroups as the sort algorithm progresses. These groups may be different with each invocation, so that it is inefficient to create and destroy communicators during the sort routine.

homepage: https://github.com/LLNL/lwgrp

version	toolchain
1.0.2	gompi/2019a, gompi/2020a, iimpi/2019a, iimpi/2020a
1.0.3	gompi/2020b
1.0.5	gompi/2022a, gompi/2023a

lxml

The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.

homepage: https://lxml.de/

version	versionsuffix	toolchain
3.5.0	-Python-2.7.11	intel/2016a
3.6.0	-Python-2.7.11	intel/2016a
3.6.4	-Python-2.7.12	intel/2016b
4.0.0	-Python-2.7.13	intel/2017a
4.1.1	-Python-2.7.14	intel/2017b
4.2.0	-Python-2.7.14	foss/2018a, intel/2018a
4.2.0	-Python-3.6.4	intel/2018a
4.2.5	-Python-2.7.15	foss/2018b, intel/2018b
4.2.5	-Python-3.6.6	foss/2018b
4.3.3		GCCcore/8.2.0
4.4.2		GCCcore/8.3.0
4.5.2		GCCcore/9.3.0
4.6.2		GCCcore/10.2.0
4.6.3		GCCcore/10.3.0, GCCcore/11.2.0
4.9.1		GCCcore/11.3.0
4.9.2		GCCcore/12.2.0, GCCcore/12.3.0
4.9.3		GCCcore/13.2.0

lynx

lynx is an alphanumeric display oriented World-Wide Web Client

homepage: http://lynx.browser.org/

version	versionsuffix	toolchain
2.8.9	-develop	foss/2016b

lz4

LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. It features an extremely fast decoder, with speed in multiple GB/s per core.

homepage: https://lz4.github.io/lz4/

version	toolchain
1.8.2	GCCcore/5.4.0, GCCcore/6.4.0
1.9.0	GCCcore/7.3.0
1.9.1	GCCcore/8.2.0
1.9.2	GCCcore/10.2.0, GCCcore/8.3.0, GCCcore/9.3.0
1.9.3	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0
1.9.4	GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

LZO

Portable lossless data compression library

homepage: http://www.oberhumer.com/opensource/lzo/

version	toolchain
2.09	intel/2016b, intel/2017b
2.10	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0, foss/2016a, foss/2016b, foss/2017a, foss/2018a, foss/2018b, fosscuda/2018b, intel/2017a

M

M1QN3 - M3GNet - M4 - m4ri - m4rie - MACH - MACS2 - MACS3 - MACSE - maeparser - MAFFT - MAGeCK - magick - Magics - magma - MAGMA-gene-analysis - MagresPython - mahotas - MAJIQ - make - makedepend - makedepf90 - makeinfo - MAKER - Mako - Mamba - mandrake - mannkendall - manta - mapDamage - Maple - MapSplice - Maq - MariaDB - MariaDB-connector-c - Markdown - MARS - Mash - Mashtree - MaSuRCA - Mathematica - MathGL - MATIO - MATLAB - MATLAB-Engine - matlab-proxy - matplotlib - matplotlib-inline - MATSim - maturin - Maude - mauveAligner - Maven - mawk - MaxBin - MaxQuant - mayavi - maze - MbedTLS - MBROLA - mbuffer - mc - MCL - MCR - mctc-lib - mcu - MDAnalysis - MDBM - MDI - MDSplus - MDSplus-Java - MDSplus-Python - mdtest - MDTraj - mdust - meboot - medaka - medImgProc - MedPy - Meep - MEGA - MEGACC - MEGAHIT - Megalodon - MEGAN - Meld - MEM - MEME - memkind - memory-profiler - MEMOTE - memtester - meRanTK - MERCKX - Mercurial - Mesa - Mesa-demos - meshalyzer - meshio - meshtool - Meson - meson-python - Mesquite - MESS - MetaBAT - MetaboAnalystR - MetaDecoder - metaerg - MetaEuk - MetaGeneAnnotator - Metagenome-Atlas - Metal - MetaMorpheus - MetaPhlAn - MetaPhlAn2 - metaWRAP - Metaxa2 - methylartist - MethylDackel - methylpy - METIS - mfqe - mgen - mgltools - mhcflurry - mhcnuggets - MicrobeAnnotator - microctools - MiGEC - MIGRATE-N - Mikado - Miller - mimalloc - MINC - MinCED - Mini-XML - miniasm - minibar - MiniCARD - Miniconda2 - Miniconda3 - minieigen - Miniforge3 - Minimac4 - minimap2 - Minipolish - MiniSat - minizip - MINPACK - MinPath - MIRA - miRDeep2 - Mish-Cuda - misha - MITgcmutils - MITObim - MitoHiFi - MitoZ - MiXCR - MixMHC2pred - mkl-dnn - mkl-service - mkl_fft - MLC - MLflow - MLxtend - mm-common - Mmg - MMSEQ - MMseqs2 - mmtf-cpp - MNE-Python - MOABB - MOABS - MOB-suite - ModelTest-NG - MODFLOW - modred - Molcas - mold - Molden - molecularGSM - Molekel - molmod - Molpro - MONA - MONAI - MONAI-Label - mongolite - Mono - Monocle3 - moonjit - MOOSE - mordecai - MoreRONN - morphosamplers - mosdepth - Mothur - motif - MotionCor2 - MotionCor3 - motionSegmentation - MoviePy - mpath - MPB - MPC - MPFI - MPFR - mpi4py - MPICH - MPICH2 - mpifileutils - mpiP - MPJ-Express - mpmath - MrBayes - mrcfile - MRChem - MRCPP - MRIcron - MRPRESSO - MRtrix - MSFragger - msgpack-c - MSM - MSPC - msprime - mstore - MTL4 - MuJoCo - mujoco-py - multicharge - multichoose - MultilevelEstimators - MultiNest - multiprocess - MultiQC - Multiwfn - muMerge - MUMmer - MUMPS - muParser - muparserx - MuPeXI - MUSCLE - MUSCLE3 - MuSiC - MUST - MuTect - mutil - MVAPICH2 - MView - mxml - mxmlplus - MXNet - MyCC - mygene - MyMediaLite - mympingpong - Myokit - mypy - MySQL - MySQL-python - mysqlclient

M1QN3

A solver of large-scale unconstrained minimization problems

homepage: https://who.rocq.inria.fr/Jean-Charles.Gilbert/modulopt/optimization-routines/m1qn3/m1qn3.html

version	toolchain
3.3	GCC/10.3.0

M3GNet

" M3GNet is a new materials graph neural network architecture that incorporates 3-body interactions. A key difference with prior materials graph implementations such as MEGNet is the addition of the coordinates for atoms and the 3×3 lattice matrix in crystals, which are necessary for obtaining tensorial quantities such as forces and stresses via auto-differentiation.

homepage: https://materialsvirtuallab.github.io/m3gnet/

version	toolchain
0.2.4	foss/2022a

M4

GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.

homepage: https://www.gnu.org/software/m4/m4.html

version	toolchain
1.4.16	GCC/4.8.1, GCC/4.8.2, system
1.4.17	GCC/4.8.2, GCC/4.8.4, GCC/4.9.2, GCC/4.9.2-binutils-2.25, GCC/4.9.3, GCC/4.9.3-2.25, GCC/4.9.3-binutils-2.25, GCC/5.1.0-binutils-2.25, GCC/5.2.0, GCC/5.4.0-2.26, GCCcore/4.9.2, GCCcore/4.9.3, GCCcore/4.9.4, GCCcore/5.3.0, GCCcore/5.4.0, GCCcore/6.1.0, GCCcore/6.2.0, GNU/4.9.2-2.25, GNU/4.9.3-2.25, GNU/5.1.0-2.25, foss/2016.04, foss/2016a, foss/2016b, gimkl/2.11.5, intel/2016.02-GCC-4.9, intel/2016a, intel/2016b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25, system
1.4.18	FCC/4.5.0, GCCcore/10.1.0, GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.1.0, GCCcore/5.3.0, GCCcore/5.4.0, GCCcore/5.5.0, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.1.0, GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/7.4.0, GCCcore/8.1.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/8.4.0, GCCcore/9.1.0, GCCcore/9.2.0, GCCcore/9.3.0, GCCcore/system, system
1.4.19	GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/11.4.0, GCCcore/12.1.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.1.0, GCCcore/13.2.0, GCCcore/9.4.0, GCCcore/9.5.0, system

m4ri

M4RI is a library for fast arithmetic with dense matrices over F2.

homepage: https://github.com/malb/m4ri

version	toolchain
20200125	GCC/11.3.0

m4rie

M4RIE is a library for fast arithmetic with dense matrices.

homepage: https://github.com/malb/m4rie

version	toolchain
20200125	GCC/11.3.0

MACH

MACH 1.0 is a Markov Chain based haplotyper that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.

homepage: http://csg.sph.umich.edu/abecasis/MACH/

version	toolchain
1.0.18	system

MACS2

Model Based Analysis for ChIP-Seq data

homepage: https://github.com/taoliu/MACS

version	versionsuffix	toolchain
2.1.1.20160309	-Python-2.7.14	intel/2017b
2.1.2.1	-Python-2.7.14	foss/2017b, intel/2017b
2.1.2.1	-Python-2.7.15	intel/2019a
2.2.5	-Python-3.6.6	foss/2018b
2.2.7.1		foss/2021a, foss/2021b
2.2.9.1		foss/2022a, foss/2022b

MACS3

Model Based Analysis for ChIP-Seq data

homepage: https://macs3-project.github.io/MACS/

version	toolchain
3.0.0	foss/2022b
3.0.0b2	foss/2022b
3.0.1	gfbf/2023a

MACSE

MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure.

homepage: https://bioweb.supagro.inra.fr/macse/index.php

version	versionsuffix	toolchain
2.06	-Java-15	system

maeparser

maeparser is a parser for Schrodinger Maestro files.

homepage: https://github.com/schrodinger/maeparser

version	toolchain
1.2.2	gompi/2019a, iimpi/2019a
1.3.0	gompi/2019b, gompi/2021a, gompi/2022a, iimpi/2020a
1.3.1	gompi/2023a

MAFFT

MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.

homepage: https://mafft.cbrc.jp/alignment/software/source.html

version	versionsuffix	toolchain
7.305	-with-extensions	foss/2016b
7.397	-with-extensions	intel/2018a
7.427	-with-extensions	foss/2018b, intel/2018b
7.429	-with-extensions	GCC/8.2.0-2.31.1
7.453	-with-extensions	GCC/8.3.0, GCC/9.3.0, gompi/2020a, iccifort/2019.5.281, iimpi/2020a
7.470	-with-extensions	GCC/9.3.0, gompi/2020a
7.471	-with-extensions	iimpi/2020a
7.475	-with-extensions	GCC/10.2.0, gompi/2020b
7.487	-with-extensions	gompi/2021a
7.490	-with-extensions	GCC/10.3.0, GCC/11.2.0, gompi/2021b
7.505	-with-extensions	GCC/11.3.0, GCC/12.2.0
7.520	-with-extensions	GCC/12.3.0

MAGeCK

Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens (or GeCKO) technology. MAGeCK is developed by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute, and is being actively updated by Wei Li lab from Children's National Medical Center.

homepage: https://sourceforge.net/p/mageck/wiki/Home/

version	toolchain
0.5.9.4	foss/2021a, foss/2022a
0.5.9.5	gfbf/2022b

magick

R bindings to the open-source image processing library ImageMagick

homepage: https://cran.r-project.org/web/packages/magick/

version	versionsuffix	toolchain
2.0	-R-3.5.1	foss/2018b

Magics

Magics is ECMWF's meteorological plotting software and can be either accessed directly through its Python or Fortran interfaces or by using Metview.

homepage: https://confluence.ecmwf.int/display/MAGP/

version	toolchain
4.13.0	gompi/2022a

magma

The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.

homepage: https://icl.cs.utk.edu/magma/

version	versionsuffix	toolchain
2.3.0		fosscuda/2017b, intelcuda/2017b
2.3.0	-CUDA-9.1.85	foss/2018a
2.4.0		fosscuda/2018b
2.5.0		fosscuda/2018b
2.5.1		fosscuda/2019a, fosscuda/2019b
2.5.4		fosscuda/2019a, fosscuda/2019b, fosscuda/2020a, fosscuda/2020b, intelcuda/2019b, intelcuda/2020b
2.6.1	-CUDA-11.3.1	foss/2021a
2.6.2	-CUDA-11.4.1	foss/2021b
2.6.2	-CUDA-11.5.2	foss/2021b
2.6.2	-CUDA-11.7.0	foss/2022a
2.7.1	-CUDA-12.0.0	foss/2022b
2.7.2	-CUDA-12.1.1	foss/2023a
2.7.2	-CUDA-12.4.0	foss/2023b

MAGMA-gene-analysis

MAGMA is a tool for gene analysis and generalized gene-set analysis of GWAS data. It can be used to analyse both raw genotype data as well as summary SNP p-values from a previous GWAS or meta-analysis.

homepage: https://ctg.cncr.nl/software/magma

version	toolchain
1.07b	foss/2018b
1.07bb	GCC/8.3.0
1.09b	GCC/11.2.0

MagresPython

MagresPython is a Python library for parsing the CCP-NC ab-initio magnetic resonance file format. This is used in the latest version of the CASTEP and Quantum ESPRESSO (PWSCF) codes.

homepage: http://tfgg.me/magres-python

version	versionsuffix	toolchain
20160329	-Python-2.7.15	foss/2018b

mahotas

Mahotas is a computer vision and image processing library for Python

homepage: https://mahotas.readthedocs.io/

version	versionsuffix	toolchain
1.4.3	-Python-2.7.12	intel/2016b
1.4.13		foss/2022a

MAJIQ

MAJIQ and Voila are two software packages that together detect, quantify, and visualize local splicing variations (LSV) from RNA-Seq data.

homepage: https://majiq.biociphers.org

version	versionsuffix	toolchain
1.1.1	-Python-3.6.4	intel/2018a

make

GNU version of make utility

homepage: https://www.gnu.org/software/make/make.html

version	toolchain
3.82	GCC/4.8.2
4.1	GCC/4.9.2
4.2.1	GCC/7.3.0-2.30, GCCcore/8.3.0
4.3	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/9.3.0
4.4.1	GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

makedepend

The makedepend package contains a C-preprocessor like utility to determine build-time dependencies.

homepage: https://linux.die.net/man/1/makedepend

version	toolchain
1.0.5	GCCcore/6.3.0, GCCcore/6.4.0, foss/2016a, gimkl/2.11.5, intel/2016a
1.0.6	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/7.3.0, GCCcore/8.3.0, GCCcore/9.3.0
1.0.7	GCCcore/11.3.0, GCCcore/12.3.0

makedepf90

Makedepf90 is a program for automatic creation of Makefile-style dependency lists for Fortran source code.

homepage: https://linux.die.net/man/1/makedepf90

version	toolchain
2.8.8	foss/2017a

makeinfo

makeinfo is part of the Texinfo project, the official documentation format of the GNU project.

homepage: https://www.gnu.org/software/texinfo/

version	versionsuffix	toolchain
6.7		FCC/4.5.0, GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/8.3.0, GCCcore/9.3.0
6.7	-minimal	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/8.3.0, GCCcore/9.3.0
6.8		GCCcore/11.2.0, GCCcore/11.3.0
7.0.3		GCCcore/12.2.0, GCCcore/12.3.0
7.1		GCCcore/13.2.0

MAKER

MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.

homepage: https://yandell-lab.org/software/maker.html

version	toolchain
3.01.04	foss/2022a

Mako

A super-fast templating language that borrows the best ideas from the existing templating languages

homepage: https://www.makotemplates.org

version	versionsuffix	toolchain
1.0.4	-Python-2.7.12	foss/2016b, intel/2016b
1.0.6	-Python-2.7.13	foss/2017a, intel/2017a
1.0.7	-Python-2.7.14	foss/2017b, foss/2018a, fosscuda/2017b, fosscuda/2018a, intel/2017b, intel/2018.01, intel/2018a, intelcuda/2017b, iomkl/2018a
1.0.7	-Python-2.7.15	foss/2018b, fosscuda/2018b, intel/2018b
1.0.7	-Python-3.6.4	intel/2018a
1.0.7	-Python-3.6.6	fosscuda/2018b
1.0.8		GCCcore/8.2.0
1.1.0		GCCcore/8.3.0
1.1.2		GCCcore/9.3.0
1.1.3		GCCcore/10.2.0
1.1.4		GCCcore/10.3.0, GCCcore/11.2.0
1.2.0		GCCcore/11.3.0
1.2.4		GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

Mamba

Mamba is a fast, robust, and cross-platform package manager. It runs on Windows, OS X and Linux (ARM64 and PPC64LE included) and is fully compatible with conda packages and supports most of conda's commands.

homepage: https://mamba.readthedocs.io/

version	toolchain
4.14.0-0	system
23.1.0-4	system
23.11.0-0	system

mandrake

Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding.

homepage: https://mandrake.readthedocs.io

version	toolchain
1.2.2	foss/2022a

mannkendall

A python package for non parametric Mann Kendall family of trend tests.

homepage: https://github.com/mmhs013/pymannkendall

version	toolchain
1.1.1	foss/2022a

manta

Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow.

homepage: https://github.com/Illumina/manta

version	versionsuffix	toolchain
1.1.1		system
1.6.0		system
1.6.0	-Python-2.7.16	gompi/2019b
1.6.0	-Python-2.7.18	GCC/10.2.0, gompi/2020a

mapDamage

mapDamage2 is a computational framework written in Python and R, which tracks and quantifies DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.

homepage: https://ginolhac.github.io/mapDamage/

version	versionsuffix	toolchain
2.2.1		foss/2021b, foss/2022a
2.2.1	-R-4.0.4	foss/2020b
2.2.1	-R-4.1.0	foss/2021a

Maple

Maple combines the world's most powerful mathematical computation engine with an intuitive, 'clickable' user interface.

homepage: http://www.maplesoft.com/products/maple/

version	toolchain
15	system
2017.2	system
2022.1	system

MapSplice

MapSplice is a software for mapping RNA-seq data to reference genome for splice junction discovery that depends only on reference genome, and not on any further annotations.

homepage: http://www.netlab.uky.edu/p/bioinfo/MapSplice2

version	versionsuffix	toolchain
2.2.1	-Python-2.7.12	foss/2016b
2.2.1	-Python-2.7.15	intel/2018b

Maq

Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing machines.

homepage: http://maq.sourceforge.net/maq-man.shtml

version	toolchain
0.7.0	system

MariaDB

MariaDB is an enhanced, drop-in replacement for MySQL. Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.

homepage: https://mariadb.org/

version	toolchain
10.0.21	GNU/4.9.3-2.25
10.1.13	intel/2016a
10.1.14	foss/2016a, intel/2016a
10.1.17	intel/2016b
10.1.24	intel/2017a
10.2.11	foss/2017b, intel/2017b
10.3.7	intel/2018a
10.3.10	foss/2018b
10.3.14	foss/2019a
10.4.13	gompi/2019b
10.5.8	GCC/10.2.0
10.6.4	GCC/10.3.0, GCC/11.2.0
10.9.3	GCC/11.3.0
10.11.2	GCC/12.2.0

MariaDB-connector-c

MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases.

homepage: https://downloads.mariadb.org/connector-c/

version	toolchain
2.3.4	foss/2017b, intel/2017b
2.3.5	intel/2018a, iomkl/2018a
2.3.7	GCCcore/8.2.0, GCCcore/8.3.0, foss/2018b
3.1.7	GCCcore/9.3.0
3.1.11	GCCcore/10.2.0
3.2.2	GCCcore/10.3.0

Markdown

This is a Python implementation of John Gruber's Markdown. It is almost completely compliant with the reference implementation, though there are a few known issues. Additional features are supported by the Available Extensions.

homepage: https://python-markdown.github.io/

version	toolchain
3.6	GCCcore/12.2.0, GCCcore/13.2.0

MARS

improving Multiple circular sequence Alignment using Refined Sequences

homepage: https://github.com/lorrainea/MARS

version	toolchain
20191101	GCCcore/8.3.0

Mash

Fast genome and metagenome distance estimation using MinHash

homepage: http://mash.readthedocs.org

version	toolchain
2.0	foss/2018a
2.1	foss/2018b
2.2	GCC/9.3.0
2.3	GCC/10.3.0, GCC/11.2.0, GCC/11.3.0, GCC/12.2.0, GCC/12.3.0, intel-compilers/2021.4.0

Mashtree

Create a tree using Mash distances.

homepage: https://github.com/lskatz/mashtree

version	toolchain
1.4.6	GCC/12.2.0

MaSuRCA

MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore).

homepage: https://www.genome.umd.edu/masurca.html

version	versionsuffix	toolchain
3.2.2		foss/2016a
3.2.2	-Perl-5.26.0	foss/2017b
3.2.4		foss/2018a
3.2.5	-Perl-5.26.0	foss/2017b
3.3.1	-Perl-5.28.0	foss/2018b
4.0.1	-Perl-5.30.2	foss/2020a
4.0.9	-Perl-5.32.1	foss/2021a
4.1.0		GCC/11.3.0

Mathematica

Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields.

homepage: http://www.wolfram.com/mathematica

version	toolchain
9.0.1	system
10.0.2	system
10.1.0	system
10.4.1	system
11.0.1	system
11.1.1	system
11.3.0	system
12.0.0	system
12.1.1	system
13.0.0	system
13.1.0	system

MathGL

MathGL is ... a library for making high-quality scientific graphics under Linux and Windows; a library for the fast data plotting and data processing of large data arrays; a library for working in window and console modes and for easy embedding into other programs; a library with large and growing set of graphics.

homepage: http://mathgl.sourceforge.net/doc_en/Main.html

version	toolchain
2.4.1	foss/2018a

MATIO

matio is an C library for reading and writing Matlab MAT files.

homepage: http://sourceforge.net/projects/matio/

version	toolchain
1.5.9	GCCcore/5.4.0
1.5.11	foss/2017b
1.5.12	GCCcore/6.4.0
1.5.17	GCCcore/8.3.0
1.5.19	GCCcore/9.3.0
1.5.21	GCCcore/10.2.0
1.5.22	GCCcore/11.2.0
1.5.23	GCCcore/11.3.0, GCCcore/12.1.0, GCCcore/12.2.0
1.5.26	GCCcore/12.3.0, GCCcore/13.2.0

MATLAB

MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.

homepage: https://www.mathworks.com/products/matlab

version	versionsuffix	toolchain
2012b		system
2013b		system
2015a		system
2016a		system
2017a		system
2018b		system
2019b		system
2020a		system
2020b		system
2021a		system
2021b		system
2022a		system
2022a	-r3	system
2022b		system
2022b	-r5	system
2023a		system
2023b		system

MATLAB-Engine

The MATLAB Engine API for Python provides a package for Python to call MATLAB as a computational engine.

homepage: https://www.mathworks.com/help/matlab/matlab-engine-for-python.html

version	versionsuffix	toolchain
2018b	-Python-2.7.14	foss/2017b, intel/2017b
2018b	-Python-3.6.3	foss/2017b, intel/2017b
2019b		GCCcore/8.3.0
2021a-9.10.1		GCCcore/10.2.0
2021b-9.11.19		GCCcore/11.2.0

matlab-proxy

A Python package which enables you to launch MATLAB and access it from a web browser.

homepage: https://github.com/mathworks/matlab-proxy

version	toolchain
0.5.4	GCCcore/11.3.0

matplotlib

matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.

homepage: https://matplotlib.org

version	versionsuffix	toolchain
1.4.3	-Python-2.7.12	intel/2016b
1.5.1	-Python-2.7.11	foss/2016a, intel/2016a
1.5.1	-Python-2.7.11-freetype-2.6.3	foss/2016a, intel/2016a
1.5.1	-Python-2.7.12	intel/2016b
1.5.1	-Python-3.5.1	foss/2016a, intel/2016a
1.5.1	-Python-3.5.2	intel/2016b
1.5.2	-Python-2.7.12	foss/2016b, intel/2016b
1.5.2	-Python-3.5.2	intel/2016b
1.5.3	-Python-2.7.12	foss/2016b, intel/2016b
1.5.3	-Python-3.5.2	foss/2016b, intel/2016b
2.0.0	-Python-2.7.12	foss/2016b, intel/2016b
2.0.0	-Python-2.7.13	intel/2017a
2.0.1	-Python-3.6.1	intel/2017a
2.0.2	-Python-2.7.13	foss/2017a, intel/2017a
2.0.2	-Python-2.7.13-Qt-4.8.7	intel/2017a
2.0.2	-Python-2.7.13-libpng-1.6.29	intel/2017a
2.0.2	-Python-3.6.1	foss/2017a
2.0.2	-Python-3.6.1-libpng-1.6.29	intel/2017a
2.1.0	-Python-2.7.14	foss/2017b, fosscuda/2017b, intel/2017b, intelcuda/2017b
2.1.0	-Python-3.6.2	foss/2017b
2.1.0	-Python-3.6.3	foss/2017b, fosscuda/2017b, intel/2017b, intelcuda/2017b
2.1.1	-Python-2.7.14	intel/2017b
2.1.1	-Python-3.6.3	foss/2017b, intel/2017b
2.1.2	-Python-2.7.14	foss/2018a, intel/2018a
2.1.2	-Python-3.6.4	foss/2018a, intel/2018a, iomkl/2018.02, iomkl/2018a
2.2.3	-Python-2.7.15	foss/2018b, fosscuda/2018b, intel/2018b
2.2.3	-Python-3.6.6	intel/2018b
2.2.4	-Python-2.7.15	foss/2019a, fosscuda/2019a, intel/2019a, intelcuda/2019a
2.2.4	-Python-2.7.16	foss/2019b, fosscuda/2019b, intel/2019b
2.2.5	-Python-2.7.16	foss/2019b
2.2.5	-Python-2.7.18	foss/2020a, foss/2020b, foss/2021b, fosscuda/2020a, intel/2020a
3.0.0	-Python-3.6.6	foss/2018b, fosscuda/2018b, intel/2018b, iomkl/2018b
3.0.2	-Python-3.6.6	foss/2018b
3.0.3	-Python-3.7.2	foss/2019a, fosscuda/2019a, intel/2019a, intelcuda/2019a
3.1.1	-Python-3.7.4	foss/2019b, fosscuda/2019b, intel/2019b, intelcuda/2019b
3.2.1	-Python-3.8.2	foss/2020a, fosscuda/2020a, intel/2020a, intelcuda/2020a
3.3.3		foss/2020b, fosscuda/2020b, intel/2020b, intelcuda/2020b
3.4.2		foss/2021a, gomkl/2021a, intel/2021a
3.4.3		foss/2021b, intel/2021b
3.5.1		foss/2020b, intel/2020b
3.5.2		foss/2021b, foss/2022a, intel/2022a
3.7.0		gfbf/2022b
3.7.2		gfbf/2023a, iimkl/2023a
3.8.2		gfbf/2023b

matplotlib-inline

Matplotlib Inline Back-end for IPython and Jupyter.

homepage: https://github.com/ipython/matplotlib-inline

version	toolchain
0.1.3	GCCcore/10.2.0

MATSim

MATSim is an open-source framework to implement large-scale agent-based transport simulations.

homepage: https://www.matsim.org/

version	versionsuffix	toolchain
0.8.1	-Java-1.8.0_112	intel/2016b
14.0	-Java-11	GCCcore/11.2.0, system

maturin

This project is meant as a zero configuration replacement for setuptools-rust and milksnake. It supports building wheels for python 3.5+ on windows, linux, mac and freebsd, can upload them to pypi and has basic pypy and graalpy support.

homepage: https://github.com/pyo3/maturin

version	versionsuffix	toolchain
1.1.0		GCCcore/12.2.0, GCCcore/12.3.0
1.3.1		GCCcore/13.2.0
1.3.2	-Rust-1.65.0	GCCcore/11.3.0
1.4.0	-Rust-1.75.0	GCCcore/12.2.0, GCCcore/12.3.0
1.5.0	-Rust-1.76.0	GCCcore/13.2.0

Maude

Maude is a high-performance reflective language and system supporting both equational and rewriting logic specification and programming for a wide range of applications. Maude has been influenced in important ways by the OBJ3 language, which can be regarded as an equational logic sublanguage. Besides supporting equational specification and programming, Maude also supports rewriting logic computation.

homepage: https://maude.cs.illinois.edu/w/index.php/The_Maude_System

version	toolchain
3.1	GCCcore/10.2.0

mauveAligner

Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignments provide a basis for research into comparative genomics and the study of genome-wide evolutionary dynamics. This version was built without Graphical User Interface.

homepage: https://darlinglab.org/mauve/mauve.html

version	toolchain
4736	gompi/2020a

Maven

Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information.

homepage: https://maven.apache.org/index.html

version	toolchain
3.2.3	system
3.3.3	system
3.3.9	system
3.5.0	system
3.5.2	system
3.6.0	system
3.6.3	system

mawk

mawk is an interpreter for the AWK Programming Language.

homepage: https://invisible-island.net/mawk/

version	toolchain
1.3.4-20141206	GCC/4.9.2
1.3.4-20171017	foss/2018a, foss/2018b, foss/2019a, intel/2018a, intel/2018b, intel/2019a

MaxBin

MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.

homepage: https://sourceforge.net/projects/maxbin/

version	versionsuffix	toolchain
2.2.6	-Perl-5.28.0	foss/2018b
2.2.7		gompi/2020b, gompi/2021a, gompi/2021b
2.2.7	-Perl-5.28.1	GCC/8.2.0-2.31.1

MaxQuant

MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling techniques as well as label-free quantification are supported.

homepage: https://maxquant.org/maxquant

version	toolchain
1.6.10.43	foss/2018b
2.0.3.0	GCCcore/11.2.0
2.2.0.0	GCCcore/11.2.0
2.4.2.0	system

mayavi

The Mayavi scientific data 3-dimensional visualizer

homepage: http://code.enthought.com/projects/mayavi/

version	versionsuffix	toolchain
4.4.4	-Python-2.7.11	intel/2016a
4.6.2	-Python-3.6.6	foss/2018b
4.7.1	-Python-2.7.15	foss/2019a
4.7.1	-Python-3.7.2	foss/2019a
4.7.4		foss/2021b

maze

In a similar manner to dot plots, maze highlights local sequence similarity between two DNA sequences. In particular, maximal exact substring matches are computed with MUMmer3 and visualised.

homepage: https://github.com/dellytools/maze

version	toolchain
20170124	foss/2020b

MbedTLS

An open source, portable, easy to use, readable and flexible SSL library.

homepage: https://tls.mbed.org/

version	toolchain
2.26.0	GCCcore/10.2.0

MBROLA

MBROLA is a speech synthesizer based on the concatenation of diphones. It takes a list of phonemes as input, together with prosodic information (duration of phonemes and a piecewise linear description of pitch), and produces speech samples on 16 bits (linear), at the sampling frequency of the diphone database. MBROLA voices project provides list of MBROLA speech synthesizer voices. It is intended to provide easier collaboration and automatic updates for individual users and packagers.

homepage: <['https://github.com/numediart/MBROLA', 'https://github.com/numediart/MBROLA-voices']>

version	versionsuffix	toolchain
3.3	-voices-20200330	GCCcore/12.3.0, GCCcore/9.3.0

mbuffer

mbuffer is a tool for buffering data streams with a large set of unique features.

homepage: https://www.maier-komor.de/mbuffer.html

version	toolchain
20191016	GCCcore/9.3.0

mc

mc-4.6.1: User-friendly file manager and visual shell

homepage: https://www.midnight-commander.org/

version	toolchain
4.8.13	GCC/4.9.2

MCL

The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs.

homepage: https://micans.org/mcl/

version	versionsuffix	toolchain
02.063		intel/2016b
14.137		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.3.0, GCCcore/8.3.0, GCCcore/9.3.0, foss/2016a, intel/2016b
14.137	-Perl-5.26.1	GCCcore/6.4.0
14.137	-Perl-5.28.0	GCCcore/7.3.0
22.282		GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.3.0

MCR

The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.

homepage: https://www.mathworks.com/products/compiler/mcr/

version	versionsuffix	toolchain
R2013a		system
R2013b		system
R2014a		system
R2014b		system
R2015a		system
R2015b		system
R2016a		system
R2016b		system
R2018a		system
R2018b		system
R2019a		system
R2019b	.8	system
R2020a	.6	system
R2020b	.5	system
R2021a	.0	system
R2021a	.3	system
R2021b		system
R2021b	.1	system
R2021b	.2	system
R2022a		system
R2022a	.1	system
R2022a	.5	system
R2023a		system

mctc-lib

Common tool chain for working with molecular structure data in various applications. This library provides a unified way to perform operations on molecular structure data, like reading and writing to common geometry file formats.

homepage: https://grimme-lab.github.io/mctc-lib

version	toolchain
0.3.1	GCC/11.3.0, GCC/12.2.0, intel-compilers/2022.1.0, intel-compilers/2022.2.1

mcu

A package for periodic wavefunction and crystallography analysis. mcu is designed to support large scale analysis and topological descriptions for periodic wavefunction.

homepage: https://hungqpham.com/mcu/

version	toolchain
2021-04-06	gomkl/2021a

MDAnalysis

MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats.

homepage: https://www.mdanalysis.org/

version	versionsuffix	toolchain
0.20.1	-Python-3.7.4	foss/2019b, intel/2019b
1.1.1		foss/2020b
2.0.0		foss/2021a, foss/2021b, intel/2021b
2.2.0		foss/2022a
2.4.2		foss/2021a, foss/2022b
2.7.0		foss/2023a

MDBM

MDBM is a super-fast memory-mapped key/value store

homepage: https://github.com/yahoo/mdbm

version	toolchain
4.13.0	GCCcore/6.4.0, GCCcore/9.3.0

MDI

The MolSSI Driver Interface (MDI) project provides a standardized API for fast, on-the-fly communication between computational chemistry codes. This greatly simplifies the process of implementing methods that require the cooperation of multiple software packages and enables developers to write a single implementation that works across many different codes. The API is sufficiently general to support a wide variety of techniques, including QM/MM, ab initio MD, machine learning, advanced sampling, and path integral MD, while also being straightforwardly extensible. Communication between codes is handled by the MDI Library, which enables tight coupling between codes using either the MPI or TCP/IP methods.

homepage: https://github.com/MolSSI-MDI/MDI_Library

version	toolchain
1.4.16	gompi/2022b
1.4.26	gompi/2023a

MDSplus

MDSplus is a set of software tools for data acquisition and storage and a methodology for management of complex scientific data.

homepage: https://mdsplus.org/

version	versionsuffix	toolchain
7.0.67	-Java-1.7.0_79-Python-2.7.11	foss/2016a
7.46.1		foss/2018a
7.96.8		GCCcore/9.3.0
7.96.12		GCCcore/9.3.0

MDSplus-Java

MDSplus is a set of software tools for data acquisition and storage and a methodology for management of complex scientific data.

homepage: https://mdsplus.org

version	versionsuffix	toolchain
7.96.12	-Java-13	GCCcore/9.3.0

MDSplus-Python

MDSplus is a set of software tools for data acquisition and storage and a methodology for management of complex scientific data.

homepage: https://mdsplus.org

version	versionsuffix	toolchain
7.96.12	-Python-3.8.2	foss/2020a

mdtest

mdtest is an MPI-coordinated metadata benchmark test that performs open/stat/close operations on files and directories and then reports the performance.

homepage: http://sourceforge.net/projects/mdtest/

version	toolchain
1.9.3	intel/2017a

MDTraj

Read, write and analyze MD trajectories with only a few lines of Python code.

homepage: https://mdtraj.org

version	versionsuffix	toolchain
1.9.1	-Python-3.6.3	intel/2017b
1.9.2	-Python-3.6.6	intel/2018b
1.9.3	-Python-3.7.4	foss/2019b, intel/2019b
1.9.4	-Python-3.8.2	foss/2020a, intel/2020a
1.9.5		foss/2020b, fosscuda/2020b, intel/2020b
1.9.7		foss/2021a, foss/2021b, foss/2022a, intel/2021b, intel/2022a

mdust

mdust from DFCI Gene Indices Software Tools (archived for a historical record only)

homepage: https://github.com/lh3/mdust

version	toolchain
20150102	GCC/10.3.0

meboot

Maximum entropy density based dependent data bootstrap. An algorithm is provided to create a population of time series (ensemble) without assuming stationarity.

homepage: https://cran.r-project.org/web/packages/meboot/index.html

version	versionsuffix	toolchain
1.4-9.2	-R-4.2.1	foss/2022a

medaka

medaka is a tool to create a consensus sequence from nanopore sequencing data.

homepage: https://github.com/nanoporetech/medaka

version	versionsuffix	toolchain
0.4.3	-Python-3.6.6	foss/2018b
0.11.4	-Python-3.6.6	foss/2018b
0.12.0	-Python-3.6.6	foss/2018b
1.1.1	-Python-3.7.4	foss/2019b
1.1.3	-Python-3.7.4	foss/2019b
1.2.0	-Python-3.7.4	foss/2019b
1.4.3		foss/2020b
1.4.3	-Python-3.7.4	foss/2019b
1.5.0		foss/2021a
1.6.0		foss/2021b
1.8.1		foss/2022a
1.9.1		foss/2022a, foss/2022b
1.11.3		foss/2022a, foss/2023a

medImgProc

Motion correction, explicit spatio-temporal regularization of motion tracking, random speckles enhancement, and segmentation.

homepage: https://github.com/WeiXuanChan/motionSegmentation

version	versionsuffix	toolchain
2.5.7	-Python-3.7.4	foss/2019b

MedPy

MedPy is a library and script collection for medical image processing in Python, providing basic functionalities for reading, writing and manipulating large images of arbitrary dimensionality. Its main contributions are n-dimensional versions of popular image filters, a collection of image feature extractors, ready to be used with scikit-learn, and an exhaustive n-dimensional graph-cut package.

homepage: https://pypi.org/project/MedPy/

version	versionsuffix	toolchain
0.4.0		foss/2020b, fosscuda/2020b
0.4.0	-Python-3.7.4	foss/2019b

Meep

Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems.

homepage: https://meep.readthedocs.io/en/latest/

version	versionsuffix	toolchain
1.3		foss/2016a
1.4.3		intel/2020a
1.6.0	-Python-2.7.14	foss/2017b, foss/2018a, intel/2018a
1.26.0		foss/2020b

MEGA

MEGA-CC (Molecular Evolutionary Genetics Analysis Computational Core) is an integrated suite of tools for statistics-based comparative analysis of molecular sequence data based on evolutionary principles.

homepage: http://www.megasoftware.net/

version	toolchain
7.0.20-1	system
10.0.5	system
11.0.10	system

MEGACC

MEGA-Computing Core - Sophisticated and user-friendly software suite for analyzing DNA and protein sequence data from species and populations.

homepage: http://www.megasoftware.net

version	toolchain
7.0.18-1	system

MEGAHIT

An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

homepage: https://github.com/voutcn/megahit

version	versionsuffix	toolchain
1.1.2	-Python-2.7.14	foss/2018a
1.1.3	-Python-2.7.14	foss/2017b, foss/2018a
1.1.3	-Python-3.6.3	foss/2017b
1.1.4	-Python-2.7.15	foss/2018b
1.1.4	-Python-3.6.6	foss/2018b
1.2.8		GCCcore/8.2.0
1.2.9		GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/9.3.0, foss/2018b
1.2.9	-Python-2.7.18	GCCcore/10.2.0

Megalodon

Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.

homepage: https://github.com/nanoporetech/megalodon

version	versionsuffix	toolchain
2.3.5		foss/2020b, fosscuda/2020b
2.5.0		foss/2021a
2.5.0	-CUDA-11.3.1	foss/2021a

MEGAN

MEGAN is a comprehensive toolbox for interactively analyzing microbiome data

homepage: http://megan.informatik.uni-tuebingen.de/

version	versionsuffix	toolchain
6.22.0	-Java-17	system
6.25.3	-Java-17	system

Meld

Meld is a visual diff and merge tool targeted at developers. Meld helps you compare files, directories, and version controlled projects. It provides two- and three-way comparison of both files and directories, and has support for many popular version control systems.

homepage: https://meldmerge.org/

version	versionsuffix	toolchain
3.20.1	-Python-3.7.2	GCCcore/8.2.0

MEM

Marker Enrichment Modeling (MEM) is a tool designed to calculate enrichment scores.

homepage: https://github.com/cytolab/mem

version	versionsuffix	toolchain
20191023		foss/2019b
20191023	-R-4.0.0	foss/2020a

MEME

The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment using SpaMo or CentriMo.

homepage: https://meme-suite.org/meme/index.html

version	versionsuffix	toolchain
5.0.4	-Perl-5.26.0-Python-2.7.14	foss/2017b, intel/2017b
5.0.4	-Perl-5.26.0-Python-3.6.3	foss/2017b, intel/2017b
5.1.1	-Python-3.6.6	foss/2018b
5.1.1	-Python-3.7.4	foss/2019b, intel/2019b
5.4.1		GCC/10.3.0, gompi/2021b
5.4.1	-Python-2.7.18	gompi/2021b
5.5.4		gompi/2022b

memkind

User Extensible Heap Manager built on top of jemalloc which enables control of memory characteristics and a partitioning of the heap between kinds of memory.

homepage: http://memkind.github.io

version	toolchain
1.5.0	GCCcore/5.4.0

memory-profiler

memory-profiler is a Python module for monitoring memory consumption of a process as well as line-by-line analysis of memory consumption for python programs.

homepage: https://pypi.org/project/memory-profiler

version	toolchain
0.55.0	foss/2019a, intel/2019a

MEMOTE

The genome-scale metabolic model test suite

homepage: https://github.com/opencobra/memote

version	toolchain
0.13.0	foss/2021a

memtester

A userspace utility for testing the memory subsystem for faults

homepage: https://pyropus.ca./software/memtester/

version	toolchain
4.5.1	GCCcore/11.3.0

meRanTK

meRanTK is a versatile high performance toolkit for complete analysis of methylated RNA data.

homepage: http://www.icbi.at/index.html

version	toolchain
1.1.1b	system

MERCKX

Multilingual Entity/Resource Combiner & Knowledge eXtractor

homepage: https://github.com/madewild/MERCKX

version	versionsuffix	toolchain
20170330	-Python-2.7.13	intel/2017a

Mercurial

Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface.

homepage: https://www.mercurial-scm.org

version	versionsuffix	toolchain
3.8.3	-Python-2.7.11	foss/2016a
5.7.1		GCCcore/10.2.0
5.7.1	-Python-3.8.2	GCCcore/9.3.0
5.8		GCCcore/10.3.0
6.2		GCCcore/11.3.0
6.4.5		GCCcore/12.3.0

Mesa

Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.

homepage: https://www.mesa3d.org/

version	toolchain
11.1.2	foss/2016a, gimkl/2.11.5, intel/2016a
11.2.1	foss/2016a, intel/2016a
12.0.2	foss/2016b, intel/2016b
17.0.2	foss/2017a, intel/2017a
17.2.4	intel/2017b, intelcuda/2017b
17.2.5	foss/2017b, fosscuda/2017b
17.3.6	foss/2018a, fosscuda/2018a, intel/2018a, iomkl/2018a
18.1.1	foss/2018b, fosscuda/2018b, intel/2018b
19.0.1	GCCcore/8.2.0
19.1.7	GCCcore/8.3.0
19.2.1	GCCcore/8.3.0
20.0.2	GCCcore/9.3.0
20.2.1	GCCcore/10.2.0
21.1.1	GCCcore/10.3.0
21.1.7	GCCcore/11.2.0
22.0.3	GCCcore/11.3.0
22.2.4	GCCcore/12.2.0
23.1.4	GCCcore/12.3.0
23.1.9	GCCcore/13.2.0

Mesa-demos

Mesa utility and demo programs, including glxinfo and eglinfo.

homepage: https://www.mesa3d.org/

version	toolchain
8.4.0	GCCcore/10.3.0

meshalyzer

Graphical program for display time dependent data on 3D finite element meshes

homepage: https://git.opencarp.org/openCARP/meshalyzer

version	versionsuffix	toolchain
2.0	-Python-3.8.2	foss/2020a
2.2		foss/2020b
20200308	-Python-3.8.2	foss/2020a

meshio

meshio is a tool for reading/writing various mesh formats representing unstructured meshes

homepage: https://github.com/nschloe/meshio

version	versionsuffix	toolchain
1.7.1	-Python-2.7.12	intel/2016b
2.0.2	-Python-2.7.14	intel/2018a
2.0.2	-Python-3.6.4	intel/2018a
5.3.4		foss/2022b

meshtool

Meshtool is a comand-line tool written in C++. It is designed to apply various manipulations to volumetric meshes.

homepage: https://bitbucket.org/aneic/meshtool

version	toolchain
16	GCC/10.2.0, GCC/9.3.0

Meson

Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.

homepage: https://mesonbuild.com

version	versionsuffix	toolchain
0.43.0	-Python-3.6.3	intel/2017b
0.46.1	-Python-3.6.4	foss/2018a
0.48.1	-Python-3.6.4	foss/2018a, intel/2018a
0.48.1	-Python-3.6.6	foss/2018b, fosscuda/2018b
0.50.0	-Python-3.7.2	GCCcore/8.2.0
0.51.2	-Python-3.7.4	GCCcore/8.3.0
0.53.1	-Python-3.6.3	intel/2017b
0.53.2	-Python-3.8.2	GCCcore/9.3.0
0.55.1	-Python-3.8.2	GCCcore/9.3.0
0.55.3		GCCcore/10.2.0
0.58.0		GCCcore/10.3.0
0.58.2		GCCcore/11.2.0
0.59.1	-Python-3.7.4	GCCcore/8.3.0
0.62.1		GCCcore/11.3.0
0.64.0		GCCcore/12.2.0
1.1.1		GCCcore/12.3.0
1.2.3		GCCcore/13.2.0
1.3.1		GCCcore/12.3.0

meson-python

Python build backend (PEP 517) for Meson projects

homepage: https://github.com/mesonbuild/meson-python

version	toolchain
0.11.0	GCCcore/12.2.0
0.13.2	GCCcore/12.3.0
0.15.0	GCCcore/12.3.0, GCCcore/13.2.0

Mesquite

Mesh-Quality Improvement Library

homepage: https://software.sandia.gov/mesquite/

version	toolchain
2.3.0	GCCcore/10.2.0, GCCcore/6.4.0, GCCcore/8.3.0, gimkl/2.11.5, intel/2016a, intel/2017a

MESS

Master Equation System Solver (MESS)

homepage: https://github.com/PACChem/MESS

version	toolchain
0.1.6	foss/2019b

MetaBAT

An efficient tool for accurately reconstructing single genomes from complex microbial communities

homepage: https://bitbucket.org/berkeleylab/metabat

version	versionsuffix	toolchain
2.12.1	-Python-2.7.15	foss/2018b
2.14		gompi/2019a
2.15		GCC/11.2.0, gompi/2021a, gompi/2021b
2.15	-Python-2.7.18	gompi/2020b

MetaboAnalystR

MetaboAnalystR contains the R functions and libraries underlying the popular MetaboAnalyst web server, including > 500 functions for metabolomic data analysis, visualization, and functional interpretation.

homepage: https://www.metaboanalyst.ca

version	versionsuffix	toolchain
2.0.1-20190827	-R-3.6.0	foss/2019a

MetaDecoder

An algorithm for clustering metagenomic sequences

homepage: https://github.com/liu-congcong/MetaDecoder

version	toolchain
1.0.19	foss/2023b

metaerg

MetaErg is a stand-alone and fully automated metagenomic and metaproteomic data annotation pipeline.

homepage: https://github.com/xiaoli-dong/metaerg

version	versionsuffix	toolchain
1.2.3	-Python-2.7.16	intel/2019b

MetaEuk

MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs.

homepage: https://metaeuk.soedinglab.org

version	toolchain
4	GCC/10.2.0
5	GCC/10.3.0
6	GCC/11.2.0, GCC/11.3.0, GCC/12.2.0

MetaGeneAnnotator

MetaGeneAnnotator is a gene-finding program for prokaryote and phage.

homepage: http://metagene.nig.ac.jp/

version	versionsuffix	toolchain
20080819	-x86-64	system

Metagenome-Atlas

Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, to Annotation.

homepage: https://github.com/metagenome-atlas/atlas

version	versionsuffix	toolchain
2.4.3	-Python-3.8.2	intel/2020a

Metal

Metal - Meta Analysis Helper. The METAL software is designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner.

homepage: http://csg.sph.umich.edu/abecasis/Metal/

version	toolchain
2011-03-25	foss/2016a
2020-05-05	GCC/10.2.0

MetaMorpheus

MetaMorpheus is a bottom-up proteomics database search software with integrated post-translational modification (PTM) discovery capability. This program combines features of Morpheus and G-PTM-D in a single tool.

homepage: https://github.com/smith-chem-wisc/MetaMorpheus

version	toolchain
0.0.320	GCCcore/10.3.0

MetaPhlAn

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

homepage: https://github.com/biobakery/MetaPhlAn

version	versionsuffix	toolchain
3.0.9	-Python-3.8.2	foss/2020a
4.0.6		foss/2022a

MetaPhlAn2

MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.

homepage: https://bitbucket.org/biobakery/metaphlan2/

version	versionsuffix	toolchain
2.7.8	-Python-2.7.12	foss/2016b
2.7.8	-Python-3.6.6	foss/2018b
2.7.8	-Python-3.8.2	foss/2020a

metaWRAP

MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.

homepage: https://github.com/bxlab/metaWRAP

version	versionsuffix	toolchain
1.2	-Python-2.7.15	foss/2018b
1.2.2	-Python-2.7.15	foss/2019a
1.3	-Python-2.7.18	foss/2020b

Metaxa2

Metaxa2 -- Identifies Small Subunit (SSU) rRNAs and classifies them taxonomically

homepage: https://microbiology.se/software/metaxa2/

version	toolchain
2.2	gompi/2019a

methylartist

Tools for plotting methylation data in various ways

homepage: https://github.com/adamewing/methylartist

version	toolchain
1.2.6	foss/2021b

MethylDackel

A (mostly) universal methylation extractor for BS-seq experiments.

homepage: https://github.com/dpryan79/MethylDackel

version	toolchain
0.4.0	iccifort/2019.1.144-GCC-8.2.0-2.31.1
0.5.0	iccifort/2019.5.281
0.6.1	GCC/11.2.0

methylpy

Bisulfite sequencing data processing and differential methylation analysis.

homepage: https://pypi.python.org/pypi/methylpy

version	versionsuffix	toolchain
1.1.9	-Python-2.7.13	foss/2017a
1.2.9		foss/2021b

METIS

METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.

homepage: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview

version	versionsuffix	toolchain
5.0.2		gimkl/2.11.5
5.1.0		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0, foss/2016a, foss/2016b, foss/2017a, foss/2018b, gimkl/2.11.5, intel/2016a, intel/2016b, intel/2017a
5.1.0	-32bitIDX	foss/2016a, gimkl/2.11.5, intel/2016a
5.1.0	-int64	GCCcore/11.3.0

mfqe

extract one or more sets of reads from a FASTQ (or FASTA) file by specifying their read names.

homepage: https://github.com/wwood/mfqe

version	toolchain
0.5.0	GCC/12.3.0

mgen

Convenient matrix generation functions

homepage: https://github.com/NOhs/mgen/tree/master

version	toolchain
1.2.1	foss/2022a

mgltools

The MGLTools software suite can be used for visualization and analysis of molecular structures and comprises the Python Molecular Viewer (PMV, a general purpose molecular viewer), AutoDockTools (ADT, a set of PMV commands specifically developed to support AutoDock users) and Vision (a visual programming environment).

homepage: https://ccsb.scripps.edu/mgltools/

version	toolchain
1.5.7	system

mhcflurry

MHCflurry implements class I peptide/MHC binding affinity prediction. By default it supports 112 MHC alleles using ensembles of allele-specific models. Pan-allele predictors supporting virtually any MHC allele of known sequence are available for testing (see below). MHCflurry runs on Python 2.7 and 3.4+ using the keras neural network library. It exposes command-line and Python library interfaces.

homepage: https://github.com/openvax/mhcflurry

version	versionsuffix	toolchain
1.2.4	-Python-3.7.2	foss/2019a, fosscuda/2019a

mhcnuggets

MHCnuggets: Neoantigen peptide MHC binding prediction for class I and II.

homepage: https://github.com/KarchinLab/mhcnuggets

version	versionsuffix	toolchain
2.3		foss/2020b, fosscuda/2020b
2.3	-Python-3.7.2	foss/2019a, fosscuda/2019a

MicrobeAnnotator

Easy-to-use pipeline for the comprehensive metabolic annotation of microbial genomes.

homepage: https://github.com/cruizperez/MicrobeAnnotator

version	toolchain
2.0.5	foss/2021a

microctools

Various worker functions for microclimc package

homepage: https://github.com/ilyamaclean/microctools

version	versionsuffix	toolchain
0.1.0-20201209	-R-4.0.4	foss/2020b

MiGEC

MIGEC is a software pipeline that facilitates processing and analysis of immune repertoire sequencing data generated using molecular barcoding technique

homepage: https://milaboratory.com/software/migec/

version	versionsuffix	toolchain
1.2.8	-Java-1.8.0_162	system
1.2.9	-Java-1.8	system

MIGRATE-N

Migrate estimates population parameters, effective population sizes and migration rates of n populations, using genetic data. It uses a coalescent theory approach taking into account history of mutations and uncertainty of the genealogy.

homepage: https://peterbeerli.com/migrate-html5/index.html

version	toolchain
4.2.8	foss/2016a
4.2.14	foss/2018a
5.0.4	foss/2021b

Mikado

Mikado is a lightweight Python3 pipeline to identify the most useful or “best” set of transcripts from multiple transcript assemblies. Our approach leverages transcript assemblies generated by multiple methods to define expressed loci, assign a representative transcript and return a set of gene models that selects against transcripts that are chimeric, fragmented or with short or disrupted CDS.

homepage: https://github.com/EI-CoreBioinformatics/mikado

version	toolchain
2.3.4	foss/2022b

Miller

Miller is like awk, sed, cut, join, and sort for name-indexed data such as CSV, TSV, and tabular JSON

homepage: https://miller.readthedocs.io/

version	toolchain
6.4.0	system

mimalloc

mimalloc is a general purpose allocator with excellent performance characteristics.

homepage: https://microsoft.github.io/mimalloc/

version	toolchain
1.7.2	GCCcore/10.3.0, GCCcore/11.2.0

MINC

Medical Image NetCDF or MINC isn't netCDF.

homepage: https://github.com/BIC-MNI/libminc

version	toolchain
2.4.03	foss/2017b, foss/2018a, intel/2017b

MinCED

Mining CRISPRs in Environmental Datasets

homepage: https://github.com/ctSkennerton/minced

version	versionsuffix	toolchain
0.4.2	-Java-11	GCCcore/8.3.0

Mini-XML

Mini-XML is a small XML parsing library that you can use to read XML data files or strings in your application without requiring large non-standard libraries

homepage: https://www.msweet.org/mxml

version	toolchain
2.9	GCCcore/8.2.0
2.12	GCCcore/9.3.0
3.2	GCCcore/10.3.0
3.3.1	GCCcore/11.2.0

miniasm

Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. It simply concatenates pieces of read sequences to generate the final unitig sequences. Thus the per-base error rate is similar to the raw input reads.

homepage: https://github.com/lh3/minimap2

version	toolchain
0.3-20191007	GCCcore/10.3.0, GCCcore/11.2.0

minibar

Dual barcode and primer demultiplexing for MinION sequenced reads

homepage: https://github.com/calacademy-research/minibar

version	versionsuffix	toolchain
20200326	-Python-3.7.4	iccifort/2019.5.281
20200326	-Python-3.8.2	iccifort/2020.1.217

MiniCARD

MiniCARD is a cardinality solver based on MiniSAT [www.minisat.se]. MiniCARD handles cardinality constraints natively, using the same efficient data structures and techniques MiniSAT uses for clauses, giving it much better performance on cardinality constraints than CNF encodings of those constraints passed to a typical SAT solver. It can read the standard DIMACS CNF format, the OPB pseudo-boolean format (with linear cardinality constraints only), and CNF+, a format that extends CNF to include cardinality constraints.

homepage: https://github.com/liffiton/minicard

version	toolchain
1.2	GCC/9.3.0

Miniconda2

Miniconda is a free minimal installer for conda. It is a small, bootstrap version of Anaconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages.

homepage: https://docs.conda.io/en/latest/miniconda.html

version	toolchain
4.3.21	system
4.6.14	system
4.7.10	system

Miniconda3

Miniconda is a free minimal installer for conda. It is a small, bootstrap version of Anaconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages.

homepage: https://docs.conda.io/en/latest/miniconda.html

version	toolchain
4.4.10	system
4.5.12	system
4.6.14	system
4.7.10	system
4.8.3	system
4.9.2	system
4.12.0	system
22.11.1-1	system
23.5.2-0	system
23.9.0-0	system

minieigen

A small wrapper for core parts of EIgen, c++ library for linear algebra.

homepage: https://launchpad.net/minieigen/

version	versionsuffix	toolchain
0.5.3	-Python-2.7.11	foss/2016a, intel/2016a
0.5.3	-Python-2.7.12	foss/2016b, intel/2016b
0.5.3	-Python-2.7.12-Boost-1.63.0	intel/2016b
0.5.4	-Python-2.7.14	intel/2018a

Miniforge3

Miniforge is a free minimal installer for conda and Mamba specific to conda-forge.

homepage: https://github.com/conda-forge/miniforge

version	toolchain
24.1.2-0	system

Minimac4

Minimac4 is a latest version in the series of genotype imputation software - preceded by Minimac3 (2015), Minimac2 (2014), minimac (2012) and MaCH (2010). Minimac4 is a lower memory and more computationally efficient implementation of the original algorithms with comparable imputation quality.

homepage: https://genome.sph.umich.edu/wiki/Minimac4

version	toolchain
1.0.0	foss/2018a

minimap2

Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited test data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replace BWA-MEM for long reads and contig alignment.

homepage: https://github.com/lh3/minimap2

version	toolchain
2.0rc1	foss/2016b
2.10	foss/2018a
2.11	intel/2018a
2.12	foss/2018a
2.13	foss/2018b
2.17	GCC/8.2.0-2.31.1, GCC/8.3.0, GCCcore/9.3.0
2.18	GCCcore/10.2.0
2.20	GCCcore/10.2.0, GCCcore/10.3.0
2.22	GCCcore/11.2.0
2.24	GCCcore/11.2.0, GCCcore/11.3.0
2.26	GCCcore/12.2.0, GCCcore/12.3.0

Minipolish

A tool for Racon polishing of miniasm assemblies

homepage: https://github.com/rrwick/Minipolish

version	toolchain
0.1.3	GCC/11.2.0

MiniSat

MiniSat is a minimalistic, open-source SAT solver, developed to help researchers and developers alike to get started on SAT.

homepage: http://minisat.se/

version	toolchain
2.2.0	GCC/9.3.0
20130925	GCC/9.3.0

minizip

Mini zip and unzip based on zlib

homepage: https://www.winimage.com/zLibDll/minizip.html

version	toolchain
1.1	GCCcore/11.2.0

MINPACK

Minpack includes software for solving nonlinear equations and nonlinear least squares problems. Five algorithmic paths each include a core subroutine and an easy-to-use driver. The algorithms proceed either from an analytic specification of the Jacobian matrix or directly from the problem functions. The paths include facilities for systems of equations with a banded Jacobian matrix, for least squares problems with a large amount of data, and for checking the consistency of the Jacobian matrix with the functions.

homepage: https://www.netlib.org/minpack/

version	toolchain
19961126	GCC/10.3.0

MinPath

MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset.

homepage: https://omics.informatics.indiana.edu/MinPath

version	versionsuffix	toolchain
1.4	-Python-2.7.15	foss/2018b, intel/2018b
1.4	-Python-2.7.16	intel/2019b
1.6		GCCcore/11.2.0

MIRA

MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the latter at the moment only CCS and error-corrected CLR reads).

homepage: https://sourceforge.net/p/mira-assembler/wiki/Home/

version	versionsuffix	toolchain
4.0.2		foss/2018b, gompi/2019b, intel/2017b
4.0.2	-Python-2.7.11	foss/2016a
4.9.6		intel/2017b
5.0rc2		foss/2020b

miRDeep2

miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs

homepage: https://www.mdc-berlin.de/8551903/en/

version	versionsuffix	toolchain
0.1.1	-Python-3.6.6	foss/2018b
2.0.0.8		intel/2016b

Mish-Cuda

Mish-Cuda: Self Regularized Non-Monotonic Activation Function

homepage: https://github.com/JunnYu/mish-cuda

version	versionsuffix	toolchain
20210309	-PyTorch-1.9.0	fosscuda/2020b

misha

The misha package is intended to help users to efficiently analyze genomic data achieved from various experiments.

homepage: https://github.com/tanaylab/misha

version	versionsuffix	toolchain
4.0.10	-R-4.0.0	foss/2020a

MITgcmutils

A numerical model designed for study of the atmosphere, ocean, and climate, MITgcm’s flexible non-hydrostatic formulation enables it to efficiently simulate fluid phenomena over a wide range of scales; its adjoint capabilities enable it to be applied to sensitivity questions and to parameter and state estimation problems. By employing fluid equation isomorphisms, a single dynamical kernel can be used to simulate flow of both the atmosphere and ocean. The model is developed to perform efficiently on a wide variety of computational platforms.

homepage: https://mitgcm.org/

version	toolchain
0.1.2	foss/2022a

MITObim

The MITObim procedure (mitochondrial baiting and iterative mapping) represents a highly efficient approach to assembling novel mitochondrial genomes of non-model organisms directly from total genomic DNA derived NGS reads.

homepage: https://github.com/chrishah/MITObim

version	toolchain
1.9.1	foss/2018b, foss/2020b, gompi/2019b

MitoHiFi

MitoHiFi is a Python workflow that assembles mitogenomes from Pacbio HiFi reads

homepage: https://github.com/marcelauliano/MitoHiFi

version	toolchain
3.2	foss/2022b

MitoZ

MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome visualization.

homepage: https://github.com/linzhi2013/MitoZ

version	versionsuffix	toolchain
2.3	-Python-3.6.6	foss/2018b

MiXCR

MiXCR is a universal software for fast and accurate extraction of T- and B- cell receptor repertoires from any type of sequencing data.

homepage: https://milaboratory.com/software/mixcr

version	versionsuffix	toolchain
2.1.9	-Java-1.8.0_162	system
3.0.3	-Java-1.8	system
3.0.13	-Java-1.8	system
3.0.13	-Java-11	system
4.6.0	-Java-17	system

MixMHC2pred

MixMHC2pred is a predictor of HLA class II ligands and epitopes. It is described in publication Racle, J., et al. Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes

homepage: https://github.com/GfellerLab/MixMHC2pred

version	toolchain
1.2	system

mkl-dnn

Intel(R) Math Kernel Library for Deep Neural Networks (Intel(R) MKL-DNN)

homepage: https://01.org/mkl-dnn

version	toolchain
0.11	intel/2017b
0.13	intel/2018a
0.16	foss/2018b, intel/2018b
0.17.2	foss/2018a

mkl-service

Python hooks for Intel(R) Math Kernel Library runtime control settings.

homepage: https://github.com/IntelPython/mkl-service

version	versionsuffix	toolchain
2.0.2		intel/2019a
2.3.0		intel/2020b, intel/2021b
2.3.0	-Python-3.7.4	intel/2019b

mkl_fft

NumPy-based Python interface to Intel(R) MKL FFT functionality

homepage: https://github.com/IntelPython/mkl_fft

version	versionsuffix	toolchain
1.0.14	-Python-3.6.6	intel/2018b

MLC

Intel Memory Latency Checker (Intel MLC) is a tool used to measure memory latencies and b/w, and how they change with increasing load on the system.

homepage: https://software.intel.com/en-us/articles/intelr-memory-latency-checker

version	toolchain
3.0	system

MLflow

MLflow is a platform to streamline machine learning development, including tracking experiments, packaging code into reproducible runs, and sharing and deploying models.

homepage: https://mlflow.org

version	toolchain
2.10.2	gfbf/2023a

MLxtend

Mlxtend (machine learning extensions) is a Python library of useful tools for the day-to-day data science tasks.

homepage: https://rasbt.github.io/mlxtend/

version	versionsuffix	toolchain
0.17.3	-Python-3.8.2	foss/2020a

mm-common

The mm-common module provides the build infrastructure and utilities shared among the GNOME C++ binding libraries.

homepage: https://gitlab.gnome.org/GNOME/mm-common

version	toolchain
1.0.4	GCCcore/10.3.0
1.0.5	GCCcore/11.3.0

Mmg

Mmg is an open source software for simplicial remeshing. It provides 3 applications and 4 libraries: the mmg2d application and the libmmg2d library: adaptation and optimization of a two-dimensional triangulation and generation of a triangulation from a set of points or from given boundary edges the mmgs application and the libmmgs library: adaptation and optimization of a surface triangulation and isovalue discretization the mmg3d application and the libmmg3d library: adaptation and optimization of a tetrahedral mesh and implicit domain meshing the libmmg library gathering the libmmg2d, libmmgs and libmmg3d libraries.

homepage: https://www.mmgtools.org/

version	toolchain
5.3.9	foss/2017b
5.6.0	gompi/2021a, gompi/2021b
5.7.2	gompi/2022a

MMSEQ

The MMSEQ package contains a collection of statistical tools for analysing RNA-seq expression data.

homepage: https://github.com/eturro/mmseq

version	versionsuffix	toolchain
1.0.8	-linux64-static	system

MMseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

homepage: https://mmseqs.com

version	toolchain
1-c7a89	foss/2016b
5-9375b	intel/2018a
8-fac81	intel/2018b
10-6d92c	gompi/2019b, iimpi/2019b
11-e1a1c	iimpi/2019b
13-45111	gompi/2020b, gompi/2021a, gompi/2021b
13-45111-20211006	gompi/2020b
13-45111-20211019	gompi/2020b
14-7e284	gompi/2022a, gompi/2023a

mmtf-cpp

The Macromolecular Transmission Format (MMTF) is a new compact binary format to transmit and store biomolecular structures for fast 3D visualization and analysis.

homepage: https://mmtf.rcsb.org/

version	toolchain
1.0.0	GCCcore/10.2.0

MNE-Python

MNE-Python software is an open-source Python package for exploring, visualizing, and analyzing human neurophysiological data such as MEG, EEG, sEEG, ECoG, and more. It includes modules for data input/output, preprocessing, visualization, source estimation, time-frequency analysis, connectivity analysis, machine learning, and statistics.

homepage: https://mne.tools/

version	toolchain
0.24.1	foss/2021a
1.6.1	foss/2023a

MOABB

Build a comprehensive benchmark of popular Brain-Computer Interface (BCI) algorithms applied on an extensive list of freely available EEG datasets.

homepage: https://neurotechx.github.io/moabb/

version	toolchain
0.4.6	foss/2021a
1.0.0	foss/2023a

MOABS

MOABS: MOdel based Analysis of Bisulfite Sequencing data

homepage: https://github.com/sunnyisgalaxy/moabs

version	toolchain
1.3.9.6	gompi/2019b

MOB-suite

Software tools for clustering, reconstruction and typing of plasmids from draft assemblies

homepage: https://github.com/phac-nml/mob-suite

version	versionsuffix	toolchain
3.1.0	-Python-3.7.4	foss/2019b

ModelTest-NG

ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments. ModelTest-NG supersedes jModelTest and ProtTest in one single tool, with graphical and command console interfaces.

homepage: https://github.com/ddarriba/modeltest

version	toolchain
0.1.7	gompi/2021b

MODFLOW

MODFLOW is the USGS's modular hydrologic model. MODFLOW is considered an international standard for simulating and predicting groundwater conditions and groundwater/surface-water interactions.

homepage: https://www.usgs.gov/mission-areas/water-resources/science/modflow-and-related-programs

version	toolchain
6.4.4	foss/2023a

modred

Compute modal decompositions and reduced-order models, easily, efficiently, and in parallel.

homepage: https://pypi.python.org/pypi/modred/

version	versionsuffix	toolchain
2.0.2	-Python-3.5.2	foss/2016b

Molcas

Molcas is an ab initio quantum chemistry software package developed by scientists to be used by scientists. The basic philosophy is is to be able to treat general electronic structures for molecules consisting of atoms from most of the periodic table. As such, the primary focus of the package is on multiconfigurational methods with applications typically connected to the treatment of highly degenerate states.

homepage: http://www.molcas.org

version	versionsuffix	toolchain
8.0-15.06.18	_CentOS_6.6_x86_64	system
8.2	-centos-mkl-par	system
8.2	-centos-par	system

mold

mold is a high-performance drop-in replacement for existing Unix linkers.

homepage: https://github.com/rui314/mold

version	toolchain
0.9.6	GCCcore/11.2.0
1.0.0	GCCcore/11.2.0
1.2.1	GCCcore/11.3.0
1.3.0	GCCcore/11.3.0
1.7.1	GCCcore/12.2.0
1.11.0	GCCcore/12.3.0
2.3.1	GCCcore/13.2.0

Molden

Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac

homepage: https://www.theochem.ru.nl/molden/

version	toolchain
5.6	foss/2016a
5.7	intel/2016b
5.8	foss/2018a
6.1	GCCcore/8.2.0
6.8	GCCcore/10.2.0, GCCcore/9.3.0
7.1	GCCcore/11.3.0
7.3	GCCcore/12.3.0

molecularGSM

Code for single-ended and double-ended molecular GSM. The growing string method is a reaction path and transition state finding method developed in c++.

homepage: https://github.com/ZimmermanGroup/molecularGSM

version	toolchain
20190826	intel/2020b

Molekel

Molekel is an open-source multi-platform molecular visualization program.

homepage: http://ugovaretto.github.io/molekel/wiki/pmwiki.php/Main/HomePage.html

version	versionsuffix	toolchain
5.4.0	-Linux_x86_64	system

molmod

MolMod is a Python library with many compoments that are useful to write molecular modeling programs.

homepage: https://molmod.github.io/molmod/

version	versionsuffix	toolchain
1.1	-Python-2.7.11	intel/2016a
1.1	-Python-2.7.12	intel/2016b
1.1	-Python-2.7.13	intel/2017a
1.4.3	-Python-2.7.14	intel/2017b
1.4.3	-Python-3.6.3	intel/2017b
1.4.4	-Python-2.7.14	foss/2018a, intel/2018a
1.4.4	-Python-2.7.15	intel/2018b
1.4.4	-Python-3.7.2	intel/2019a
1.4.5	-Python-3.7.4	foss/2019b, intel/2019b
1.4.5	-Python-3.8.2	foss/2020a, intel/2020a
1.4.8		foss/2020b, foss/2021a, foss/2021b, foss/2023a

Molpro

Molpro is a complete system of ab initio programs for molecular electronic structure calculations.

homepage: https://www.molpro.net

version	versionsuffix	toolchain
2010.1.23	.Linux_x86_64	system
2015.1.0	.linux_x86_64_intel	system
2015.1.3	.linux_x86_64_openmp	system
2015.1.10	.linux_x86_64_openmp	system

MONA

MONA is a tool that translates formulas to finite-state automata. The formulas may express search patterns, temporal properties of reactive systems, parse tree constraints, etc. MONA analyses the automaton resulting from the compilation and prints out "valid" or a counter-example.

homepage: https://www.brics.dk/mona/index.html

version	toolchain
1.4-18	GCC/11.2.0

MONAI

MONAI is a PyTorch-based, open-source framework for deep learning in healthcare imaging, part of PyTorch Ecosystem.

homepage: https://monai.io/

version	versionsuffix	toolchain
0.8.0		foss/2021a
0.8.0	-CUDA-11.3.1	foss/2021a
1.0.1		foss/2022a
1.0.1	-CUDA-11.7.0	foss/2022a
1.3.0		foss/2023a

MONAI-Label

MONAI Label is an intelligent open source image labeling and learning tool that enables users to create annotated datasets and build AI annotation models for clinical evaluation. MONAI Label enables application developers to build labeling apps in a serverless way, where custom labeling apps are exposed as a service through the MONAI Label Server.

homepage: https://docs.monai.io/projects/label/en/latest/

version	versionsuffix	toolchain
0.5.2	-PyTorch-1.12.0	foss/2022a
0.5.2	-PyTorch-1.12.0-CUDA-11.7.0	foss/2022a

mongolite

High-performance MongoDB client based on 'mongo-c-driver' and 'jsonlite'. Includes support for aggregation, indexing, map-reduce, streaming, encryption, enterprise authentication, and GridFS. The online user manual provides an overview of the available methods in the package: https://jeroen.github.io/mongolite/.

homepage: https://cran.r-project.org/web/packages/mongolite

version	versionsuffix	toolchain
2.3.0	-R-4.0.0	foss/2020a
2.3.0	-R-4.0.3	foss/2020b
2.3.0	-R-4.0.4	foss/2020b

Mono

An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET.

homepage: https://www.mono-project.com/

version	toolchain
2.10.6	intel/2016b
4.6.2.7	intel/2016b, system
4.8.0.495	intel/2017a
5.4.1.6	foss/2017b, intel/2017b
5.10.0.160	foss/2018a
5.18.1.0	foss/2018a
6.4.0.198	foss/2018b
6.8.0.105	GCCcore/8.3.0
6.12.0.122	GCCcore/11.2.0

Monocle3

An analysis toolkit for single-cell RNA-seq.

homepage: https://cole-trapnell-lab.github.io/monocle3/

version	versionsuffix	toolchain
0.2.0	-Python-3.7.2-R-3.6.0	foss/2019a
0.2.3	-R-4.0.3	foss/2020b
1.3.1	-R-4.2.1	foss/2022a
1.3.1	-R-4.2.2	foss/2022b

moonjit

Moonjit is a Just-In-Time Compiler (JIT) for the Lua programming language. Lua is a powerful, dynamic and light-weight programming language. It may be embedded or used as a general-purpose, stand-alone language.

homepage: https://github.com/moonjit/moonjit

version	toolchain
2.2.0	GCCcore/9.3.0

MOOSE

The Multiphysics Object-Oriented Simulation Environment (MOOSE) is a finite-element, multiphysics framework primarily developed by Idaho National Laboratory

homepage: https://mooseframework.inl.gov

version	versionsuffix	toolchain
2021-05-18	-Python-3.7.4	foss/2019b

mordecai

mordecai is a full text geoparsing as a Python library. Extract the place names from a piece of text, resolve them to the correct place, and return their coordinates and structured geographic information.

homepage: https://github.com/openeventdata/mordecai

version	versionsuffix	toolchain
2.0.1	-Python-3.6.4	foss/2018a

MoreRONN

MoreRONN is the spiritual successor of RONN and is useful for surveying disorder in proteins as well as designing expressible constructs for X-ray crystallography.

homepage: https://github.com/varun-ramraj/MoreRONN

version	toolchain
4.9	GCC/8.3.0

morphosamplers

A library for sampling image data along morphological objects such as splines and surfaces.

homepage: https://github.com/kevinyamauchi/morphosamplers

version	toolchain
0.0.10	gfbf/2023a

mosdepth

Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

homepage: https://github.com/brentp/mosdepth

version	toolchain
0.2.2	intel/2018a
0.2.3	intel/2018a
0.2.4	foss/2018b
0.3.3	GCC/11.2.0

Mothur

Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.

homepage: https://www.mothur.org/

version	versionsuffix	toolchain
1.39.5	-Python-2.7.13	intel/2017a
1.41.0	-Python-2.7.15	foss/2018b
1.43.0	-Python-3.7.2	foss/2019a

motif

Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix.

homepage: https://motif.ics.com/

version	toolchain
2.3.5	foss/2016a, intel/2016a
2.3.7	intel/2017a
2.3.8	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/8.3.0, GCCcore/9.3.0, foss/2017b, foss/2018a, foss/2018b, foss/2019a, intel/2017b, intel/2018a, intel/2019a

MotionCor2

MotionCor2 correct anisotropic image motion at the single pixel level across the whole frame, suitable for both single particle and tomographic images. Iterative, patch-based motion detection is combined with spatial and temporal constraints and dose weighting. Cite publication: Shawn Q. Zheng, Eugene Palovcak, Jean-Paul Armache, Yifan Cheng and David A. Agard (2016) Anisotropic Correction of Beam-induced Motion for Improved Single-particle Electron Cryo-microscopy, Nature Methods, submitted. BioArxiv: https://biorxiv.org/content/early/2016/07/04/061960

homepage: https://msg.ucsf.edu/

version	toolchain
1.2.6	GCCcore/8.2.0
1.3.1	GCCcore/8.3.0
1.3.2	GCCcore/8.3.0
1.4.2	GCCcore/10.2.0
1.4.4	GCCcore/10.2.0, GCCcore/10.3.0
1.5.0	GCCcore/11.3.0

MotionCor3

Anisotropic correction of beam induced motion for cryo-electron microscopy and cryo-electron tomography images. MotionCor3, an improved implementation of MotionCor2 with addition of CTF (Contrast Transfer Function) estimation, is a multi-GPU accelerated software package that enables single-pixel level correction of anisotropic beam induced sample motion for cryo-electron microscopy and cryo-electron tomography images. The iterative, patch-based motion detection combined with spatial and temporal constraints and dose weighting provides robust and accurate correction. By refining the measurement of early motion, MotionCor3 further improves correction on tilted samples. The efficiency achieved by multi-GPU acceleration and parallelization enables correction to keep pace with automated data collection. The recent addition of a very robust GPU-accelerated CTF estimation makes MotionCor3 more versatile in cryoEM and cryoET processing pipeline.

homepage: https://github.com/czimaginginstitute/MotionCor3

version	versionsuffix	toolchain
1.0.1	-CUDA-12.1.1	GCCcore/12.3.0

motionSegmentation

Motion correction, explicit spatio-temporal regularization of motion tracking, random speckles enhancement, and segmentation.

homepage: https://github.com/WeiXuanChan/motionSegmentation

version	versionsuffix	toolchain
2.7.9	-Python-3.7.4	foss/2019b

MoviePy

MoviePy (full documentation) is a Python library for video editing: cutting, concatenations, title insertions, video compositing (a.k.a. non-linear editing), video processing, and creation of custom effects.

homepage: https://zulko.github.io/moviepy/

version	versionsuffix	toolchain
1.0.1	-Python-3.7.2	foss/2019a
1.0.3		foss/2021a, foss/2021b

mpath

For now it's quit simple and get_path_info() method returns information about given path. It can be either a directory or a file path.

homepage: https://pypi.org/project/mpath/

version	toolchain
1.1.3	GCCcore/11.3.0

MPB

MPB is a free and open-source software package for computing the band structures, or dispersion relations, and electromagnetic modes of periodic dielectric structures, on both serial and parallel computers. MPB is an acronym for MIT Photonic Bands.

homepage: https://mpb.readthedocs.io/en/latest/

version	versionsuffix	toolchain
1.6.2	-Python-2.7.14	foss/2017b, foss/2018a, intel/2018a
1.11.1		foss/2020b

MPC

Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result. It extends the principles of the IEEE-754 standard for fixed precision real floating point numbers to complex numbers, providing well-defined semantics for every operation. At the same time, speed of operation at high precision is a major design goal.

homepage: http://www.multiprecision.org/

version	versionsuffix	toolchain
1.0.3		intel/2017a
1.0.3	-MPFR-3.1.6	foss/2017b, intel/2017b
1.1.0		GCC/8.3.0, GCC/9.3.0, GCCcore/9.3.0
1.2.1		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0
1.3.1		GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

MPFI

MPFI stands for Multiple Precision Floating-point Interval library.

homepage: https://perso.ens-lyon.fr/nathalie.revol/software.html

version	toolchain
1.5.4	GCCcore/11.3.0

MPFR

The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.

homepage: https://www.mpfr.org

version	toolchain
2.4.2	system
3.1.4	foss/2016a, foss/2016b, intel/2016a, intel/2016b
3.1.5	GCCcore/6.4.0, intel/2017a
3.1.6	GCCcore/6.4.0
4.0.1	GCCcore/6.4.0, GCCcore/7.3.0
4.0.2	GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
4.1.0	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0
4.2.0	GCCcore/12.2.0, GCCcore/12.3.0
4.2.1	GCCcore/13.2.0

mpi4py

MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.

homepage: https://github.com/mpi4py/mpi4py

version	versionsuffix	toolchain
1.3.1	-Python-2.7.11-timed-pingpong	intel/2016a
1.3.1	-Python-2.7.12-timed-pingpong	intel/2016b
2.0.0	-Python-2.7.12	intel/2016b
2.0.0	-Python-2.7.13-timed-pingpong	intel/2017a
3.0.0	-Python-2.7.14-timed-pingpong	intel/2018a
3.0.0	-Python-3.6.3	intel/2017b
3.0.1	-Python-3.6.6	intel/2018b
3.0.2	-timed-pingpong	gompi/2019a, iimpi/2019a
3.1.4		gompi/2022b, gompi/2023a
3.1.5		gompi/2023b

MPICH

MPICH is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3).

homepage: https://www.mpich.org/

version	toolchain
3.0.4	GCC/4.8.1
3.2	GCC/4.9.3-2.25, GCC/7.2.0-2.29
3.2.1	GCC/7.2.0-2.29
3.3.2	GCC/10.2.0, GCC/9.3.0
3.4.2	GCC/10.3.0

MPICH2

MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).

homepage: http://www.mpich.org/

version	toolchain
1.1	GCC/4.8.1

mpifileutils

MPI-Based File Utilities For Distributed Systems

homepage: https://hpc.github.io/mpifileutils/

version	toolchain
0.9.1	gompi/2019a, iimpi/2019a
0.10	gompi/2020a, iimpi/2020a
0.10.1	gompi/2020a
0.11.1	gompi/2022a, gompi/2023a

mpiP

mpiP is a lightweight profiling library for MPI applications. Because it only collects statistical information about MPI functions, mpiP generates considerably less overhead and much less data than tracing tools. All the information captured by mpiP is task-local. It only uses communication during report generation, typically at the end of the experiment, to merge results from all of the tasks into one output file.

homepage: http://mpip.sourceforge.net/

version	toolchain
3.4.1	gompi/2019a, iimpi/2019a, iompi/2019.01

MPJ-Express

MPJ Express is an open source Java message passing library that allows application developers to write and execute parallel applications for multicore processors and compute clusters/clouds.

homepage: http://mpj-express.org/

version	versionsuffix	toolchain
0.44	-Java-1.8.0_92	foss/2016a

mpmath

mpmath can be used as an arbitrary-precision substitute for Python's float/complex types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation can be performed just as well at 10-digit or 1000-digit precision, with either real or complex numbers, and in many cases mpmath implements efficient algorithms that scale well for extremely high precision work.

homepage: https://mpmath.org/

version	versionsuffix	toolchain
0.19	-Python-2.7.11	foss/2016a, intel/2016a
1.0.0	-Python-2.7.14	intel/2018a
1.0.0	-Python-2.7.15	foss/2018b
1.1.0	-Python-3.8.2	GCCcore/9.3.0
1.2.1		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0

MrBayes

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models.

homepage: https://nbisweden.github.io/MrBayes/

version	toolchain
3.2.6	foss/2016a, foss/2017a, gompi/2020b
3.2.7	gompi/2020b, gompi/2022a, gompic/2019b
3.2.7a	foss/2020a, iimpi/2019a

mrcfile

mrcfile is a Python implementation of the MRC2014 file format, which is used in structural biology to store image and volume data. It allows MRC files to be created and opened easily using a very simple API, which exposes the file’s header and data as numpy arrays. The code runs in Python 2 and 3 and is fully unit-tested. This library aims to allow users and developers to read and write standard- compliant MRC files in Python as easily as possible, and with no dependencies on any compiled libraries except numpy. You can use it interactively to inspect files, correct headers and so on, or in scripts and larger software packages to provide basic MRC file I/O functions.

homepage: https://github.com/ccpem/mrcfile

version	toolchain
1.3.0	foss/2020b, foss/2021a, fosscuda/2020b
1.4.3	foss/2022a
1.5.0	foss/2023a

MRChem

MRChem is a numerical real-space code for molecular electronic structure calculations within the self-consistent field (SCF) approximations of quantum chemistry: Hartree-Fock and Density Functional Theory.

homepage: https://mrchem.readthedocs.io

version	versionsuffix	toolchain
1.0.0	-Python-3.8.2	foss/2020a
1.1.1		foss/2022a

MRCPP

MultiResolution Computation Program Package

homepage: https://mrcpp.readthedocs.io

version	toolchain
1.3.6	foss/2020a
1.4.1	foss/2022a

MRIcron

MRIcron allows viewing of medical images. It includes tools to complement SPM and FSL. Native format is NIFTI but includes a conversion program (see dcm2nii) for converting DICOM images. Features layers, ROIs, and volume rendering.

homepage: http://www.mccauslandcenter.sc.edu/mricro/mricron/

version	toolchain
1.0.20180614	system
20150601	system

MRPRESSO

Performs the Mendelian Randomization Pleiotropy RESidual Sum and Outlier (MR-PRESSO) method..

homepage: https://github.com/rondolab/MR-PRESSO

version	toolchain
1.0-20230502	foss/2022a

MRtrix

MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines.

homepage: http://www.brain.org.au/software/index.html#mrtrix

version	versionsuffix	toolchain
0.3.14	-Python-2.7.11	intel/2016a
0.3.15	-Python-2.7.12	intel/2016b
3.0-rc-20191217	-Python-2.7.16	foss/2019b
3.0-rc-20191217	-Python-3.7.4	foss/2019b
3.0.0	-Python-3.8.2	foss/2020a
3.0.3		foss/2021a
3.0.4		foss/2022b
3.0_RC2	-Python-2.7.13	foss/2017a
3.0_RC3	-Python-2.7.14	intel/2018a

MSFragger

MSFragger is an ultrafast database search tool for peptide identification in mass spectrometry-based proteomics. It has demonstrated excellent performance across a wide range of datasets and applications. MSFragger is suitable for standard shotgun proteomics analyses as well as large datasets (including timsTOF PASEF data), enzyme unconstrained searches (e.g., peptidome), open database searches (e.g., precursor mass tolerance set to hundreds of Daltons) for identification of modified peptides, and glycopeptide identification (N-linked and O-linked).

homepage: https://msfragger.nesvilab.org/

version	versionsuffix	toolchain
4.0	-Java-11	system

msgpack-c

MessagePack is an efficient binary serialization format, which lets you exchange data among multiple languages like JSON, except that it's faster and smaller. Small integers are encoded into a single byte while typical short strings require only one extra byte in addition to the strings themselves.

homepage: http://msgpack.org/

version	toolchain
3.3.0	GCCcore/10.2.0
6.0.0	GCC/12.2.0

MSM

Multimodal Surface Matching with Higher order Clique Reduction

homepage: https://github.com/ecr05/MSM_HOCR

version	toolchain
1.0	foss/2017b, intel/2017b

MSPC

Using combined evidence from replicates to evaluate ChIP-seq peaks

homepage: https://genometric.github.io/MSPC/

version	toolchain
3.3.1	system

msprime

msprime is a coalescent simulator and library for processing tree-based genetic data.

homepage: https://msprime.readthedocs.io

version	versionsuffix	toolchain
0.7.0	-Python-3.7.2	intel/2019a
1.2.0		foss/2021b, foss/2022a

mstore

Molecular structure store for testing

homepage: https://github.com/grimme-lab/mstore

version	toolchain
0.2.0	GCC/11.2.0, GCC/11.3.0, GCC/12.2.0, intel-compilers/2022.1.0, intel-compilers/2022.2.1

MTL4

The Matrix Template Library 4 incorporates the most modern programming techniques to provide an easy and intuitive interface to users while enabling optimal performance. The natural mathematical notation in MTL4 empowers all engineers and scientists to implement their algorithms and models in minimal time. All technical aspects are encapsulated in the library.

homepage: http://www.simunova.com/mtl4

version	toolchain
4.0.8878	system
4.0.9555	system

MuJoCo

MuJoCo stands for Multi-Joint dynamics with Contact. It is a general purpose physics engine that aims to facilitate research and development in robotics, biomechanics, graphics and animation, machine learning, and other areas which demand fast and accurate simulation of articulated structures interacting with their environment.

homepage: https://mujoco.org/

version	toolchain
2.1.1	GCCcore/11.2.0
2.2.2	GCCcore/11.3.0

mujoco-py

MuJoCo is a physics engine for detailed, efficient rigid body simulations with contacts. mujoco-py allows using MuJoCo from Python 3.

homepage: https://github.com/openai/mujoco-py

version	toolchain
2.1.2.14	foss/2021b

multicharge

Electronegativity equilibration model for atomic partial charges.

homepage: https://github.com/grimme-lab/multicharge

version	toolchain
0.2.0	gfbf/2022b, iimkl/2022a, iimkl/2022b

multichoose

generate multiset combinations (n multichoose k).

homepage: https://github.com/ekg/multichoose

version	toolchain
1.0.3	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.3.0, GCCcore/9.3.0

MultilevelEstimators

The Julia module for Multilevel Monte Carlo methods

homepage: https://github.com/PieterjanRobbe/MultilevelEstimators.jl

version	versionsuffix	toolchain
0.1.0	-Julia-1.7.2	GCC/11.2.0

MultiNest

MultiNest is a Bayesian inference tool which calculates the evidence and explores the parameter space which may contain multiple posterior modes and pronounced (curving) degeneracies in moderately high dimensions.

homepage: https://ccpforge.cse.rl.ac.uk/gf/project/multinest/

version	toolchain
3.10	intel/2016a

multiprocess

better multiprocessing and multithreading in python

homepage: https://github.com/uqfoundation/multiprocess

version	toolchain
0.70.15	gfbf/2023a

MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report. MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.

homepage: https://multiqc.info

version	versionsuffix	toolchain
0.9	-Python-2.7.12	foss/2016b
1.2	-Python-2.7.14	foss/2017b, intel/2017b
1.2	-Python-3.6.3	foss/2017b, intel/2017b
1.6	-Python-2.7.14	foss/2017b, intel/2017b
1.6	-Python-3.6.3	foss/2017b, intel/2017b
1.7	-Python-2.7.15	intel/2018b
1.7	-Python-3.6.6	foss/2018b, intel/2018b
1.8	-Python-2.7.16	intel/2019b
1.8	-Python-3.7.4	foss/2019b, intel/2019b
1.9	-Python-3.7.4	foss/2019b
1.9	-Python-3.8.2	foss/2020a, intel/2020a
1.10.1		foss/2020b
1.11		foss/2021a
1.12		foss/2021b
1.14		foss/2022a, foss/2022b

Multiwfn

Multiwfn is an extremely powerful program for realizingi electronic wavefunction analysis, which is a key ingredient of quantum chemistry. Multiwfn is free, open-source, high-efficient, very user-friendly and flexible, it supports almost all of the most important wavefunction analysis methods.

homepage: http://sobereva.com/multiwfn/

version	toolchain
3.4.1	intel/2017b
3.6	intel/2019a, intel/2019b

muMerge

muMerge is a tool for combining bed regions from multiple bed files that overlap.

homepage: https://github.com/Dowell-Lab/mumerge

version	toolchain
1.1.0	foss/2022a

MUMmer

MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it.

homepage: https://mummer.sourceforge.net/

version	toolchain
3.23	GCCcore/10.3.0, GCCcore/9.3.0, foss/2016b
4.0.0beta2	GCCcore/10.2.0, GCCcore/11.2.0, GCCcore/9.3.0, foss/2018b
4.0.0rc1	GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0

MUMPS

A parallel sparse direct solver

homepage: https://graal.ens-lyon.fr/MUMPS/

version	versionsuffix	toolchain
5.1.2	-metis	foss/2017b
5.2.1	-metis	foss/2018b, foss/2019a, foss/2019b, foss/2020a, intel/2019a, intel/2019b, intel/2020a
5.2.1	-metis-seq	foss/2019a, intel/2019a
5.3.5	-metis	foss/2020b, intel/2020b
5.4.0	-metis	foss/2021a, intel/2021a
5.4.1	-metis	foss/2021b, intel/2021b
5.5.0	-metis	foss/2021a
5.5.1	-metis	foss/2022a
5.6.1	-metis	foss/2022b, foss/2023a

muParser

muParser is an extensible high performance math expression parser library written in C++. It works by transforming a mathematical expression into bytecode and precalculating constant parts of the expression.

homepage: https://beltoforion.de/article.php?a=muparser

version	toolchain
2.2.5	GCCcore/6.4.0
2.3.2	GCCcore/10.2.0, GCCcore/9.3.0
2.3.3	GCCcore/10.3.0
2.3.4	GCCcore/11.3.0, GCCcore/12.2.0

muparserx

A C++ Library for Parsing Expressions with Strings, Complex Numbers, Vectors, Matrices and more.

homepage: https://beltoforion.de/en/muparserx/

version	toolchain
4.0.8	GCCcore/10.3.0, GCCcore/11.2.0

MuPeXI

MuPeXI: Mutant Peptide eXtractor and Informer. Given a list of somatic mutations (VCF file) as input, MuPeXI returns a table containing all mutated peptides (neo-peptides) of user-defined lengths, along with several pieces of information relevant for identifying which of these neo-peptides are likely to serve as neo-epitopes.

homepage: https://github.com/ambj/MuPeXI

version	versionsuffix	toolchain
1.2.0	-Perl-5.28.0-Python-2.7.15	foss/2018b

MUSCLE

MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes-only a handful of command-line options are needed to perform common alignment tasks.

homepage: https://drive5.com/muscle/

version	versionsuffix	toolchain
3.8.31		GCC/7.3.0-2.30, GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/9.3.0, foss/2016a, foss/2017b, foss/2018a, intel/2016a, intel/2017b, intel/2018a, intel/2018b
3.8.31	-i86linux64	system
3.8.1551		GCC/10.2.0, GCC/8.2.0-2.31.1, GCC/8.3.0
5.0.1428		GCCcore/10.3.0
5.1		GCCcore/11.2.0
5.1.0		GCCcore/10.3.0, GCCcore/11.3.0, GCCcore/12.3.0

MUSCLE3

MUSCLE3 allows connecting multiple simulation models together into a multiscale simulation. Simulation models can be as simple as a single Python file, or as complex as a combination of multiple separate simulation codes written in C++ or Fortran, and running on an HPC machine.

homepage: https://muscle3.readthedocs.io/en/latest/index.html

version	toolchain
0.7.0	foss/2022b

MuSiC

Multi-subject Single Cell deconvolution (MuSiC) is a deconvolution method that utilizes cross-subject scRNA-seq to estimate cell type proportions in bulk RNA-seq data.

homepage: https://github.com/xuranw/MuSiC

version	versionsuffix	toolchain
1.6.2	-R-3.5.1	foss/2018b

MUST

MUST detects usage errors of the Message Passing Interface (MPI) and reports them to the user. As MPI calls are complex and usage errors common, this functionality is extremely helpful for application developers that want to develop correct MPI applications. This includes errors that already manifest – segmentation faults or incorrect results – as well as many errors that are not visible to the application developer or do not manifest on a certain system or MPI implementation.

homepage: https://hpc.rwth-aachen.de/must/

version	versionsuffix	toolchain
1.6	-Python-3.6.6	foss/2018b
1.6	-Python-3.7.4	foss/2019b
1.7.1		foss/2020b
1.7.2		foss/2021a

MuTect

MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.

homepage: http://www.broadinstitute.org/cancer/cga/mutect

version	versionsuffix	toolchain
1.1.4	-Java-1.7.0_76	system
1.1.4	-Java-1.7.0_80	system
1.1.7	-Java-1.7.0_80	system

mutil

Mutil is a set of standard utilities that have been parallelized to maximize performance on modern file systems. These currently include multi-threaded drop-in replacements for cp and md5sum from GNU coreutils, which have achieved 10/30x rates on one/many nodes.

homepage: http://people.nas.nasa.gov/~kolano/projects/mutil.html

version	toolchain
1.822.3	intel/2016a

MVAPICH2

This is an MPI 3.0 implementation. It is based on MPICH2 and MVICH.

homepage: http://mvapich.cse.ohio-state.edu/overview/mvapich2/

version	toolchain
2.0.1	GCC/4.8.4
2.1	GCC/4.9.3-2.25
2.2b	GCC/4.9.3-2.25

MView

MView reformats the results of a sequence database search or a multiple alignment, optionally adding HTML markup.

homepage: https://desmid.github.io/mview/

version	toolchain
1.67	GCC/11.3.0

mxml

Mini-XML is a tiny XML library that you can use to read and write XML and XML-like data files in your application without requiring large non-standard libraries.

homepage: https://github.com/michaelrsweet/mxml

version	toolchain
3.2	GCCcore/8.3.0

mxmlplus

Mxml is a pure C library (yet having an object oriented layout) that is meant to help developers implementing XML file interpretation in their projects.

homepage: http://mxml.sourceforge.net

version	toolchain
0.9.2	GCC/9.3.0

MXNet

Flexible and Efficient Library for Deep Learning

homepage: https://mxnet.io/

version	versionsuffix	toolchain
0.9.3	-Python-2.7.12-R-3.3.3	foss/2016b
1.9.1		foss/2022a

MyCC

MyCC is built and delivered as a tailored solution for metagenomics sequencesclassfication.

homepage: https://sourceforge.net/projects/sb2nhri/files/MyCC/

version	versionsuffix	toolchain
2017-03-01	-Python-2.7.16	intel/2019b

mygene

Python Client for MyGene.Info services.

homepage: https://github.com/biothings/mygene.py

version	toolchain
3.1.0	intel/2019a
3.2.2	foss/2022a, foss/2022b

MyMediaLite

MyMediaLite is a lightweight, multi-purpose library of recommender system algorithms.

homepage: http://www.ismll.uni-hildesheim.de/mymedialite/

version	toolchain
3.10	intel/2016b
3.11	intel/2016b
3.12	intel/2017a

mympingpong

A mpi4py based random pair pingpong network stress test.

homepage: https://github.com/hpcugent/mympingpong

version	versionsuffix	toolchain
0.7.0	-Python-2.7.11	intel/2016a
0.7.1	-Python-2.7.12	intel/2016b
0.8.0	-Python-2.7.13	intel/2017a
0.8.0	-Python-2.7.14	intel/2018a
0.8.0	-Python-2.7.15	foss/2019a, intel/2019a

Myokit

Myokit is an open-source Python-based toolkit that facilitates modeling and simulation of cardiac cellular electrophysiology.

homepage: http://myokit.org

version	toolchain
1.32.0	foss/2020b, fosscuda/2020b

mypy

Optional static typing for Python

homepage: http://www.mypy-lang.org/

version	toolchain
0.4.5	intel/2016b

MySQL

MySQL is one of the world's most widely used open-source relational database management system (RDBMS).

homepage: http://www.mysql.com/

version	versionsuffix	toolchain
5.6.26	-clientonly	GNU/4.9.3-2.25
5.7.21	-clientonly	GCCcore/6.4.0

MySQL-python

MySQL database connector for Python

homepage: https://github.com/farcepest/MySQLdb1

version	versionsuffix	toolchain
1.2.5	-Python-2.7.11	intel/2016a
1.2.5	-Python-2.7.11-MariaDB-10.1.14	intel/2016a

mysqlclient

Python interface to MySQL

homepage: https://github.com/PyMySQL/mysqlclient-python

version	versionsuffix	toolchain
1.3.7	-Python-2.7.11	foss/2016a, intel/2016a

N

n2v - NAG - NAGfor - NAMD - namedlist - nano - NanoCaller - NanoComp - nanocompore - NanoFilt - nanoflann - nanoget - NanoLyse - nanomath - nanomax-analysis-utils - nanonet - NanoPlot - nanopolish - NanopolishComp - NanoStat - napari - NASM - nauty - nbclassic - NBO - NCBI-Toolkit - ncbi-vdb - NCCL - NCCL-tests - ncdf4 - ncdu - NCIPLOT - NCL - NCO - ncolor - ncompress - ncurses - ncview - nd2reader - ne - NECI - NEdit - Nek5000 - Nektar++ - neon - neptune-client - Net-core - netCDF - netCDF-C++ - netCDF-C++4 - netCDF-Fortran - netcdf4-python - netloc - NetLogo - netMHC - netMHCII - netMHCIIpan - netMHCpan - NetPIPE - NetPyNE - nettle - networkTools - networkx - NeuroKit - NEURON - NewHybrids - Nextflow - NextGenMap - NEXUS-CL - nf-core - nf-core-mag - NFFT - nghttp2 - nghttp3 - NGLess - nglview - NGS - NGS-Python - NGSadmix - NGSpeciesID - ngspice - ngtcp2 - NiBabel - nichenetr - NIfTI - nifti2dicom - Nilearn - Nim - NIMBLE - Ninja - Nipype - NLMpy - nlohmann_json - NLopt - NLTK - nnU-Net - Node-RED - nodejs - noise - Normaliz - nose-parameterized - nose3 - novaSTA - novoalign - NOVOPlasty - npstat - NRGLjubljana - Nsight-Compute - Nsight-Systems - NSPR - NSS - nsync - ntCard - ntEdit - ntHits - NTL - NTPoly - num2words - numactl - numba - numdiff - numexpr - numpy - NVHPC - nvofbf - nvompi - NVSHMEM - nvtop - NWChem - NxTrim

n2v

Learning Denoising from Single Noisy Images

homepage: https://github.com/juglab/n2v

version	versionsuffix	toolchain
0.3.2		foss/2022a
0.3.2	-CUDA-11.3.1	foss/2021a

NAG

The worlds largest collection of robust, documented, tested and maintained numerical algorithms.

homepage: http://www.nag.co.uk

version	toolchain
7.1	gompi/2022b
24	PGI/17.4-GCC-6.4.0-2.28
26	GCCcore/6.4.0, intel/2018a

NAGfor

The checking compiler for improved code portability and detailed error reporting.

homepage: http://www.nag.co.uk

version	toolchain
6.2.14	system
7.1	system

NAMD

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

homepage: https://www.ks.uiuc.edu/Research/namd/

version	versionsuffix	toolchain
2.11	-mpi	intel/2016a
2.12	-CUDA-8.0.61	foss/2016b
2.12	-mpi	foss/2017a, foss/2017b, intel/2017a, intel/2017b
2.13		fosscuda/2018b
2.13	-mpi	foss/2018b, foss/2019b, intel/2018b
2.14		fosscuda/2019b, fosscuda/2020b
2.14	-CUDA-11.3.1	foss/2021a
2.14	-CUDA-11.7.0	foss/2022a
2.14	-mpi	foss/2019b, foss/2020a, foss/2020b, foss/2022a, foss/2023a, intel/2020a

namedlist

A Python object, similar to namedtuple, but for lists.

homepage: https://gitlab.com/ericvsmith/namedlist

version	toolchain
1.8	GCCcore/11.2.0

nano

a simple editor, inspired by Pico

homepage: https://www.nano-editor.org/

version	toolchain
6.4	GCCcore/11.3.0
7.0	GCCcore/11.3.0
7.1	GCCcore/12.2.0
7.2	GCCcore/12.2.0

NanoCaller

NanoCaller is a computational method that integrates long reads in deep convolutional neural network for the detection of SNPs/indels from long-read sequencing data.

homepage: https://github.com/WGLab/NanoCaller

version	toolchain
3.4.1	foss/2022a

NanoComp

Comparing runs of Oxford Nanopore sequencing data and alignments

homepage: https://github.com/wdecoster/NanoComp

version	versionsuffix	toolchain
1.10.1	-Python-3.7.4	intel/2019b
1.13.1		intel/2020b

nanocompore

Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples

homepage: https://nanocompore.rna.rocks/

version	versionsuffix	toolchain
1.0.0rc3-2	-Python-3.8.2	intel/2020a

NanoFilt

Filtering and trimming of long read sequencing data.

homepage: https://github.com/wdecoster/nanofilt

version	versionsuffix	toolchain
2.5.0	-Python-3.6.6	foss/2018b
2.6.0	-Python-3.7.4	foss/2019b, intel/2019b
2.6.0	-Python-3.8.2	intel/2020a
2.8.0		foss/2021b

nanoflann

nanoflann is a C++11 header-only library for building KD-Trees of datasets with different topologies.

homepage: https://github.com/jlblancoc/nanoflann

version	toolchain
1.4.0	GCCcore/10.3.0
1.5.0	GCCcore/11.3.0

nanoget

Functions to extract information from Oxford Nanopore sequencing data and alignments

homepage: https://github.com/wdecoster/nanoget

version	versionsuffix	toolchain
1.12.1	-Python-3.7.4	intel/2019b
1.15.0		intel/2020b
1.18.1		foss/2021a, foss/2022a

NanoLyse

Remove reads mapping to the lambda phage genome from a fastq file.

homepage: https://github.com/wdecoster/nanolyse

version	toolchain
1.2.1	foss/2021a

nanomath

A few simple math function for other Oxford Nanopore processing scripts

homepage: https://github.com/wdecoster/nanomath

version	versionsuffix	toolchain
0.23.1	-Python-3.7.4	intel/2019b
1.2.0		intel/2020b
1.2.1		foss/2021a
1.3.0		foss/2022a

nanomax-analysis-utils

A set of tools for handling and analysing data at the NanoMAX beamline.

homepage: https://github.com/maxiv-science/nanomax-analysis-utils

version	versionsuffix	toolchain
0.4	-Python-3.7.4	foss/2019b, fosscuda/2019b
0.4.3		foss/2020b, fosscuda/2020b
0.4.4		foss/2021b

nanonet

Nanonet provides recurrent neural network basecalling for Oxford Nanopore MinION data.

homepage: https://github.com/nanoporetech/nanonet

version	versionsuffix	toolchain
2.0.0	-Python-2.7.13	intel/2017a

NanoPlot

Plotting suite for long read sequencing data and alignments

homepage: https://github.com/wdecoster/NanoPlot

version	versionsuffix	toolchain
1.28.4	-Python-3.7.4	intel/2019b
1.33.0		foss/2021a, intel/2020b

nanopolish

Software package for signal-level analysis of Oxford Nanopore sequencing data.

homepage: https://github.com/jts/nanopolish

version	versionsuffix	toolchain
0.9.2		intel/2018a
0.10.2	-Python-2.7.15	foss/2018b, intel/2018b
0.13.1	-Python-3.6.6	foss/2018b
0.13.2	-Python-3.8.2	foss/2020a
0.13.3		foss/2020b
0.14.0		foss/2022a

NanopolishComp

NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files

homepage: https://adrienleger.com/NanopolishComp/

version	versionsuffix	toolchain
0.6.11	-Python-3.8.2	foss/2020a

NanoStat

Calculate various statistics from a long read sequencing dataset in fastq, bam or albacore sequencing summary format.

homepage: https://github.com/wdecoster/nanostat

version	toolchain
1.6.0	foss/2021a, foss/2022a

napari

napari is a fast, interactive, multi-dimensional image viewer for Python. It's designed for browsing, annotating, and analyzing large multi-dimensional images. It's built on top of Qt (for the GUI), vispy (for performant GPU-based rendering), and the scientific Python stack (numpy, scipy).

homepage: https://napari.org/

version	toolchain
0.4.15	foss/2021b
0.4.18	foss/2022a, foss/2023a

NASM

NASM: General-purpose x86 assembler

homepage: https://www.nasm.us/

version	toolchain
2.11.08	GCCcore/5.4.0, foss/2016a, foss/2016b, gimkl/2.11.5, intel/2016a
2.12.01	foss/2016a, intel/2016a
2.12.02	foss/2016a, foss/2016b, intel/2016b, intel/2017a, system
2.13.01	GCCcore/6.3.0, GCCcore/6.4.0
2.13.03	GCCcore/6.4.0, GCCcore/7.3.0
2.14.02	GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
2.15.05	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0
2.16.01	GCCcore/12.3.0, GCCcore/13.2.0

nauty

nauty and Traces are programs for computing automorphism groups of graphs and digraphs. They can also produce a canonical label.

homepage: https://pallini.di.uniroma1.it/

version	toolchain
2.6r12	GCC/8.2.0-2.31.1
2.7rc2	GCC/8.2.0-2.31.1
2.7rc5	GCC/8.3.0
2.8.6	GCC/11.3.0

nbclassic

NbClassic provides a backwards compatible Jupyter Notebook interface that you can install side-by-side with the latest versions: That way, you can fearlessly upgrade without worrying about your classic extensions and customizations breaking.

homepage: https://jupyter.org/

version	toolchain
1.0.0	GCCcore/12.3.0

NBO

The Natural Bond Orbital (NBO) program is a discovery tool for chemical insights from complex wavefunctions.

homepage: http://nbo.chem.wisc.edu/

version	toolchain
1.1	intel/2016a
7.0	intel/2017b
7.0.10	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/9.3.0, gfbf/2022a, gfbf/2022b

NCBI-Toolkit

The NCBI Toolkit is a collection of utilities developed for the production and distribution of GenBank, Entrez, BLAST, and related services by the National Center for Biotechnology Information.

homepage: http://ncbi.github.io/cxx-toolkit/

version	toolchain
18.0.0	intel/2017a

ncbi-vdb

The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.

homepage: https://github.com/ncbi/ncbi-vdb

version	toolchain
2.5.8-1	foss/2016b, intel/2016a
2.7.0	foss/2016b
2.8.2	foss/2017b, intel/2017a, intel/2017b
2.9.1-1	foss/2018a, intel/2018a
2.9.3	foss/2018b
2.10.4	gompi/2019b
2.10.7	gompi/2020a
2.10.9	gompi/2020b, gompi/2021a
2.11.2	gompi/2021b
3.0.0	gompi/2021b, gompi/2022a
3.0.2	gompi/2022a
3.0.5	gompi/2021a, gompi/2022b
3.0.10	gompi/2023a

NCCL

The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs.

homepage: https://developer.nvidia.com/nccl

version	versionsuffix	toolchain
2.1.4	-CUDA-9.0.176	system
2.2.13	-CUDA-9.2.148.1	system
2.3.7		fosscuda/2018b
2.4.2		gcccuda/2019a
2.4.8		gcccuda/2019b
2.8.3	-CUDA-11.0.2	GCCcore/9.3.0, system
2.8.3	-CUDA-11.1.1	GCCcore/10.2.0, system
2.9.9	-CUDA-11.3.1	system
2.10.3	-CUDA-11.3.1	GCCcore/10.3.0
2.10.3	-CUDA-11.4.1	GCCcore/11.2.0
2.10.3	-CUDA-11.5.2	GCCcore/11.2.0
2.11.4		gcccuda/2019b
2.12.12	-CUDA-11.7.0	GCCcore/11.3.0
2.16.2	-CUDA-12.0.0	GCCcore/12.2.0
2.18.3	-CUDA-12.1.1	GCCcore/12.3.0
2.20.5	-CUDA-12.4.0	GCCcore/13.2.0

NCCL-tests

Tests check both the performance and the correctness of NCCL operations.

homepage: https://github.com/NVIDIA/nccl-tests

version	versionsuffix	toolchain
2.0.0		gompic/2019b
2.13.6	-CUDA-11.7.0	gompi/2022a

ncdf4

ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files

homepage: https://cran.r-project.org/web/packages/ncdf4

version	versionsuffix	toolchain
1.16	-R-3.4.0	intel/2017a
1.16	-R-3.4.3	intel/2017b
1.16	-R-3.4.4	intel/2018a
1.16.1	-R-3.5.1	foss/2018b, intel/2018b
1.16.1	-R-3.6.0	foss/2019a
1.17		foss/2019b
1.17	-R-4.0.0	foss/2020a
1.17	-R-4.0.3	foss/2020b
1.17	-R-4.1.0	foss/2021a

ncdu

Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find space hogs on a remote server where you don't have an entire graphical setup available, but it is a useful tool even on regular desktop systems. Ncdu aims to be fast, simple and easy to use, and should be able to run in any minimal POSIX-like environment with ncurses installed.

homepage: https://dev.yorhel.nl/ncdu

version	toolchain
1.13	GCCcore/7.3.0
1.14	GCCcore/7.3.0
1.15.1	GCCcore/9.3.0
1.16	GCC/10.3.0, GCC/11.2.0
1.17	GCC/11.3.0
1.18	GCC/12.3.0

NCIPLOT

NCIPLOT is a program for revealing non covalent interactions based on the reduced density gradient.

homepage: https://www.lct.jussieu.fr/pagesperso/contrera/index-nci.html

version	toolchain
4.0-20190718	iccifort/2019.5.281
4.0-20200106	iccifort/2019.5.281
4.0-20200624	GCC/11.2.0

NCL

NCL is an interpreted language designed specifically for scientific data analysis and visualization.

homepage: https://www.ncl.ucar.edu

version	toolchain
6.4.0	intel/2017a, intel/2017b, intel/2018a
6.5.0	intel/2018a
6.6.2	foss/2018b, foss/2020a, foss/2020b, foss/2021a, intel/2018b, intel/2019b, intel/2020a

NCO

The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5.

homepage: https://github.com/nco/nco

version	toolchain
4.6.0	foss/2016a
4.6.6	intel/2017a
4.7.0	intel/2017b
4.7.1	intel/2017b
4.7.4	foss/2017b
4.7.6	intel/2018a
4.7.9	foss/2018b, intel/2018b
4.8.1	foss/2019a
4.9.3	foss/2019b
4.9.7	foss/2020a, foss/2020b
5.0.1	foss/2021a
5.0.3	foss/2021b, intel/2021b
5.0.6	intel/2019b
5.1.0	foss/2022a
5.1.3	foss/2021a, foss/2022a
5.1.9	intel/2022a

ncolor

Fast remapping of instance labels 1,2,3,...,M to a smaller set of repeating, disjoint labels, 1,2,...,N.

homepage: https://github.com/kevinjohncutler/ncolor

version	toolchain
1.2.1	foss/2022a

ncompress

Compress is a fast, simple LZW file compressor. Compress does not have the highest compression rate, but it is one of the fastest programs to compress data. Compress is the defacto standard in the UNIX community for compressing files.

homepage: http://ncompress.sourceforge.net/

version	toolchain
4.2.4.4	GCCcore/6.4.0

ncurses

The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.

homepage: https://www.gnu.org/software/ncurses/

version	toolchain
5.9	GCC/4.8.1, GCC/4.8.2, GCC/4.8.3, GCC/4.8.4, GCC/4.9.2, GNU/4.9.3-2.25, gimkl/2.11.5, system
6.0	GCC/4.9.3-2.25, GCC/5.4.0-2.26, GCCcore/4.9.3, GCCcore/5.3.0, GCCcore/5.4.0, GCCcore/6.2.0, GCCcore/6.3.0, GCCcore/6.4.0, GNU/4.9.3-2.25, foss/2016.04, foss/2016a, foss/2016b, gimkl/2017a, intel/2016.02-GCC-4.9, intel/2016a, intel/2016b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25, system
6.1	GCCcore/6.4.0, GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, system
6.2	FCC/4.5.0, GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/9.3.0, system
6.3	GCCcore/11.3.0, GCCcore/12.1.0, GCCcore/12.2.0, system
6.4	GCCcore/12.3.0, GCCcore/13.1.0, GCCcore/13.2.0, system

ncview

Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc.

homepage: http://meteora.ucsd.edu/~pierce/ncview_home_page.html

version	toolchain
2.1.7	foss/2017b, foss/2018b, foss/2019b, gompi/2019a, intel/2016b, intel/2017a, intel/2017b, intel/2018a, intel/2018b, intel/2019b, iomkl/2018b
2.1.8	gompi/2020a, gompi/2021a, gompi/2021b, gompi/2022a, gompi/2023a

nd2reader

nd2reader is a pure-Python package that reads images produced by NIS Elements 4.0+.

homepage: https://www.lighthacking.nl/nd2reader/

version	versionsuffix	toolchain
3.0.6	-Python-2.7.14	intel/2017b

ne

ne is a free (GPL'd) text editor based on the POSIX standard that runs (we hope) on almost any UN*X machine. ne is easy to use for the beginner, but powerful and fully configurable for the wizard, and most sparing in its resource usage.

homepage: http://ne.di.unimi.it/

version	toolchain
3.0.1	gimkl/2017a

NECI

Standalone NECI codebase designed for FCIQMC and other stochastic quantum chemistry methods.

homepage: https://github.com/ghb24/NECI_STABLE

version	toolchain
20220711	foss/2022a
20230620	foss/2022b

NEdit

NEdit is a multi-purpose text editor for the X Window System, which combines a standard, easy to use, graphical user interface with the thorough functionality and stability required by users who edit text eight hours a day.

homepage: http://www.nedit.org

version	versionsuffix	toolchain
5.5	-Linux-x86	system

Nek5000

a fast and scalable high-order solver for computational fluid dynamics

homepage: https://nek5000.mcs.anl.gov/

version	toolchain
17.0	intel/2018a

Nektar++

Nektar++ is a tensor product based finite element package designed to allow one to construct efficient classical low polynomial order h-type solvers (where h is the size of the finite element) as well as higher p-order piecewise polynomial order solvers.

homepage: https://www.nektar.info

version	toolchain
5.0.1	foss/2020b

neon

neon is an HTTP/1.1 and WebDAV client library, with a C interface.

homepage: https://github.com/notroj/neon

version	toolchain
0.31.2	GCCcore/8.3.0

neptune-client

Neptune is an experiment tracking hub that brings organization and collaboration to your data science team.

homepage: https://docs.neptune.ai

version	versionsuffix	toolchain
0.4.129	-Python-3.8.2	foss/2020a
0.10.5		foss/2020b
0.16.2		foss/2021a, foss/2022a

Net-core

.NET Core is a free and open-source managed computer software framework for the Windows, Linux, and macOS operating systems .NET Core fully supports C# and F# and partially supports Visual Basic

homepage: https://dotnet.microsoft.com/

version	toolchain
2.1.8	system
2.2.5	system
3.0.0	system

netCDF

NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

homepage: https://www.unidata.ucar.edu/software/netcdf/

version	versionsuffix	toolchain
4.3.3.1		foss/2016a, intel/2016.02-GCC-4.9, intel/2016a
4.4.0		foss/2016a, intel/2016a, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25
4.4.1		foss/2016a, foss/2016b, intel/2016a, intel/2016b
4.4.1.1		foss/2016b, foss/2017b, fosscuda/2017b, intel/2016b, intel/2017a, intel/2017b, intelcuda/2017b
4.4.1.1	-HDF5-1.10.1	foss/2017a, intel/2017a
4.4.1.1	-HDF5-1.8.18	intel/2017a
4.4.1.1	-HDF5-1.8.19	foss/2017a, foss/2017b, intel/2017b
4.5.0		foss/2017b, intel/2017b, intel/2018.00, intel/2018.01
4.6.0		foss/2018a, intel/2018a, iomkl/2018a
4.6.1		PGI/18.4-GCC-6.4.0-2.28, foss/2018b, fosscuda/2018b, intel/2018b, iomkl/2018b
4.6.2		gompi/2019a, iimpi/2019a
4.7.1		gompi/2019b, gompic/2019b, iimpi/2019b, iimpic/2019b
4.7.4		gompi/2020a, gompi/2020b, gompic/2020a, gompic/2020b, iimpi/2020a, iimpi/2020b, iimpic/2020b, iompi/2020a
4.8.0		gompi/2021a, iimpi/2021a
4.8.1		gompi/2021b, iimpi/2021b
4.9.0		gompi/2022a, gompi/2022b, iimpi/2022a, iimpi/2022b
4.9.2		gompi/2023a, gompi/2023b, iimpi/2023a, iimpi/2023b

netCDF-C++

NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

homepage: http://www.unidata.ucar.edu/software/netcdf/

version	toolchain
4.2	foss/2016a

netCDF-C++4

NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

homepage: https://www.unidata.ucar.edu/software/netcdf/

version	versionsuffix	toolchain
4.3.0		foss/2018b, gompi/2019a, iimpi/2019a, intel/2016a, intel/2016b, intel/2017a, intel/2018a, intel/2018b, iomkl/2018b
4.3.0	-HDF5-1.8.18	intel/2017a
4.3.0	-HDF5-1.8.19	intel/2017b
4.3.1		gompi/2019b, gompi/2020a, gompi/2020b, gompi/2021a, gompi/2021b, gompi/2022a, gompi/2023a, gompi/2023b, iimpi/2019b, iimpi/2020a, iimpi/2020b, iimpi/2021a, iimpi/2021b, iimpi/2022a, iimpi/2023b

netCDF-Fortran

NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

homepage: https://www.unidata.ucar.edu/software/netcdf/

version	versionsuffix	toolchain
4.4.1		foss/2016b, intel/2016b
4.4.2		intel/2016.02-GCC-4.9
4.4.3		foss/2016a, intel/2016a
4.4.4		PGI/18.4-GCC-6.4.0-2.28, foss/2016b, foss/2017b, foss/2018a, foss/2018b, fosscuda/2017b, fosscuda/2018b, intel/2016a, intel/2016b, intel/2017a, intel/2017b, intel/2018a, intel/2018b, intelcuda/2017b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25, iomkl/2018b
4.4.4	-HDF5-1.8.18	intel/2017a
4.4.4	-HDF5-1.8.19	foss/2017b, intel/2017b
4.4.5		gompi/2019a, iimpi/2019a
4.5.2		gompi/2019b, gompi/2020a, gompic/2019b, gompic/2020a, iimpi/2019b, iimpi/2020a, iimpic/2019b
4.5.3		gompi/2020b, gompi/2021a, gompi/2021b, gompic/2020b, iimpi/2020b, iimpi/2021a, iimpi/2021b
4.6.0		gompi/2022a, gompi/2022b, iimpi/2022a
4.6.1		gompi/2023a, gompi/2023b, iimpi/2023a, iimpi/2023b

netcdf4-python

Python/numpy interface to netCDF.

homepage: https://unidata.github.io/netcdf4-python/

version	versionsuffix	toolchain
1.2.9	-Python-2.7.13	intel/2017a
1.3.1	-Python-3.6.3	intel/2017b
1.3.1	-Python-3.6.3-HDF5-1.8.19	intel/2017b
1.4.0	-Python-3.6.2-HDF5-1.8.19	foss/2017b
1.4.0	-Python-3.6.4	intel/2018a
1.4.1	-Python-2.7.15	intel/2018b
1.4.1	-Python-3.6.6	foss/2018b, intel/2018b
1.4.2	-Python-3.6.4	foss/2018a
1.4.3	-Python-3.6.6	foss/2018b
1.5.2		intel/2019a
1.5.3	-Python-2.7.16	foss/2019b
1.5.3	-Python-3.7.4	foss/2019b, intel/2019b
1.5.3	-Python-3.8.2	foss/2020a, intel/2020a
1.5.5.1		foss/2020b, fosscuda/2020b, intel/2020b
1.5.7		foss/2021a, foss/2021b, intel/2021b
1.6.1		foss/2022a, intel/2022a
1.6.3		foss/2022b
1.6.4		foss/2023a
1.6.5		foss/2023b

netloc

The Portable Network Locality (netloc) software package provides network topology discovery tools, and an abstract representation of those networks topologies for a range of network types and configurations. It is provided as a companion to the Portable Hardware Locality (hwloc) package.

homepage: http://www.open-mpi.org/software/netloc

version	toolchain
0.5	GCC/4.8.3

NetLogo

NetLogo is a multi-agent programmable modeling environment. It is used by tens of thousands of students, teachers and researchers worldwide. It also powers HubNet participatory simulations. It is authored by Uri Wilensky and developed at the CCL.

homepage: https://ccl.northwestern.edu/netlogo/

version	versionsuffix	toolchain
5.3.1	-64	system
6.0.4	-64	system
6.2.0	-64	system
6.2.2	-64	system
6.3.0	-64	system

netMHC

NetMHC 4.0 predicts binding of peptides to a number of different HLA alleles using artificial neural networks (ANN).

homepage: https://www.cbs.dtu.dk/services/NetMHC/

version	toolchain
4.0a	system

netMHCII

NetMHCII 2.3 server predicts binding of peptides to HLA-DR, HLA-DQ, HLA-DP and mouse MHC class II alleles using articial neuron networks. Predictions can be obtained for 25 HLA-DR alleles, 20 HLA-DQ, 9 HLA-DP, and 7 mouse H2 class II alleles.

homepage: https://www.cbs.dtu.dk/services/NetMHCII/

version	toolchain
2.3	system

netMHCIIpan

NetMHCIIpan 3.2 server predicts binding of peptides to MHC class II molecules. The predictions are available for the three human MHC class II isotypes HLA-DR, HLA-DP and HLA-DQ, as well as mouse molecules (H-2).

homepage: https://www.cbs.dtu.dk/services/NetMHCIIpan/

version	toolchain
3.2	GCCcore/7.3.0, GCCcore/8.2.0

netMHCpan

The NetMHCpan software predicts binding of peptides to any known MHC molecule using artificial neural networks (ANNs).

homepage: https://www.cbs.dtu.dk/services/NetMHCpan/

version	toolchain
4.0a	system

NetPIPE

NetPIPE is a protocol independent communication performance benchmark that visually represents the network performance under a variety of conditions.

homepage: https://netpipe.cs.ksu.edu/

version	toolchain
5.1	intel/2018a
5.1.4	gompi/2020b, iimpi/2020b

NetPyNE

NetPyNE is an open-source Python package to facilitate the development, parallel simulation, analysis, and optimization of biological neuronal networks using the NEURON simulator.

homepage: http://www.netpyne.org

version	toolchain
1.0.2.1	foss/2021b

nettle

Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space.

homepage: https://www.lysator.liu.se/~nisse/nettle/

version	toolchain
3.1.1	GNU/4.9.3-2.25, foss/2016a, intel/2016a
3.2	GCCcore/5.4.0, foss/2016b, intel/2016b
3.3	GCCcore/6.3.0, GCCcore/6.4.0, intel/2017a
3.4	GCCcore/6.4.0, GCCcore/7.3.0, foss/2018a, foss/2018b, fosscuda/2018b, intel/2018a, intel/2018b, iomkl/2018a
3.4.1	GCCcore/8.2.0
3.5.1	GCCcore/8.3.0
3.6	GCCcore/10.2.0, GCCcore/9.3.0
3.7.2	GCCcore/10.3.0
3.7.3	GCCcore/11.2.0
3.8	GCCcore/11.3.0
3.8.1	GCCcore/12.2.0
3.9.1	GCCcore/12.3.0, GCCcore/13.2.0

networkTools

Dynamical Network Analysis is a method of characterizing allosteric signalling through biomolecular complexes.

homepage: http://faculty.scs.illinois.edu/schulten/software/networkTools/

version	toolchain
2	GCC/9.3.0

networkx

NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.

homepage: https://pypi.python.org/pypi/networkx

version	versionsuffix	toolchain
1.1	-Python-2.7.12	intel/2016b
1.11	-Python-2.7.11	foss/2016a
1.11	-Python-2.7.14	intel/2017b
1.11	-Python-3.5.1	foss/2016a
2.0	-Python-2.7.14	intel/2017b
2.1	-Python-2.7.14	intel/2017b
2.2	-Python-2.7.15	foss/2018b, foss/2019a, intel/2018b
2.2	-Python-2.7.16	foss/2019b
2.2	-Python-3.6.6	foss/2018b, intel/2018b
2.3	-Python-3.7.2	foss/2019a, intel/2019a
2.4	-Python-3.7.2	foss/2019a, intel/2019a
2.4	-Python-3.7.4	foss/2019b, fosscuda/2019b, intel/2019b, intelcuda/2019b
2.4	-Python-3.8.2	foss/2020a, fosscuda/2020a, intel/2020a
2.5		foss/2020b, fosscuda/2020b, intel/2020b, intelcuda/2020b
2.5.1		foss/2021a
2.6.2		foss/2020b
2.6.3		foss/2021a, foss/2021b, intel/2021b
2.8.4		foss/2022a, intel/2022a
2.8.8		gfbf/2022b
3.0		gfbf/2022b
3.1		gfbf/2023a
3.2.1		gfbf/2023b

NeuroKit

NeuroKit is a Python module that provides high-level integrative functions with good and flexible defaults, allowing users to focus on what’s important.

homepage: https://neurokit.readthedocs.io

version	versionsuffix	toolchain
0.2.7	-Python-3.6.4	intel/2018a

NEURON

Empirically-based simulations of neurons and networks of neurons.

homepage: https://www.neuron.yale.edu/neuron

version	versionsuffix	toolchain
7.4		intel/2016b
7.6.5	-Python-2.7.15	intel/2018b
7.8.2		foss/2021b

NewHybrids

This implements a Gibbs sampler to estimate the posterior probability that genetically sampled individuals fall into each of a set of user-defined hybrid categories.

homepage: https://ib.berkeley.edu/labs/slatkin/eriq/software/software.htm#NewHybs

version	toolchain
1.1_Beta3	GCC/10.2.0

Nextflow

Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data

homepage: https://www.nextflow.io/

version	toolchain
19.04.0	system
19.07.0	system
19.12.0	system
20.01.0	system
20.04.1	system
20.10.0	system
21.03.0	system
21.08.0	system
21.10.6	system
22.04.0	system
22.10.0	system
22.10.1	system
22.10.5	system
22.10.6	system
23.04.2	system
23.10.0	system

NextGenMap

NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime.

homepage: http://cibiv.github.io/NextGenMap/

version	toolchain
0.5.5	GCC/11.2.0, foss/2016b

NEXUS-CL

The NEXUS Class Library is a C++ library for parsing NEXUS files.

homepage: https://ncl.sourceforge.net/

version	toolchain
2.1.18	GCC/8.2.0-2.31.1

nf-core

Python package with helper tools for the nf-core community.

homepage: https://github.com/nf-core/tools

version	toolchain
2.10	foss/2022b
2.13.1	foss/2023b

nf-core-mag

The Nextflow pipeline 'mag' ported to EasyBuild/EESSI.

homepage: https://nf-co.re/mag

version	toolchain
20221110	foss/2021a

NFFT

The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more dimensions, of arbitrary input size, and of complex data.

homepage: https://www-user.tu-chemnitz.de/~potts/nfft/

version	toolchain
3.1.3	foss/2020b, fosscuda/2020b
3.5.1	foss/2018b, foss/2019a
3.5.2	foss/2020a, foss/2021a, foss/2021b
3.5.3	foss/2022a, foss/2023a

nghttp2

This is an implementation of the Hypertext Transfer Protocol version 2 in C. The framing layer of HTTP/2 is implemented as a reusable C library. On top of that, we have implemented an HTTP/2 client, server and proxy. We have also developed load test and benchmarking tools for HTTP/2. An HPACK encoder and decoder are available as a public API.

homepage: https://github.com/nghttp2/nghttp2

version	toolchain
1.48.0	GCC/11.2.0, GCC/11.3.0

nghttp3

nghttp3 is an implementation of RFC 9114 HTTP/3 mapping over QUIC and RFC 9204 QPACK in C. It does not depend on any particular QUIC transport implementation.

homepage: https://github.com/ngtcp2/nghttp3

version	toolchain
0.6.0	GCCcore/11.2.0, GCCcore/11.3.0

NGLess

NGLess is a domain-specific language for NGS (next-generation sequencing data) processing.

homepage: https://ngless.embl.de/

version	versionsuffix	toolchain
1.1.1	-static-Linux64	system

nglview

IPython widget to interactively view molecular structures and trajectories.

homepage: https://github.com/arose/nglview

version	versionsuffix	toolchain
2.7.0	-Python-3.7.2	intel/2019a
2.7.7	-Python-3.8.2	intel/2020a
3.0.3		foss/2021a, foss/2022a

NGS

NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing.

homepage: https://github.com/ncbi/ngs

version	versionsuffix	toolchain
1.2.3		foss/2016b, intel/2016a
1.2.5		foss/2016b
1.3.0		GCCcore/6.4.0, intel/2017a
2.9.1	-Java-1.8.0_162	foss/2018a, intel/2018a
2.9.3	-Java-1.8	foss/2018b
2.10.0	-Java-1.8	GCCcore/8.2.0
2.10.0	-Java-11	GCCcore/8.2.0
2.10.4	-Java-11	GCCcore/8.3.0
2.10.5		GCCcore/9.3.0
2.10.9		GCCcore/10.2.0, GCCcore/10.3.0
2.11.2		GCCcore/11.2.0

NGS-Python

NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing.

homepage: https://github.com/ncbi/ngs

version	versionsuffix	toolchain
1.2.3	-Python-2.7.11	intel/2016a
2.9.3	-Python-3.6.6	intel/2018b
2.10.4	-Python-2.7.16	gompi/2019b

NGSadmix

NGSadmix is a tool for finding admixture proportions from NGS data, based on genotype likelihoods.

homepage: http://www.popgen.dk/software/index.php/NgsAdmix

version	toolchain
32	GCC/7.3.0-2.30

NGSpeciesID

NGSpeciesID is a tool for clustering and consensus forming of targeted ONT reads.

homepage: https://github.com/ksahlin/NGSpeciesID

version	versionsuffix	toolchain
0.1.1.1	-Python-3.7.4	foss/2019b
0.1.2.1		foss/2021b
0.3.0		foss/2022b, foss/2023a

ngspice

Ngspice is a mixed-level/mixed-signal circuit simulator. Its code is based on three open source software packages: Spice3f5, Cider1b1 and Xspice.

homepage: https://ngspice.sourceforge.net

version	toolchain
31	foss/2019b
39	foss/2022a

ngtcp2

'Call it TCP/2. One More Time.' ngtcp2 project is an effort to implement RFC9000 QUIC protocol.

homepage: https://github.com/ngtcp2/ngtcp2

version	toolchain
0.7.0	GCC/11.2.0, GCC/11.3.0

NiBabel

NiBabel provides read/write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.

homepage: https://nipy.github.io/nibabel

version	versionsuffix	toolchain
2.0.2	-Python-2.7.11	intel/2016a
2.0.2	-Python-2.7.11-freetype-2.6.3	intel/2016a
2.1.0	-Python-2.7.13	intel/2017a
2.2.1	-Python-3.6.4	intel/2018a
2.3.0	-Python-2.7.14	foss/2017b, intel/2017b
2.3.0	-Python-3.6.3	foss/2017b, intel/2017b
2.3.0	-Python-3.6.6	foss/2018b
2.4.0		foss/2019a, intel/2019a
2.5.1	-Python-3.6.6	foss/2018b
3.1.0	-Python-3.7.4	foss/2019b, intel/2019b
3.2.0	-Python-3.8.2	foss/2020a
3.2.1		foss/2020b, foss/2021a, fosscuda/2020b
3.2.2		foss/2021b
4.0.2		foss/2022a
5.2.0		gfbf/2023a

nichenetr

R implementation of the NicheNet method, to predict active ligand-target links between interacting cells

homepage: https://github.com/saeyslab/nichenetr

version	versionsuffix	toolchain
1.1.1-20230223	-R-4.2.1	foss/2022a
2.0.4	-R-4.2.2	foss/2022b

NIfTI

Niftilib is a set of i/o libraries for reading and writing files in the nifti-1 data format.

homepage: http://niftilib.sourceforge.net/

version	toolchain
2.0.0	GCCcore/6.4.0

nifti2dicom

Nifti2Dicom is a conversion tool that converts 3D NIfTI files (and other formats supported by ITK, including Analyze, MetaImage Nrrd and VTK) to DICOM. Unlike other conversion tools, it can import a DICOM file that is used to import the patient and study DICOM tags, and allows you to edit the accession number and other DICOM tags, in order to create a valid DICOM that can be imported in a PACS.

homepage: https://github.com/biolab-unige/nifti2dicom

version	toolchain
0.4.11	foss/2019b

Nilearn

Nilearn is a Python module for fast and easy statistical learning on NeuroImaging data.

homepage: https://nilearn.github.io/

version	versionsuffix	toolchain
0.5.2		foss/2019a, intel/2019a
0.5.2	-Python-2.7.14	foss/2017b, intel/2017b
0.5.2	-Python-3.6.3	foss/2017b, intel/2017b
0.7.0	-Python-3.8.2	foss/2020a
0.7.1		foss/2020b
0.10.3		gfbf/2023a

Nim

Nim is a systems and applications programming language.

homepage: https://nim-lang.org/

version	toolchain
0.18.0	GCCcore/6.4.0
0.19.2	GCCcore/7.3.0
1.0.0	GCCcore/8.3.0
1.4.6	GCCcore/10.2.0
1.4.8	GCCcore/10.3.0
1.6.6	GCCcore/11.2.0

NIMBLE

NIMBLE is a system for building and sharing analysis methods for statistical models, especially for hierarchical models and computationally-intensive methods.

homepage: https://r-nimble.org

version	versionsuffix	toolchain
0.7.0	-R-3.5.1	foss/2018b

Ninja

Ninja is a small build system with a focus on speed.

homepage: https://ninja-build.org/

version	toolchain
1.8.2	foss/2018a, foss/2018b, fosscuda/2018b, intel/2017b, intel/2018a
1.9.0	GCCcore/8.2.0, GCCcore/8.3.0, foss/2018b
1.10.0	GCCcore/9.3.0
1.10.1	GCCcore/10.2.0
1.10.2	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0
1.11.1	GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

Nipype

Nipype is a Python project that provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow.

homepage: https://nipype.readthedocs.io

version	versionsuffix	toolchain
1.0.2	-Python-3.6.4	intel/2018a
1.1.3	-Python-3.6.6	foss/2018b
1.4.2	-Python-3.7.4	intel/2019b
1.6.0		foss/2020b
1.8.5		foss/2021a

NLMpy

NLMpy is a Python package for the creation of neutral landscape models that are widely used in the modelling of ecological patterns and processes across landscapes.

homepage: https://pypi.org/project/nlmpy

version	versionsuffix	toolchain
0.1.5	-Python-3.7.4	intel/2019b

nlohmann_json

JSON for Modern C++

homepage: https://github.com/nlohmann/json

version	toolchain
3.10.0	GCCcore/10.3.0
3.10.4	GCCcore/11.2.0
3.10.5	GCCcore/11.3.0
3.11.2	GCCcore/12.2.0, GCCcore/12.3.0
3.11.3	GCCcore/13.2.0

NLopt

NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms.

homepage: http://ab-initio.mit.edu/wiki/index.php/NLopt

version	toolchain
2.4.2	GCC/5.4.0-2.26, GCCcore/7.3.0, foss/2016a, foss/2016b, foss/2017b, foss/2018a, iccifort/2016.3.210-GCC-5.4.0-2.26, intel/2016a, intel/2016b, intel/2017a, intel/2017b, intel/2018a, iomkl/2018a
2.6.1	GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
2.6.2	GCCcore/10.2.0
2.7.0	GCCcore/10.3.0, GCCcore/11.2.0
2.7.1	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0

NLTK

NLTK is a leading platform for building Python programs to work with human language data.

homepage: https://www.nltk.org/

version	versionsuffix	toolchain
3.2.2	-Python-2.7.13	intel/2017a
3.2.4	-Python-2.7.13	intel/2017a
3.5	-Python-3.7.4	foss/2019b
3.5	-Python-3.8.2	foss/2020a, fosscuda/2020a
3.6.7		foss/2021a
3.7		foss/2021b
3.8.1		foss/2022b, foss/2023a, foss/2023b

nnU-Net

nnU-Net is the first segmentation method that is designed to deal with the dataset diversity found in the domain It condenses and automates the keys decisions for designing a successful segmentation pipeline for any given dataset.

homepage: https://github.com/MIC-DKFZ/nnUNet

version	toolchain
1.7.0	foss/2020b, fosscuda/2020b

Node-RED

Node-RED is a programming tool for wiring together hardware devices, APIs and online services in new and interesting ways.

homepage: http://nodered.org

version	toolchain
0.16.2	foss/2017a

nodejs

Node.js is a platform built on Chrome's JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices.

homepage: http://nodejs.org

version	toolchain
4.4.7	foss/2016a
6.10.3	foss/2017a
8.9.4	foss/2017a
10.15.1	foss/2018b
10.15.3	GCCcore/8.2.0
12.16.1	GCCcore/7.3.0, GCCcore/8.3.0, GCCcore/9.3.0
12.19.0	GCCcore/10.2.0
14.17.0	GCCcore/10.3.0
14.17.2	GCCcore/10.3.0
14.17.6	GCCcore/11.2.0
16.15.1	GCCcore/11.3.0
18.12.1	GCCcore/12.2.0
18.17.1	GCCcore/12.3.0
20.9.0	GCCcore/13.2.0

noise

Native-code and shader implementations of Perlin noise for Python

homepage: https://github.com/caseman/noise

version	toolchain
1.2.2	gfbf/2023a

Normaliz

Normaliz is a open source tool for computations in affine monoids, vector configurations, rational polyhedra and rational cones. Normaliz now computes rational and algebraic polyhedra, i.e., polyhedra defined over real algebraic extensions of QQ.

homepage: https://www.normaliz.uni-osnabrueck.de/

version	toolchain
3.6.3	intel/2018b
3.7.4	gompi/2019a
3.8.4	GCC/8.3.0
3.10.1	gfbf/2022a

nose-parameterized

Parameterized testing with any Python test framework.

homepage:

version	versionsuffix	toolchain
0.5.0	-Python-2.7.11	foss/2016a
0.5.0	-Python-3.5.1	foss/2016a
0.5.0	-Python-3.5.2	intel/2016b
0.6.0	-Python-3.6.1	intel/2017a

nose3

Nose extends unittest to make testing easier.

homepage: https://nose.readthedocs.io/

version	toolchain
1.3.8	GCCcore/11.3.0, GCCcore/12.3.0

novaSTA

C++ version of subtomogram averaging (SA) scripts from TOM/AV3 package https://doi.org/10.1073/pnas.0409178102. Both CPU and GPU parallelization is supported although the latter performs significantly worse in terms of processing time (the code is not well optimized) and is thus not recommended for larger datasets.

homepage: https://github.com/turonova/novaSTA

version	versionsuffix	toolchain
1.1	-CUDA-11.7.0	foss/2022a

novoalign

NovoCraft is a software bundle. NovoAlign: Market’s leading aligner with fully packed features designed for mapping of short reads onto a reference genome from Illumina, Ion Torrent, 454, and Color Spance NGS platforms. NovoAlignCS: Leading aligner packed with features designed to fully support reads from ABI SOLiD Color Space. NovoSort: Custom designed multi-threaded sort/merge tools for BAM files. NovoMethyl: It can analyse a set of alignments to identify methylated cytosine’s. WARNING! You can only use the sofware without a license (with some features disabled) if you are a non-profit organisation and use is for your own research or for use by students as part of their course. A license is required for use where these programs are part of a service where a third party is billed.

homepage: http://www.novocraft.com/

version	versionsuffix	toolchain
3.09.00		system
3.09.01	-R-3.5.1	foss/2018b

NOVOPlasty

NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.

homepage: https://github.com/ndierckx/NOVOPlasty

version	toolchain
3.7	GCCcore/8.3.0

npstat

npstat implements some population genetics tests and estimators that can be applied to pooled sequences from Next Generation Sequencing experiments.

homepage: https://code.google.com/archive/p/npstat/

version	toolchain
0.99	foss/2016a, intel/2016a

NRGLjubljana

NRG Ljubljana is an efficient implementation of the numerical renormalization group (NRG) technique for solving quantum impurity problems that arise as simplified models of magnetic impurities and as effective models in the dynamical mean field theory (DMFT) approach to bulk correlated materials.

homepage: http://nrgljubljana.ijs.si/

version	toolchain
2.4.3.23	foss/2016b

Nsight-Compute

NVIDIA® Nsight™ Compute is an interactive kernel profiler for CUDA applications. It provides detailed performance metrics and API debugging via a user interface and a command line tool. In addition, its baseline feature allows users to compare results within the tool. Nsight Compute provides a customizable and data-driven user interface and fast metric collection, which can be extended with rules-based analysis scripts for post-processing results. The rules-based guided analysis helps isolate and fix memory throughput, compute, and occupancy inefficiencies in the target application.

homepage: https://developer.nvidia.com/nsight-compute

version	toolchain
2020.3.0	system
2021.2.0	system

Nsight-Systems

NVIDIA® Nsight™ Systems is a system-wide performance analysis tool designed to visualize an application’s algorithm, help you select the largest opportunities to optimize, and tune to scale efficiently across any quantity of CPUs and GPUs in your computer; from laptops to DGX servers.

homepage: https://developer.nvidia.com/nsight-compute

version	toolchain
2020.5.1	system

NSPR

Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions.

homepage: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR

version	toolchain
4.20	GCCcore/6.4.0, GCCcore/7.3.0
4.21	GCCcore/8.2.0, GCCcore/8.3.0
4.25	GCCcore/9.3.0
4.29	GCCcore/10.2.0
4.30	GCCcore/10.3.0
4.32	GCCcore/11.2.0
4.34	GCCcore/11.3.0
4.35	GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

NSS

Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications.

homepage: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS

version	toolchain
3.39	GCCcore/6.4.0, GCCcore/7.3.0
3.42.1	GCCcore/8.2.0
3.45	GCCcore/8.3.0
3.51	GCCcore/9.3.0
3.57	GCCcore/10.2.0
3.65	GCCcore/10.3.0
3.69	GCCcore/11.2.0
3.79	GCCcore/11.3.0
3.85	GCCcore/12.2.0
3.89.1	GCCcore/12.3.0
3.94	GCCcore/13.2.0

nsync

nsync is a C library that exports various synchronization primitives, such as mutexes

homepage: https://github.com/google/nsync

version	toolchain
1.24.0	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/8.3.0, GCCcore/9.3.0
1.25.0	GCCcore/11.3.0
1.26.0	GCCcore/12.2.0, GCCcore/12.3.0

ntCard

ntCard is a streaming algorithm for estimating the frequencies of k-mers in genomics datasets.

homepage: https://www.bcgsc.ca/resources/software/ntcard

version	toolchain
1.2.1	GCC/11.2.0, GCC/8.3.0
1.2.2	GCC/12.3.0

ntEdit

ntEdit is a fast and scalable genomics application for polishing genome assembly drafts.

homepage: https://github.com/bcgsc/ntEdit

version	toolchain
1.3.1	iccifort/2018.3.222-GCC-7.3.0-2.30

ntHits

ntHits is a method for identifying repeats in high-throughput DNA sequencing data.

homepage: https://github.com/bcgsc/ntHits

version	toolchain
0.0.1	iccifort/2018.3.222-GCC-7.3.0-2.30

NTL

NTL is a high-performance, portable C++ library providing data structures and algorithms for manipulating signed, arbitrary length integers, and for vectors, matrices, and polynomials over the integers and over finite fields.

homepage: https://shoup.net/ntl/

version	toolchain
11.3.4	GCC/8.2.0-2.31.1
11.5.1	GCC/11.2.0, GCC/11.3.0, GCC/12.2.0, GCC/13.2.0

NTPoly

is a massively parallel library for computing the functions of sparse, symmetric matrices based on polynomial expansions. For sufficiently sparse matrices, most of the matrix functions in NTPoly can be computed in linear time.

homepage: https://github.com/william-dawson/NTPoly

version	toolchain
2.5.1	foss/2020b, intel/2020b
2.7.0	foss/2021a, intel/2021a
2.7.1	intel/2020b

num2words

Modules to convert numbers to words. 42 --> forty-two

homepage: https://github.com/savoirfairelinux/num2words

version	toolchain
0.5.10	GCCcore/10.3.0

numactl

The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.

homepage: http://oss.sgi.com/projects/libnuma/

version	toolchain
2.0.9	GCC/4.8.3
2.0.10	GCC/4.8.4, GCC/4.9.2, GNU/4.9.2-2.25, GNU/4.9.3-2.25
2.0.11	GCC/4.9.3, GCC/4.9.3-2.25, GCC/5.2.0, GCC/5.3.0-2.26, GCC/5.4.0-2.26, GCC/6.1.0-2.27, GCC/6.2.0-2.27, GCC/6.3.0-2.27, GCCcore/4.9.2, GCCcore/4.9.3, GCCcore/5.3.0, GCCcore/5.4.0, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.2.0, GCCcore/7.3.0, foss/2016a, iccifort/2016.3.210-GCC-4.9.3-2.25, iccifort/2016.3.210-GCC-5.4.0-2.26, intel/2016a, intel/2016b
2.0.12	GCCcore/8.2.0, GCCcore/8.3.0
2.0.13	GCCcore/10.2.0, GCCcore/9.2.0, GCCcore/9.3.0
2.0.14	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0
2.0.16	GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

numba

Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.

homepage: https://numba.pydata.org/

version	versionsuffix	toolchain
0.24.0	-Python-2.7.11	intel/2016a
0.24.0	-Python-3.5.1	intel/2016a
0.26.0	-Python-2.7.11	intel/2016a
0.32.0	-Python-2.7.13	intel/2017a
0.37.0	-Python-2.7.14	foss/2018a, intel/2017b
0.37.0	-Python-3.6.4	foss/2018a, intel/2018a
0.39.0	-Python-3.6.6	foss/2018b
0.43.1		intel/2019a
0.46.0		foss/2019a
0.47.0	-Python-3.7.4	foss/2019b, fosscuda/2019b
0.50.0	-Python-3.8.2	foss/2020a, intel/2020a
0.50.1	-Python-3.8.2	foss/2020a
0.52.0		foss/2020b, fosscuda/2020b, intel/2020b
0.52.0	-Python-3.8.2	foss/2020a
0.53.1		foss/2020b, foss/2021a, fosscuda/2020b
0.54.1		foss/2021b, intel/2021b
0.54.1	-CUDA-11.4.1	foss/2021b
0.56.4		foss/2022a
0.56.4	-CUDA-11.7.0	foss/2022a
0.58.1		foss/2022b, foss/2023a

numdiff

Numdiff (which I will also write numdiff) is a little program that can be used to compare putatively similar files line by line and field by field, ignoring small numeric differences or/and different numeric formats. Equivalently, Numdiff is a program with the capability to appropriately compare files containing numerical fields (and not only).

homepage: https://www.nongnu.org/numdiff/

version	toolchain
5.9.0	GCCcore/10.2.0, GCCcore/12.2.0

numexpr

The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a compiler at runtime.

homepage: https://numexpr.readthedocs.io/en/latest/

version	versionsuffix	toolchain
2.5.2	-Python-2.7.11	intel/2016a
2.6.1	-Python-2.7.12	foss/2016b, intel/2016b
2.6.1	-Python-3.5.2	intel/2016b
2.6.4	-Python-2.7.13	foss/2017a
2.6.4	-Python-2.7.14	intel/2018a
2.6.4	-Python-3.5.1	foss/2016a
2.6.4	-Python-3.6.1	intel/2017a
2.6.4	-Python-3.6.3	intel/2017b
2.6.4	-Python-3.6.4	foss/2018a, intel/2018a
2.6.5	-Python-2.7.15	foss/2018b, intel/2018b
2.6.5	-Python-3.6.6	foss/2018b, fosscuda/2018b, intel/2018b
2.7.0		intel/2019a
2.7.1	-Python-2.7.16	intel/2019b
2.7.1	-Python-3.7.4	foss/2019b, fosscuda/2019b
2.7.1	-Python-3.8.2	foss/2020a, intel/2020a
2.8.1		foss/2021a, intel/2021a
2.8.4		foss/2022a

numpy

NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.

homepage: http://www.numpy.org

version	versionsuffix	toolchain
1.8.2	-Python-2.7.11	foss/2016a, intel/2016a
1.9.2	-Python-2.7.12	intel/2016b
1.10.4	-Python-2.7.11	intel/2016a
1.11.0	-Python-2.7.11	intel/2016a
1.12.1	-Python-3.5.2	intel/2016b
1.13.0	-Python-2.7.13	intel/2017a
1.13.1	-Python-3.6.1	intel/2017a

NVHPC

C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)

homepage: https://developer.nvidia.com/hpc-sdk/

version	versionsuffix	toolchain
20.7		system
20.9		system
20.11		system
21.2		system
21.3		system
21.5		system
21.7		system
21.9		system
21.11		system
22.7	-CUDA-11.7.0	system
22.9	-CUDA-11.7.0	system
22.11	-CUDA-11.7.0	system
23.1	-CUDA-12.0.0	system
23.7	-CUDA-12.1.1	system
23.7	-CUDA-12.2.0	system
24.1	-CUDA-12.3.0	system

nvofbf

NVHPC based toolchain, including OpenMPI for MPI support, OpenBLAS (via FlexiBLAS for BLAS and LAPACK support), FFTW and ScaLAPACK.

homepage: <(none)>

version	toolchain
2022.07	system

nvompi

NVHPC based compiler toolchain, including OpenMPI for MPI support.

homepage: <(none)>

version	toolchain
2022.07	system

NVSHMEM

NVSHMEM is a parallel programming interface based on OpenSHMEM that provides efficient and scalable communication for NVIDIA GPU clusters. NVSHMEM creates a global address space for data that spans the memory of multiple GPUs and can be accessed with fine-grained GPU-initiated operations, CPU-initiated operations, and operations on CUDA streams.

homepage: https://developer.nvidia.com/nvshmem

version	versionsuffix	toolchain
2.4.1	-CUDA-11.4.1	gompi/2021b
2.5.0	-CUDA-11.7.0	gompi/2022a
2.7.0	-CUDA-11.7.0	gompi/2022a
2.8.0	-CUDA-11.7.0	gompi/2022a

nvtop

htop-like GPU usage monitor

homepage: https://github.com/Syllo/nvtop

version	toolchain
1.0.0	fosscuda/2018b
1.1.0	fosscuda/2019b
1.2.1	GCCcore/10.2.0, GCCcore/10.3.0
1.2.2	GCCcore/10.2.0, GCCcore/10.3.0
2.0.2	GCCcore/11.3.0
3.0.1	GCCcore/12.2.0

NWChem

NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity.

homepage: https://nwchemgit.github.io/

version	versionsuffix	toolchain
6.6.revision27746	-2015-10-20-Python-2.7.12	iomkl/2017a
6.6.revision27746	-2015-10-20-patches-20170814-Python-2.7.13	intel/2017a
6.8.revision47	-2017-12-14-Python-2.7.14	intel/2017b, intel/2018a
7.0.0	-Python-3.7.4	intel/2019b
7.0.2		intel/2021a, intel/2022a
7.0.2	-Python-3.7.4	intel/2019b
7.2.2		intel/2023a

NxTrim

NxTrim is a software to remove Nextera Mate Pair junction adapters and categorise reads according to the orientation implied by the adapter location.

homepage: https://github.com/sequencing/NxTrim

version	toolchain
0.4.3	foss/2018a

O

Oases - OBITools - OBITools3 - OCaml - occt - oceanspy - OCNet - Octave - Octopus-vcf - OGDF - olaFlow - olego - OMA - OmegaFold - OMERO.insight - OMERO.py - Omnipose - onedrive - ONNX - ONNX-Runtime - ont-fast5-api - ont-guppy - ont-remora - OOMPA - OPARI2 - Open-Data-Cube-Core - OpenAI-Gym - OpenBabel - OpenBLAS - openCARP - OpenCensus-python - OpenCoarrays - OpenColorIO - OpenCV - OpenEXR - OpenFace - OpenFAST - OpenFOAM - OpenFOAM-Extend - OpenFold - OpenForceField - OpenImageIO - OpenJPEG - OpenKIM-API - openkim-models - OpenMEEG - OpenMM - OpenMM-PLUMED - OpenMMTools - OpenMolcas - OpenMPI - OpenMS - OpenNLP - OpenPGM - OpenPIV - openpyxl - OpenRefine - OpenSceneGraph - OpenSees - OpenSlide - OpenSlide-Java - openslide-python - OpenSSL - OpenStackClient - OPERA - OPERA-MS - OptaDOS - Optax - OptiType - OptiX - Optuna - OR-Tools - ORCA - ORFfinder - OrfM - OrthoFinder - OrthoMCL - Osi - OSPRay - OSU-Micro-Benchmarks - OTF2 - OVITO - ownCloud - oxDNA - oxford_asl

Oases

Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.

homepage: http://www.ebi.ac.uk/~zerbino/oases/

version	versionsuffix	toolchain
0.2.08		foss/2016b
0.2.08	-kmer_101	intel/2017b
20180312		GCC/12.3.0

OBITools

The OBITools programs aims to help you to manipulate various data and sequence files in a convenient way using the Unix command line interface. They follow the standard Unix interface for command line program, allowing to chain a set of commands using the pipe mecanism.

homepage: http://www.grenoble.prabi.fr/trac/OBITools

version	versionsuffix	toolchain
1.2.9	-Python-2.7.11	foss/2016a
1.2.13	-Python-2.7.15	foss/2019a

OBITools3

A package for the management of analyses and data in DNA metabarcoding.

homepage: https://metabarcoding.org/obitools3

version	toolchain
3.0.1b8	GCCcore/10.2.0
3.0.1b26	GCCcore/12.3.0

OCaml

OCaml is a general purpose industrial-strength programming language with an emphasis on expressiveness and safety. Developed for more than 20 years at Inria it benefits from one of the most advanced type systems and supports functional, imperative and object-oriented styles of programming.

homepage: http://ocaml.org/

version	toolchain
4.02.3	foss/2016a
4.07.1	foss/2018b
4.14.0	GCC/11.3.0

occt

Open CASCADE Technology (OCCT) is an object-oriented C++ class library designed for rapid production of sophisticated domain-specific CAD/CAM/CAE applications.

homepage: https://www.opencascade.com/

version	toolchain
7.3.0p4	foss/2019b
7.5.0p1	foss/2021a, foss/2022a
7.8.0	GCCcore/12.3.0

oceanspy

OceanSpy - A Python package to facilitate ocean model data analysis and visualization.

homepage: https://github.com/hainegroup/oceanspy

version	toolchain
0.2.0	foss/2022a

OCNet

Generate and analyze Optimal Channel Networks (OCNs): oriented spanning trees reproducing all scaling features characteristic of real, natural river networks. As such, they can be used in a variety of numerical experiments in the fields of hydrology, ecology and epidemiology.

homepage: https://cran.r-project.org/web/packages/OCNet

version	versionsuffix	toolchain
0.2.0	-R-3.6.0	foss/2019a

Octave

GNU Octave is a high-level interpreted language, primarily intended for numerical computations.

homepage: https://www.gnu.org/software/octave/

version	versionsuffix	toolchain
4.0.0		foss/2016a
4.0.3		intel/2016b
4.2.1		foss/2018a, intel/2016b, intel/2017a
4.2.1	-mt	intel/2017a
4.2.2		foss/2018a
4.4.1		foss/2018b
5.1.0		foss/2019a, foss/2019b
6.2.0		foss/2020b
7.1.0		foss/2021b

Octopus-vcf

Octopus is a mapping-based variant caller that implements several calling models within a unified haplotype-aware framework. Octopus takes inspiration from particle filtering by constructing a tree of haplotypes and dynamically pruning and extending the tree based on haplotype posterior probabilities in a sequential manner. This allows octopus to implicitly consider all possible haplotypes at a given loci in reasonable time.

homepage: https://github.com/luntergroup/octopus

version	toolchain
0.7.1	foss/2020b
0.7.2	foss/2020b

OGDF

OGDF is a self-contained C++ library for graph algorithms, in particular for (but not restricted to) automatic graph drawing. It offers sophisticated algorithms and data structures to use within your own applications or scientific projects.

homepage: https://ogdf.uos.de/

version	toolchain
dogwood-202202	GCC/11.2.0

olaFlow

olaFlow CFD Suite is a free and open source project committed to bringing the latest advances for the simulation of wave dynamics to the OpenFOAM® and FOAM-extend communities.

homepage: https://olaflow.github.io/

version	toolchain
20210820	foss/2021b

olego

OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a seed-and-extend scheme, and does not rely on a separate external mapper.

homepage: https://github.com/chaolinzhanglab/olego

version	toolchain
1.1.9	GCC/11.2.0

OMA

The OMA ('Orthologous MAtrix') project is a method and database for the inference of orthologs among complete genomes

homepage: https://omabrowser.org/standalone/

version	toolchain
2.1.1	system

OmegaFold

OmegaFold: High-resolution de novo Structure Prediction from Primary Sequence

homepage: https://github.com/HeliXonProtein/OmegaFold

version	versionsuffix	toolchain
1.1.0	-CUDA-11.7.0	foss/2022a

OMERO.insight

The OMERO.insight Project is a sub-project of the Open Microscopy Environment Project, OME that focuses on delivering a client for the visualization and manipulation of both image data and metadata maintained at an OMERO server site.

homepage: https://github.com/ome/omero-insight

version	versionsuffix	toolchain
5.8.3	-Java-11	system

OMERO.py

OMERO.py provides Python bindings to the OMERO.blitz server as well as a pluggable command-line interface.

homepage: https://github.com/ome/omero-py

version	toolchain
5.17.0	gfbf/2023a

Omnipose

Omnipose is a general image segmentation tool that builds on Cellpose in a number of ways described in our paper. It works for both 2D and 3D images and on any imaging modality or cell shape, so long as you train it on representative images.

homepage: https://omnipose.readthedocs.io

version	versionsuffix	toolchain
0.4.4		foss/2022a
0.4.4	-CUDA-11.7.0	foss/2022a

onedrive

A free Microsoft OneDrive Client which supports OneDrive Personal, OneDrive for Business, OneDrive for Office365 and SharePoint.

homepage: https://abraunegg.github.io/

version	toolchain
2.4.11	GCCcore/10.2.0
2.4.21	GCCcore/11.3.0
2.4.25	GCCcore/12.3.0

ONNX

Open Neural Network Exchange (ONNX) is an open ecosystem that empowers AI developers to choose the right tools as their project evolves. ONNX provides an open source format for AI models, both deep learning and traditional ML. It defines an extensible computation graph model, as well as definitions of built-in operators and standard data types. Currently we focus on the capabilities needed for inferencing (scoring).

homepage: https://onnx.ai

version	toolchain
1.11.0	foss/2021a
1.15.0	foss/2022b

ONNX-Runtime

ONNX Runtime inference can enable faster customer experiences and lower costs, supporting models from deep learning frameworks such as PyTorch and TensorFlow/Keras as well as classical machine learning libraries such as scikit-learn, LightGBM, XGBoost, etc. ONNX Runtime is compatible with different hardware, drivers, and operating systems, and provides optimal performance by leveraging hardware accelerators where applicable alongside graph optimizations and transforms.

homepage: https://onnxruntime.ai

version	versionsuffix	toolchain
1.10.0		foss/2021a
1.10.0	-CUDA-11.3.1	foss/2021a
1.16.3		foss/2022b

ont-fast5-api

ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format.

homepage: https://github.com/nanoporetech/ont_fast5_api

version	versionsuffix	toolchain
3.3.0		foss/2020b, fosscuda/2020b
3.3.0	-Python-3.7.4	foss/2019b
4.0.0		foss/2021a
4.0.2		foss/2021a, foss/2021b
4.1.1		foss/2022a, foss/2022b
4.1.2		foss/2023a

ont-guppy

Guppy is a bioinformatics toolkit that enables real-time basecalling and several post-processing features that works on Oxford Nanopore Technologies™ sequencing platforms. For Research Use Only

homepage: https://community.nanoporetech.com/protocols/Guppy-protocol

version	versionsuffix	toolchain
6.4.6		system
6.4.6	-CUDA-11.7.0	system
6.4.8	-CUDA-11.7.0	system

ont-remora

Methylation/modified base calling separated from basecalling. Remora primarily provides an API to call modified bases for basecaller programs such as Bonito. Remora also provides the tools to prepare datasets, train modified base models and run simple inference.

homepage: https://github.com/nanoporetech/remora

version	versionsuffix	toolchain
0.1.2		foss/2021a
0.1.2	-CUDA-11.3.1	foss/2021a
1.0.0		foss/2021a
1.0.0	-CUDA-11.3.1	foss/2021a

OOMPA

OOMPA is a suite of R packages for the analysis of gene expression (RNA), proteomics profiling, and other high throughput molecular biology data.

homepage: https://r-forge.r-project.org/projects/oompa

version	versionsuffix	toolchain
3.1.2	-R-3.3.1	intel/2016b

OPARI2

OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface.

homepage: https://www.score-p.org

version	toolchain
2.0	foss/2016a
2.0.5	GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
2.0.6	GCCcore/10.2.0, GCCcore/10.3.0
2.0.7	GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0
2.0.8	GCCcore/13.2.0

Open-Data-Cube-Core

The Open Data Cube Core provides an integrated gridded data analysis environment for decades of analysis ready earth observation satellite and related data from multiple satellite and other acquisition systems.

homepage: https://github.com/opendatacube/datacube-core

version	versionsuffix	toolchain
1.8.3	-Python-3.8.2	foss/2020a

OpenAI-Gym

A toolkit for developing and comparing reinforcement learning algorithms.

homepage: https://gym.openai.com

version	versionsuffix	toolchain
0.17.1	-Python-3.7.4	foss/2019b
0.21.0		foss/2021b
0.26.2		foss/2022a

OpenBabel

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.

homepage: https://openbabel.org

version	versionsuffix	toolchain
2.3.2	-Python-2.7.11	foss/2016a
2.4.1	-Python-2.7.14	intel/2017b
2.4.1	-Python-2.7.15	intel/2018b
2.4.1	-Python-3.6.6	intel/2018b
2.4.1	-Python-3.7.2	intel/2019a
3.0.0	-Python-3.7.4	gompi/2019b
3.1.1		gompi/2021a, gompi/2022a, gompi/2023a
3.1.1	-Python-3.7.4	gompi/2019b
3.1.1	-Python-3.8.2	iimpi/2020a

OpenBLAS

OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.

homepage: https://xianyi.github.com/OpenBLAS/

version	versionsuffix	toolchain
0.2.9	-LAPACK-3.5.0	GCC/4.8.3
0.2.12	-LAPACK-3.5.0	GCC/4.9.2
0.2.13	-LAPACK-3.5.0	GCC/4.8.4, GCC/4.9.2
0.2.14	-LAPACK-3.5.0	GNU/4.9.2-2.25, GNU/4.9.3-2.25
0.2.15	-LAPACK-3.6.0	GCC/4.9.3-2.25
0.2.18	-LAPACK-3.6.0	GCC/4.9.4-2.25, GCC/5.3.0-2.26, GCC/5.4.0-2.26
0.2.18	-LAPACK-3.6.1	GCC/5.4.0-2.26, gompi/2016.07
0.2.19	-LAPACK-3.6.1	gompi/2016.09
0.2.19	-LAPACK-3.7.0	GCC/5.4.0-2.26, GCC/6.3.0-2.27
0.2.20		GCC/5.4.0-2.26, GCC/6.4.0-2.28, GCC/7.2.0-2.29
0.3.0		GCC/6.4.0-2.28, GCC/7.3.0-2.30
0.3.1		GCC/7.3.0-2.30
0.3.3		GCC/8.2.0-2.31.1
0.3.4		GCC/8.2.0-2.31.1
0.3.5		GCC/8.2.0-2.31.1
0.3.6		GCC/8.3.0-2.32
0.3.7		GCC/8.3.0
0.3.8		GCC/9.2.0
0.3.9		GCC/9.3.0
0.3.12		GCC/10.2.0
0.3.15		GCC/10.3.0
0.3.17		GCC/10.3.0, GCC/11.2.0
0.3.18		GCC/11.2.0
0.3.20		GCC/11.2.0, GCC/11.3.0, NVHPC/22.7-CUDA-11.7.0
0.3.21		GCC/12.2.0
0.3.23		GCC/12.3.0
0.3.24		GCC/13.2.0

openCARP

openCARP is an open cardiac electrophysiology simulator for in-silico experiments.

homepage: https://opencarp.org

version	versionsuffix	toolchain
3.2	-Python-3.8.2	foss/2020a
6.0		foss/2020b
8.2		foss/2021a

OpenCensus-python

OpenCensus for Python. OpenCensus provides a framework to measure a server's resource usage and collect performance stats. This repository contains Python related utilities and supporting software needed by OpenCensus.

homepage: https://opencensus.io/

version	toolchain
0.8.0	GCCcore/11.2.0

OpenCoarrays

OpenCoarrays is an open-source software project that supports the coarray Fortran (CAF) parallel programming features of the Fortran 2008 standard and several features proposed for Fortran 2015 in the draft Technical Specification TS 18508 Additional Parallel Features in Fortran.

homepage: https://github.com/sourceryinstitute/opencoarrays

version	toolchain
1.9.0	gompi/2017a
2.2.0	gompi/2018b
2.8.0	gompi/2019b
2.9.2	gompi/2020a

OpenColorIO

OpenColorIO (OCIO) is a complete color management solution geared towards motion picture production with an emphasis on visual effects and computer animation.

homepage: http://opencolorio.org/

version	toolchain
1.1.0	foss/2018b

OpenCV

OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. Includes extra modules for OpenCV from the contrib repository.

homepage: https://opencv.org/

version	versionsuffix	toolchain
2.4.12		intel/2016a
3.1.0		foss/2016a, foss/2016b, intel/2016a, intel/2016b
3.3.0	-Python-2.7.13	intel/2017a
3.3.0	-Python-2.7.14	foss/2017b, intel/2017b
3.3.0	-Python-3.6.1	intel/2017a
3.3.0	-Python-3.6.3	foss/2017b, intel/2017b
3.4.1	-Python-2.7.14	foss/2018a, intel/2018a
3.4.1	-Python-3.6.4	foss/2018a, intel/2018a
3.4.1	-Python-3.6.4-contrib	foss/2018a
3.4.5	-Python-2.7.15	foss/2018b
3.4.7	-Python-2.7.15	foss/2019a, fosscuda/2019a
3.4.7	-Python-3.7.2	foss/2019a, fosscuda/2019a
4.0.1	-Python-2.7.15	foss/2018b
4.0.1	-Python-3.6.6	foss/2018b
4.2.0	-Python-3.7.4	foss/2019b, fosscuda/2019b
4.2.0	-Python-3.8.2	foss/2020a
4.2.0	-Python-3.8.2-contrib	foss/2020a
4.5.1	-contrib	foss/2020b, fosscuda/2020b
4.5.3	-CUDA-11.3.1-contrib	foss/2021a
4.5.3	-contrib	foss/2021a
4.5.5	-CUDA-11.4.1-contrib	foss/2021b
4.5.5	-contrib	foss/2021b
4.6.0	-CUDA-11.7.0-contrib	foss/2022a
4.6.0	-contrib	foss/2022a
4.8.0	-contrib	foss/2022b
4.8.1	-contrib	foss/2023a

OpenEXR

OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic for use in computer imaging applications

homepage: https://www.openexr.com/

version	toolchain
2.2.0	intel/2016b, intel/2017a
2.3.0	foss/2018b, intel/2018b
2.4.0	GCCcore/8.3.0
2.4.1	GCCcore/9.3.0
2.5.5	GCCcore/10.2.0
3.0.1	GCCcore/10.3.0
3.1.1	GCCcore/11.2.0
3.1.5	GCCcore/11.3.0, GCCcore/12.2.0
3.1.7	GCCcore/12.3.0
3.2.0	GCCcore/13.2.0

OpenFace

OpenFace – a state-of-the art tool intended for facial landmark detection, head pose estimation, facial action unit recognition, and eye-gaze estimation.

homepage: https://github.com/TadasBaltrusaitis/OpenFace

version	versionsuffix	toolchain
2.2.0		foss/2021a
2.2.0	-CUDA-11.3.1	foss/2021a

OpenFAST

OpenFAST is a wind turbine simulation tool which builds on FAST v8. FAST.Farm extends the capability of OpenFAST to simulate multi-turbine wind farms

homepage: http://openfast.readthedocs.io/

version	toolchain
3.0.0	foss/2021b

OpenFOAM

OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.

homepage: https://www.openfoam.com/

version	versionsuffix	toolchain
2.2.2		intel/2016a, intel/2017a, intel/2018a
2.2.x		intel/2019a
2.3.1		intel/2017a, intel/2019b
2.4.0		intel/2017a, intel/2019a
3.0.0		foss/2016a
3.0.1		intel/2016b, intel/2018a
4.0		foss/2016b, intel/2016b
4.1		foss/2016b, intel/2017a
4.x-20170904		intel/2016b
5.0		foss/2017b, intel/2017a, intel/2017b
5.0-20180108		foss/2018a, intel/2017b, intel/2018a
5.0-20180606		foss/2019b
6		foss/2018b, foss/2019b, intel/2018a
7		foss/2019b
7	-20200508	foss/2019b, foss/2022a
7	-20200508-int64	foss/2022a
8		foss/2020a, foss/2020b
8	-20210316	foss/2020b
9		foss/2021a, intel/2021a
10		foss/2022a, foss/2023a
10	-20230119	foss/2022a
11		foss/2022a, foss/2023a
v1606+		foss/2018b
v1612+		foss/2018b
v1712		foss/2017b, intel/2017b
v1806		foss/2018b
v1812		foss/2018b
v1906		foss/2019b
v1912		foss/2019b, intel/2019b
v2006		foss/2020a, intel/2020a
v2012		foss/2020a
v2106		foss/2021a
v2112		foss/2020b, foss/2021b, foss/2022a
v2206		foss/2022a
v2206	-int64	foss/2022a
v2306		foss/2022b
v2312		foss/2023a

OpenFOAM-Extend

OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.

homepage: http://www.extend-project.de/

version	versionsuffix	toolchain
3.1		gimkl/2.11.5
3.2		gimkl/2.11.5, intel/2016a
4.0		intel/2017a
4.0	-Python-2.7.16	intel/2019b
4.1-20191120	-Python-2.7.16	intel/2019b
4.1-20200408	-Python-2.7.16	foss/2019b

OpenFold

A faithful PyTorch reproduction of DeepMind's AlphaFold 2

homepage: https://github.com/aqlaboratory/openfold

version	versionsuffix	toolchain
1.0.0	-CUDA-11.3.1	foss/2021a
1.0.1	-CUDA-11.3.1	foss/2021a
1.0.1	-CUDA-11.7.0	foss/2022a

OpenForceField

Simulation and Parameter Estimation in Geophysics - A python package for simulation and gradient based parameter estimation in the context of geophysical applications.

homepage: https://github.com/openforcefield/openforcefield/releases

version	versionsuffix	toolchain
0.7.0	-Python-3.8.2	intel/2020a

OpenImageIO

OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, and applications.

homepage: https://openimageio.org/

version	toolchain
1.6.17	intel/2016b
1.7.17	intel/2017a
1.8.16	foss/2018b, intel/2018b
2.0.12	gompi/2019b, iimpi/2019b
2.1.12.0	gompi/2020a, iimpi/2020a
2.3.17.0	GCC/11.3.0
2.4.14.0	GCC/12.3.0

OpenJPEG

OpenJPEG is an open-source JPEG 2000 codec written in C language. It has been developed in order to promote the use of JPEG 2000, a still-image compression standard from the Joint Photographic Experts Group (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as a JPEG 2000 Reference Software.

homepage: https://www.openjpeg.org/

version	toolchain
2.1	GCCcore/6.4.0
2.3.0	GCCcore/6.4.0, GCCcore/7.3.0
2.3.1	GCCcore/8.2.0, GCCcore/8.3.0
2.4.0	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/9.3.0
2.5.0	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

OpenKIM-API

Open Knowledgebase of Interatomic Models. OpenKIM is an API and a collection of interatomic models (potentials) for atomistic simulations. It is a library that can be used by simulation programs to get access to the models in the OpenKIM database. This EasyBuild only installs the API, the models have to be installed by the user by running kim-api-collections-management install user MODELNAME or kim-api-collections-management install user OpenKIM to install them all.

homepage: https://openkim.org/

version	toolchain
1.9.2	foss/2016b, foss/2017b
1.9.7	foss/2018b, intel/2018b, iomkl/2018b

openkim-models

Open Knowledgebase of Interatomic Models. OpenKIM is an API and a collection of interatomic models (potentials) for atomistic simulations. It is a library that can be used by simulation programs to get access to the models in the OpenKIM database. This EasyBuild installs the models. The API itself is in the kim-api package.

homepage: https://openkim.org/

version	toolchain
20190725	GCC/10.2.0, foss/2019a, foss/2019b, intel/2019a, intel/2019b
20210128	GCC/10.2.0
20210811	GCC/12.3.0, intel-compilers/2023.1.0

OpenMEEG

The OpenMEEG software is a C++ package for solving the forward problems of electroencephalography (EEG) and magnetoencephalography (MEG).

homepage: http://openmeeg.github.io/

version	toolchain
2.5.7	foss/2023a

OpenMM

OpenMM is a toolkit for molecular simulation.

homepage: https://openmm.org

version	versionsuffix	toolchain
7.1.1	-Python-3.6.3	intel/2017b
7.4.1	-Python-3.7.4	foss/2019b, fosscuda/2019b, intel/2019b
7.4.2	-Python-3.8.2	intel/2020a
7.5.0		foss/2020b, fosscuda/2020b, intel/2020b
7.5.0	-Python-3.8.2	fosscuda/2020a, intel/2020a
7.5.1		foss/2020b, fosscuda/2020b
7.5.1	-CUDA-11.3.1-DeepMind-patch	foss/2021a
7.5.1	-CUDA-11.4.1-DeepMind-patch	foss/2021b
7.5.1	-DeepMind-patch	foss/2021a, foss/2021b
7.7.0		foss/2021a, foss/2022a
7.7.0	-CUDA-11.3.1	foss/2021a
7.7.0	-CUDA-11.7.0	foss/2022a
8.0.0		foss/2022a, foss/2023a
8.0.0	-CUDA-11.7.0	foss/2022a

OpenMM-PLUMED

This project provides a connection between OpenMM and PLUMED. It allows you to bias or analyze an OpenMM simulation based on collective variables.

homepage: https://github.com/openmm/openmm-plumed/

version	versionsuffix	toolchain
1.0	-Python-3.8.2	intel/2020a

OpenMMTools

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine. openmmtools is a Python library layer that sits on top of OpenMM to provide access to a variety of useful tools for building full-featured molecular simulation packages.

homepage: https://github.com/choderalab/openmmtools

version	versionsuffix	toolchain
0.20.0	-Python-3.8.2	intel/2020a

OpenMolcas

OpenMolcas is a quantum chemistry software package.

homepage: https://gitlab.com/Molcas/OpenMolcas

version	versionsuffix	toolchain
18.09	-Python-3.6.6	intel/2018b
20.10	-Python-3.8.2	intel/2020a
20.10	-Python-3.8.2-noGA	intel/2020a
21.06		intel/2021a, iomkl/2021a
22.06		intel/2022a
22.10		intel/2022a
22.10	-noGA	intel/2022a
23.06		intel/2023a

OpenMPI

The Open MPI Project is an open source MPI implementation.

homepage: http://www.open-mpi.org/

version	versionsuffix	toolchain
1.6.5		GCC/4.8.1, GCC/4.8.2, GCC/4.8.3
1.6.5	-no-OFED	GCC/4.8.1, GCC/4.8.2
1.7.3		GCC/4.8.2
1.8.1		GCC/4.8.3
1.8.3		GCC/4.9.2
1.8.4		GCC/4.8.4, GCC/4.9.2
1.8.5		GNU/4.9.2-2.25
1.8.6		GNU/4.9.3-2.25
1.8.8		GNU/4.9.3-2.25
1.10.1		GCC/4.9.3-2.25
1.10.2		GCC/4.9.3-2.25, GCC/5.3.0-2.26, GCC/6.1.0-2.27, PGI/16.3-GCC-4.9.3-2.25, PGI/16.4-GCC-5.3.0-2.26
1.10.3		GCC/5.4.0-2.26, GCC/6.1.0-2.27, iccifort/2016.3.210-GCC-5.4.0-2.26
1.10.4		PGI/16.7-GCC-5.4.0-2.26, iccifort/2016.3.210-GCC-4.9.3-2.25
2.0.0		GCC/5.2.0
2.0.1		GCC/6.2.0-2.27, iccifort/2017.1.132-GCC-5.4.0-2.26
2.0.2		GCC/6.3.0-2.27, iccifort/2017.1.132-GCC-6.3.0-2.27
2.0.2	-opa	GCC/6.3.0-2.27
2.1.0		GCC/6.3.0-2.28
2.1.1		GCC/6.4.0-2.28, gcccuda/2017b, iccifort/2017.4.196-GCC-6.4.0-2.28
2.1.2		GCC/6.4.0-2.28, gcccuda/2018a, iccifort/2018.1.163-GCC-6.4.0-2.28
2.1.3		iccifort/2018.2.199-GCC-6.4.0-2.28
3.0.0		GCC/7.2.0-2.29
3.1.0		GCC/7.3.0-2.30
3.1.1		GCC/7.3.0-2.30, gcccuda/2018b, iccifort/2018.3.222-GCC-7.3.0-2.30
3.1.2		GCC/8.2.0-2.31.1
3.1.3		GCC/8.2.0-2.31.1, gcccuda/2019a, iccifort/2019.1.144-GCC-8.2.0-2.31.1
3.1.4		GCC/8.3.0, GCC/8.3.0-2.32, gcccuda/2019b, iccifort/2019.5.281
4.0.0		GCC/8.2.0-2.31.1
4.0.0	-hpcx	GCC/8.2.0-2.31.1
4.0.1		GCC/8.3.0-2.32
4.0.2		GCC/9.2.0-2.32
4.0.3		GCC/9.3.0, gcccuda/2020a, iccifort/2020.1.217, iccifortcuda/2020a
4.0.5		GCC/10.2.0, GCC/9.3.0, gcccuda/2020b, iccifort/2020.4.304
4.0.5	-CUDA-11.2.1	NVHPC/21.2
4.0.6		GCC/10.3.0
4.0.7		GCC/10.3.0
4.1.0		GCC/10.2.0
4.1.1		GCC/10.3.0, GCC/11.2.0, intel-compilers/2021.2.0, intel-compilers/2021.4.0
4.1.2		GCC/10.2.0, GCC/11.2.0
4.1.4		GCC/11.3.0, GCC/12.2.0, NVHPC/22.7-CUDA-11.7.0
4.1.5		GCC/12.2.0, GCC/12.3.0, intel-compilers/2023.1.0
4.1.6		GCC/13.2.0
system		GCC/system-2.29

OpenMS

As part of the deNBI Center for integrative Bioinformatics, OpenMS offers an open-source software C++ library (+ python bindings) for LC/MS data management and analyses. It provides an infrastructure for the rapid development of mass spectrometry related software as well as a rich toolset built on top of it.

homepage: https://www.openms.de/

version	toolchain
2.4.0	foss/2018b

OpenNLP

The Apache OpenNLP library is a machine learning based toolkit for the processing of natural language text.

homepage: https://opennlp.apache.org/

version	toolchain
1.8.1	system

OpenPGM

OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility.

homepage: http://code.google.com/p/openpgm/

version	toolchain
5.2.122	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0, foss/2016a, foss/2016b, foss/2017a, intel/2016a, intel/2016b, intel/2017a

OpenPIV

OpenPIV is an open source Particle Image Velocimetry analysis software

homepage: http://www.openpiv.net

version	versionsuffix	toolchain
0.21.8	-Python-3.7.4	intel/2019b

openpyxl

A Python library to read/write Excel 2010 xlsx/xlsm files

homepage: https://openpyxl.readthedocs.io

version	versionsuffix	toolchain
2.6.2		GCCcore/8.2.0
2.6.4	-Python-2.7.16	GCCcore/8.3.0
3.0.3	-Python-3.7.4	GCCcore/8.3.0
3.0.7		GCCcore/10.2.0, GCCcore/10.3.0
3.0.9		GCCcore/11.2.0
3.0.10		GCCcore/11.3.0
3.1.2		GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

OpenRefine

OpenRefine is a power tool that allows you to load data, understand it, clean it up, reconcile it, and augment it with data coming from the web.

homepage: https://github.com/OpenRefine/OpenRefine

version	versionsuffix	toolchain
2.7	-Java-1.8.0_144	system
3.4.1	-Java-11	system

OpenSceneGraph

The OpenSceneGraph is an open source high performance 3D graphics toolkit, used by application developers in fields such as visual simulation, games, virtual reality, scientific visualization and modelling. Written entirely in Standard C++ and OpenGL it runs on all Windows platforms, OSX, GNU/Linux, IRIX, Solaris, HP-Ux, AIX and FreeBSD operating systems. The OpenSceneGraph is now well established as the world leading scene graph technology, used widely in the vis-sim, space, scientific, oil-gas, games and virtual reality industries.

homepage: http://www.openscenegraph.org/

version	toolchain
3.6.5	foss/2021a, foss/2021b, foss/2022a

OpenSees

Open System for Earthquake Engineering Simulation

homepage: https://opensees.berkeley.edu/index.php

version	versionsuffix	toolchain
3.2.0	-Python-3.8.2	intel/2020a
3.2.0	-Python-3.8.2-parallel	intel/2020a

OpenSlide

OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides).

homepage: https://openslide.org/

version	versionsuffix	toolchain
3.4.1		GCCcore/11.2.0, GCCcore/8.2.0
3.4.1	-largefiles	GCCcore/10.3.0, GCCcore/11.3.0, GCCcore/12.3.0, GCCcore/8.2.0

OpenSlide-Java

This is a Java binding to OpenSlide.

homepage: https://github.com/openslide/openslide-java

version	versionsuffix	toolchain
0.12.4	-Java-17	GCCcore/12.3.0

openslide-python

OpenSlide Python is a Python interface to the OpenSlide library.

homepage: https://github.com/openslide/openslide-python

version	toolchain
1.1.1	GCCcore/8.2.0
1.1.2	GCCcore/10.3.0, GCCcore/11.2.0
1.2.0	GCCcore/11.3.0
1.3.1	GCCcore/12.3.0

OpenSSL

The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library.

homepage: https://www.openssl.org/

version	toolchain
1.0	system
1.0.1f	GCC/4.8.2
1.0.1k	GCC/4.9.2
1.0.1s	foss/2016a, intel/2016a
1.0.2g	GCCcore/4.9.3
1.0.2h	foss/2016.04, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25
1.1	system
1.1.0c	GCC/5.4.0-2.26
1.1.0e	intel/2016b
1.1.0h	GCCcore/7.3.0
1.1.1b	GCCcore/8.2.0
1.1.1d	GCCcore/8.3.0
1.1.1e	GCCcore/9.3.0
1.1.1h	GCCcore/10.2.0
1.1.1k	GCCcore/10.3.0, GCCcore/11.2.0
1.1.1n	GCCcore/11.3.0
1.1.1q	GCCcore/10.3.0
3	system

OpenStackClient

OpenStackClient (aka OSC) is a command-line client for OpenStack that brings the command set for Compute, Identity, Image, Network, Object Store and Block Storage APIs together in a single shell with a uniform command structure.

homepage: https://docs.openstack.org/python-openstackclient/latest/

version	toolchain
5.5.0	GCCcore/10.2.0
5.8.0	GCCcore/11.2.0
6.0.0	GCCcore/12.2.0

OPERA

An optimal genome scaffolding program

homepage: https://sourceforge.net/projects/operasf

version	versionsuffix	toolchain
2.0.6	-Perl-5.28.0	foss/2018b, intel/2018b

OPERA-MS

OPERA-MS is a hybrid metagenomic assembler which combines the advantages of short and long-read technologies to provide high quality assemblies, addressing issues of low contiguity for short-read only assemblies, and low base-pair quality for long-read only assemblies.

homepage: https://github.com/CSB5/OPERA-MS

version	versionsuffix	toolchain
0.9.0-20200802	-Python-3.8.2	foss/2020a

OptaDOS

OptaDOS is a program for calculating core-electron and low-loss electron energy loss spectra (EELS) and optical spectra along with total-, projected- and joint-density of electronic states (DOS) from single-particle eigenenergies and dipole transition coefficients.

homepage: http://www.optados.org/

version	toolchain
1.2.380	GCC/11.3.0

Optax

Optax is a gradient processing and optimization library for JAX.

homepage: https://github.com/deepmind/optax

version	toolchain
0.1.7	foss/2022a

OptiType

OptiType is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles.

homepage: https://github.com/FRED-2/OptiType

version	versionsuffix	toolchain
1.3.2	-Python-2.7.15	foss/2018b
1.3.2	-Python-3.6.6	foss/2018b

OptiX

OptiX is NVIDIA SDK for easy ray tracing performance. It provides a simple framework for accessing the GPU’s massive ray tracing power using state-of-the-art GPU algorithms.

homepage: https://developer.nvidia.com/optix

version	toolchain
3.8.0	GNU/4.9.3-2.25
3.9.0	GNU/4.9.3-2.25
6.5.0	system
7.2.0	system

Optuna

Optuna is an automatic hyperparameter optimization software framework, particularly designed for machine learning. It features an imperative, define-by-run style user API. Thanks to our define-by-run API, the code written with Optuna enjoys high modularity, and the user of Optuna can dynamically construct the search spaces for the hyperparameters.

homepage: https://optuna.org/

version	toolchain
2.9.1	foss/2021a
2.10.0	foss/2021b
3.1.0	foss/2022a
3.5.0	foss/2023a

OR-Tools

Google Optimization Tools (a.k.a., OR-Tools) is an open-source, fast and portable software suite for solving combinatorial optimization problems.

homepage: https://developers.google.com/optimization/

version	versionsuffix	toolchain
7.1	-Python-3.7.2	foss/2019a

ORCA

ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.

homepage: https://orcaforum.kofo.mpg.de

version	versionsuffix	toolchain
3_0_2-linux_x86-64	-OpenMPI-1.8.1	system
4.0.0.2	-OpenMPI-2.0.2	system
4.0.1	-OpenMPI-2.0.2	system
4.1.0	-OpenMPI-3.1.3	system
4.2.0		gompi/2019b
4.2.1		gompi/2019b
5.0.0		gompi/2021a
5.0.0	-static	gompi/2021a
5.0.1		gompi/2021a
5.0.1	-static	gompi/2021a
5.0.2		gompi/2021a, gompi/2021b
5.0.2	-static	gompi/2021a, gompi/2021b
5.0.3		gompi/2021b
5.0.4		gompi/2022a, gompi/2023a

ORFfinder

ORF finder searches for open reading frames (ORFs) in the DNA sequence you enter. The program returns the range of each ORF, along with its protein translation. Use ORF finder to search newly sequenced DNA for potential protein encoding segments, verify predicted protein using newly developed SMART BLAST or regular BLASTP.

homepage: https://www.ncbi.nlm.nih.gov/orffinder/

version	toolchain
0.4.3	system

OrfM

A simple and not slow open reading frame (ORF) caller.

homepage: https://github.com/wwood/OrfM

version	toolchain
0.6.1	foss/2016b
0.7.1	GCC/12.3.0, iccifort/2019.1.144-GCC-8.2.0-2.31.1

OrthoFinder

OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics

homepage: https://github.com/davidemms/OrthoFinder

version	versionsuffix	toolchain
2.2.7	-Python-2.7.14	intel/2018a
2.3.3	-Python-2.7.15	intel/2018b
2.3.8	-Python-2.7.16	foss/2019b
2.3.11	-Python-3.7.4	intel/2019b
2.5.2		foss/2020b
2.5.4		foss/2020b
2.5.5		foss/2023a

OrthoMCL

OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences.

homepage: http://orthomcl.org/

version	versionsuffix	toolchain
1.4	-Perl-5.24.0	intel/2016b
2.0.9	-Perl-5.24.0	intel/2016b

Osi

Osi (Open Solver Interface) provides an abstract base class to a generic linear programming (LP) solver, along with derived classes for specific solvers. Many applications may be able to use the Osi to insulate themselves from a specific LP solver. That is, programs written to the OSI standard may be linked to any solver with an OSI interface and should produce correct results. The OSI has been significantly extended compared to its first incarnation. Currently, the OSI supports linear programming solvers and has rudimentary support for integer programming.

homepage: https://github.com/coin-or/Osi

version	toolchain
0.108.5	GCCcore/7.3.0, foss/2018b
0.108.6	GCC/10.3.0, GCCcore/10.2.0
0.108.7	GCC/11.2.0
0.108.8	GCC/12.2.0
0.108.9	GCC/12.3.0

OSPRay

Open, Scalable, and Portable Ray Tracing Engine

homepage: https://www.ospray.org

version	toolchain
2.5.0	system

OSU-Micro-Benchmarks

OSU Micro-Benchmarks

homepage: https://mvapich.cse.ohio-state.edu/benchmarks/

version	versionsuffix	toolchain
5.3.2		foss/2016a, foss/2017a
5.6.2		gompi/2019a
5.6.3		gompi/2019b, gompi/2020a, gompi/2020b, gompic/2019b, gompic/2020a, iimpi/2019a, iimpi/2019b, iimpi/2020a, iimpi/2020b, iimpic/2019b, iimpic/2020a
5.7		gompi/2020b, gompic/2020b, iimpi/2020b
5.7.1		ffmpi/4.5.0, gompi/2021a, gompi/2021b, iimpi/2021a, iompi/2021a
5.7.1	-CUDA-11.3.1	gompi/2021a
5.8		iimpi/2021b
5.9		gompi/2022.05, gompi/2022a, iimpi/2022a
5.9	-CUDA-11.3.1	gompi/2021a
5.9	-CUDA-11.4.1	gompi/2021b
5.9	-CUDA-11.7.0	gompi/2022a
5.9	-ROCm-4.5.0	gompi/2021b
6.2		gompi/2022.10, gompi/2022b, iimpi/2022b
6.2	-CUDA-12.0.0	gompi/2022b
7.1-1		gompi/2023a, iimpi/2023a
7.2		gompi/2023.09, gompi/2023b
7.2	-CUDA-12.1.1	gompi/2023a

OTF2

The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus support library. It is the new standard trace format for Scalasca, Vampir, and TAU and is open for other tools.

homepage: https://www.score-p.org

version	toolchain
2.0	foss/2016a, foss/2017a
2.2	GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
2.3	GCCcore/10.2.0, GCCcore/10.3.0
3.0	GCCcore/11.3.0
3.0.2	GCCcore/11.2.0, GCCcore/11.3.0
3.0.3	GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

OVITO

OVITO is a scientific visualization and data analysis solution for atomistic and other particle-based models. It helps scientists gain meaningful and quick insights from numerical simulation results.

homepage: https://www.ovito.org

version	versionsuffix	toolchain
3.7.11	-basic	gompi/2022a

ownCloud

The ownCloud Desktop Client is a tool to synchronize files from ownCloud Server with your computer.

homepage: https://github.com/owncloud/client

version	toolchain
2.4.3	foss/2018b
2.5.4	GCCcore/8.2.0

oxDNA

oxDNA is a simulation code that was initially conceived as an implementation of the coarse-grained DNA model introduced by T. E. Ouldridge, J. P. K. Doye and A. A. Louis. It has been since reworked and it is now an extensible simulation+analysis framework. It natively supports DNA, RNA, Lennard-Jones and patchy particle simulations of different kinds on both single CPU cores and NVIDIA GPUs.

homepage: https://github.com/lorenzo-rovigatti/oxDNA

version	versionsuffix	toolchain
3.5.2	-CUDA-11.7.0	foss/2022a

oxford_asl

A command line tool for quantification of perfusion from ASL data

homepage: https://github.com/ibme-qubic/oxford_asl

version	versionsuffix	toolchain
3.9.6	-centos7-Python-2.7.13	intel/2017a

P

p11-kit - p4-phylogenetics - p4est - p4vasp - p7zip - packmol - PAGAN2 - pagmo - pairsnp - PAL2NAL - paladin - PALEOMIX - PAML - panaroo - pandapower - pandas - pandas-datareader - PANDAseq - Pandoc - Panedr - Pango - pangolin - panito - PAPI - parallel - parallel-fastq-dump - Parallel-Hashmap - ParallelIO - parameterized - paramiko - parasail - Paraver - ParaView - Parcels - PARI-GP - ParmEd - ParMETIS - ParMGridGen - Parsl - PartitionFinder - PASA - pasta - PaStiX - pastml - patch - patchelf - path.py - PAUP - pauvre - pbbam - pbcopper - pbdagcon - pbipa - pblat - pbmm2 - pbs_python - PBSuite - PBZIP2 - PCAngsd - PCC - PCL - PCMSolver - PCRaster - PCRE - PCRE2 - PDM - pdsh - PDT - peakdetect - PEAR - PennCNV - PEPT - Percolator - Perl - perl-app-cpanminus - Perl-bundle-CPAN - Perl4-CoreLibs - Perseus - PEST++ - PETSc - petsc4py - PfamScan - PFFT - pfind - pftoolsV3 - pFUnit - PGDSpider - PGI - PGPLOT - PHANOTATE - Phantompeakqualtools - PHASE - PHAST - Phenoflow - PheWAS - PheWeb - Philosopher - PhiPack - PHLAT - phonemizer - phono3py - phonopy - photontorch - phototonic - PHYLIP - PhyloBayes-MPI - phylokit - phylonaut - PhyloPhlAn - phyluce - PhyML - phyx - picard - PICI-LIGGGHTS - PICRUSt2 - pigz - PIL - PileOMeth - Pillow - Pillow-SIMD - Pilon - PIMS - Pindel - Pingouin - Pint - pip - PIPITS - PIRATE - pIRS - Pisces - piSvM - piSvM-JSC - pixman - pizzly - pkg-config - pkgconf - pkgconfig - PLAMS - plantcv - PlaScope - PlasmaPy - PLAST - Platanus - Platypus - Platypus-Opt - plc - PLINK - plinkliftover - plinkQC - PLINKSEQ - plot1cell - Ploticus - plotly - plotly-orca - plotly.py - plotutils - PLplot - PLUMED - PLY - PMIx - pmt - pmx - PnetCDF - pocl - pod5-file-format - poetry - polars - polymake - pomkl - pompi - poppler - poppunk - popscle - popt - Porechop - porefoam - poretools - Portcullis - PortMidi - Postgres-XL - PostgreSQL - POT - POV-Ray - powerlaw - pp-sketchlib - PPanGGOLiN - PPfold - ppl - pplacer - pplpy - PRANK - PRC - preCICE - PREQUAL - preseq - presto - pretty-yaml - primecount - primecountpy - Primer3 - PRINSEQ - printproto - PRISMS-PF - ProbABEL - ProBiS - prodigal - ProFit - PROJ - ProjectQ - prokka - prompt-toolkit - proovread - propy - Proteinortho - ProtHint - protobuf - protobuf-python - protozero - PRSice - PSASS - pscom - PSI - PSI4 - PsiCLASS - PSIPRED - psmc - psmpi - psmpi2 - PSolver - PSORTb - psrecord - pstoedit - psutil - psycopg - psycopg2 - ptemcee - PTESFinder - pubtcrs - pugixml - pullseq - PuLP - purge_dups - pv - py - py-aiger - py-aiger-bdd - py-c3d - py-cpuinfo - py3Dmol - pyABC - PyAMG - PyAPS3 - PyAV - pybedtools - PyBerny - pyBigWig - pybind11 - pybinding - PyBioLib - PyCairo - PyCalib - pyccel - PyCharm - PyCheMPS2 - Pychopper - PyCifRW - PyClone - pycma - pycocotools - pycodestyle - PyCogent - pycoQC - pycubescd - PyCUDA - PycURL - PyDamage - pydantic - PyDatastream - pydicom - pydicom-seg - pydlpoly - pydot - pyEGA3 - pyenchant - PyEVTK - pyFAI - pyfaidx - pyfasta - PyFFmpeg - pyFFTW - pyfits - PyFMI - PyFoam - PyFR - PyFrag - pygame - pygccxml - pyGenomeTracks - PyGEOS - pyGIMLi - Pygments - pygmo - PyGObject - pygraphviz - pygrib - PyGTK - PyGTS - PyGWAS - pyhdf - PyImageJ - PyInstaller - pyiron - Pyke3 - pylift - Pylint - pylipid - pyMannKendall - pymatgen - pymatgen-db - pymbar - PyMC - PyMC3 - pymca - pymemcache - PyMOL - PyNAST - pyobjcryst - PyOD - pyodbc - Pyomo - PyOpenCL - PyOpenGL - pyparsing - pyperf - pyplusplus - pypmt - PYPOWER - pyproj - PyPSA - PyPy - pyqstem - PyQt - PyQt-builder - PyQt5 - PyQtGraph - pyradiomics - PyRe - PyRETIS - pyringe - pyro-api - pyro-ppl - Pyro4 - PyRosetta - Pysam - pysamstats - PySAT - pyScaf - pySCENIC - PySCF - pysheds - pyshp - PySide2 - PySINDy - pyslim - pysndfx - Pysolar - pyspoa - pysqlite - PyStan - pysteps - pystran - PyTables - PyTensor - pytesseract - pytest - pytest-benchmark - pytest-cpp - pytest-flakefinder - pytest-rerunfailures - pytest-shard - pytest-workflow - pytest-xdist - pythermalcomfort - PYTHIA - Python - Python-bundle - Python-bundle-PyPI - python-casacore - python-docx - python-hl7 - python-igraph - python-irodsclient - python-isal - python-Levenshtein - python-libsbml - python-louvain - python-mujoco - python-parasail - python-telegram-bot - python-weka-wrapper3 - python-xxhash - pythran - PyTorch - pytorch-3dunet - PyTorch-bundle - pytorch-CycleGAN-pix2pix - PyTorch-Geometric - PyTorch-Ignite - PyTorch-Image-Models - PyTorch-Lightning - PyTorch3D - PyTorchVideo - PyVCF - PyVCF3 - pyWannier90 - PyWavelets - PyWBGT - pyXDF - PyYAML - PyZMQ

p11-kit

Provides a way to load and enumerate PKCS#11 modules. Provides a standard configuration setup for installing PKCS#11 modules in such a way that they're discoverable. Also solves problems with coordinating the use of PKCS#11 by different components or libraries living in the same process.

homepage: https://p11-glue.freedesktop.org/p11-kit.html

version	toolchain
0.23.2	GCCcore/5.4.0, GNU/4.9.3-2.25, foss/2016a, intel/2016a
0.24.0	GCCcore/10.3.0
0.24.1	GCCcore/11.2.0, GCCcore/11.3.0

p4-phylogenetics

A Python phyloinformatic toolkit, and an implementation of tree-heterogeneous models of evolution.

homepage: http://p4.nhm.ac.uk/

version	versionsuffix	toolchain
1.4-20210322	-Python-3.7.4	foss/2019b

p4est

p4est is a C library to manage a collection (a forest) of multiple connected adaptive quadtrees or octrees in parallel.

homepage: https://www.p4est.org

version	toolchain
2.2	foss/2019a, intel/2019a
2.8	foss/2021a

p4vasp

Visualization suite for VASP

homepage: http://www.p4vasp.at/

version	versionsuffix	toolchain
0.3.29	-Python-2.7.11	intel/2016a
0.3.30	-Python-2.7.14	intel/2017b, intel/2018a
0.3.30	-Python-2.7.15	foss/2018b

p7zip

p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip) for Unix. 7-Zip is a file archiver with highest compression ratio.

homepage: http://p7zip.sourceforge.net/

version	toolchain
9.38.1	GCC/4.9.2, system
16.02	GCC/6.4.0-2.28, iccifort/2017.4.196-GCC-6.4.0-2.28, intel/2018a
17.03	GCCcore/10.2.0
17.04	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.3.0

packmol

Packing Optimization for Molecular Dynamics Simulations

homepage: http://m3g.iqm.unicamp.br/packmol

version	toolchain
16.103	intel/2016a
18.013	foss/2018a, intel/2018a
20.2.2	GCC/10.2.0
v20.2.2	iccifort/2020.1.217

PAGAN2

PAGAN2 is a general-purpose method for the alignment of DNA, codon and amino-acid sequences as graphs. It aligns sequences either with pileup or, when related by a tree, using phylogeny-aware progressive alignment algorithm. In both cases it uses graphs to describe the uncertainty in the presence of characters at certain sequence positions. PAGAN2 is largely compatible with PAGAN but implements new algorithms for alignment anchoring and memory handling. As a result, PAGAN2 can align sequences of several hundreds of kilobases in length.

homepage: https://github.com/ariloytynoja/pagan2-msa

version	versionsuffix	toolchain
1.53_20230824	-linux64	system

pagmo

pagmo is a C++ scientific library for massively parallel optimization.

homepage: https://esa.github.io/pagmo2

version	toolchain
2.17.0	foss/2020b
2.18.0	foss/2021a, foss/2021b, foss/2022a

pairsnp

A set of scripts for very quickly obtaining pairwise SNP distance matrices from multiple sequence alignments using sparse matrix libraries to improve performance.

homepage: https://github.com/gtonkinhill/pairsnp

version	toolchain
0.0.7	foss/2021a

PAL2NAL

PAL2NAL is a program that converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment. The program automatically assigns the corresponding codon sequence even if the input DNA sequence has mismatches with the input protein sequence, or contains UTRs, polyA tails. It can also deal with frame shifts in the input alignment, which is suitable for the analysis of pseudogenes. The resulting codon alignment can further be subjected to the calculation of synonymous (d_S) and non-synonymous (d_N) subs- titution rates.

homepage: http://www.bork.embl.de/pal2nal/

version	toolchain
14	GCCcore/10.2.0, GCCcore/10.3.0

paladin

Protein ALignment And Detection INterface PALADIN is a protein sequence alignment tool designed for the accurate functional characterization of metagenomes.

homepage: https://github.com/ToniWestbrook/paladin

version	toolchain
1.4.6	GCCcore/10.3.0, GCCcore/11.2.0

PALEOMIX

The PALEOMIX pipelines are a set of pipelines and tools designed to aid the rapid processing of High-Throughput Sequencing (HTS) data.

homepage: https://github.com/MikkelSchubert/paleomix

version	toolchain
1.3.7	foss/2022a

PAML

PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.

homepage: http://abacus.gene.ucl.ac.uk/software/paml.html

version	toolchain
4.9i	GCC/6.4.0-2.28, iccifort/2017.4.196-GCC-6.4.0-2.28
4.9j	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/9.3.0
4.10.5	GCCcore/11.3.0

panaroo

A pangenome analysis pipeline.

homepage: https://gtonkinhill.github.io/panaroo/

version	toolchain
1.2.8	foss/2020b
1.2.9	foss/2021a
1.3.2	foss/2021b

pandapower

An easy to use open source tool for power system modeling, analysis and optimization with a high degree of automation

homepage: http://www.pandapower.org/

version	toolchain
2.7.0	foss/2020b

pandas

pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.

homepage: https://pypi.python.org/pypi/pandas/

version	versionsuffix	toolchain
0.18.0	-Python-2.7.11	foss/2016a, intel/2016a
0.18.0	-Python-3.5.1	foss/2016a, intel/2016a
0.18.1	-Python-2.7.12	intel/2016b
0.18.1	-Python-3.5.2	intel/2016b
0.19.0	-Python-2.7.12	foss/2016b, intel/2016b
0.19.0	-Python-3.5.2	foss/2016b, intel/2016b
0.19.1	-Python-2.7.12	intel/2016b
0.19.1	-Python-3.5.2	intel/2016b
0.20.1	-Python-3.6.1	intel/2017a
0.21.0	-Python-2.7.13	intel/2017a
0.21.0	-Python-3.6.3	intel/2017b
1.1.2	-Python-3.8.2	foss/2020a

pandas-datareader

Up to date remote data access for pandas, works for multiple versions of pandas.

homepage: https://pypi.org/project/pandas-datareader

version	versionsuffix	toolchain
0.7.0	-Python-3.6.4	intel/2018a

PANDAseq

PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

homepage: https://github.com/neufeld/pandaseq

version	toolchain
2.10	GCC/5.4.0-2.26, iccifort/2016.3.210-GCC-5.4.0-2.26
2.11	foss/2017b, intel/2017b, intel/2018a

Pandoc

If you need to convert files from one markup format into another, pandoc is your swiss-army knife

homepage: https://pandoc.org

version	toolchain
2.1.3	system
2.5	system
2.10	system
2.13	system
3.1.2	system

Panedr

Panedr uses the Pyedr library to read a Gromacs EDR binary energy XDR file and returns its contents as a pandas dataframe.

homepage: https://github.com/MDAnalysis/panedr

version	toolchain
0.7.0	foss/2021a

Pango

Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.

homepage: https://www.pango.org/

version	toolchain
1.39.0	foss/2016a, intel/2016a
1.40.1	foss/2016a, intel/2016a
1.40.3	foss/2016b, intel/2016b
1.40.5	intel/2017a
1.40.12	intel/2017a
1.40.14	foss/2017b, intel/2017b
1.41.0	foss/2017b, intel/2017b
1.41.1	foss/2018a, intel/2018a
1.42.4	foss/2018b, fosscuda/2018b
1.43.0	GCCcore/8.2.0
1.44.7	GCCcore/8.3.0, GCCcore/9.3.0
1.47.0	GCCcore/10.2.0
1.48.5	GCCcore/10.3.0
1.48.8	GCCcore/11.2.0
1.50.7	GCCcore/11.3.0
1.50.12	GCCcore/12.2.0
1.50.14	GCCcore/12.3.0
1.51.0	GCCcore/13.2.0

pangolin

Software package for assigning SARS-CoV-2 genome sequences to global lineages. This module also contains the faToVcf tool

homepage: https://cov-lineages.org/pangolin.html

version	versionsuffix	toolchain
3.1.11		foss/2020b
3.1.16	-pangoLEARN-2021-10-18	foss/2021b
3.1.16	-pangoLEARN-2021-11-25	foss/2021b

panito

Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment.

homepage: https://github.com/sanger-pathogens/panito

version	toolchain
0.0.1	GCC/10.3.0

PAPI

PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack.

homepage: https://icl.cs.utk.edu/projects/papi/

version	toolchain
5.4.3	foss/2016a
5.5.1	GCCcore/6.3.0, GCCcore/6.4.0
5.6.0	GCCcore/6.4.0
5.7.0	GCCcore/7.3.0, GCCcore/8.2.0
6.0.0	GCCcore/10.2.0, GCCcore/8.3.0, GCCcore/9.3.0
6.0.0.1	GCCcore/10.3.0, GCCcore/11.2.0
7.0.0	GCCcore/11.3.0
7.0.1	GCCcore/12.2.0, GCCcore/12.3.0
7.1.0	GCCcore/13.2.0

parallel

parallel: Build and execute shell commands in parallel

homepage: https://savannah.gnu.org/projects/parallel/

version	toolchain
20141122	GCC/4.9.2
20150322	GCC/4.9.2
20150822	GCC/4.9.2
20160622	foss/2016a
20170822	intel/2017a
20171022	intel/2017b
20171122	foss/2017b, intel/2017b
20180422	intel/2018a
20180822	foss/2018b
20181222	intel/2018b
20190222	GCCcore/7.3.0
20190622	GCCcore/8.2.0
20190922	GCCcore/8.3.0
20200422	GCCcore/9.3.0
20200522	GCCcore/9.3.0
20210322	GCCcore/10.2.0
20210622	GCCcore/10.3.0
20210722	GCCcore/11.2.0
20220722	GCCcore/11.3.0
20230722	GCCcore/12.2.0, GCCcore/12.3.0

parallel-fastq-dump

parallel fastq-dump wrapper

homepage: https://github.com/rvalieris/parallel-fastq-dump

version	versionsuffix	toolchain
0.6.5	-Python-3.7.2	GCCcore/8.2.0
0.6.6	-Python-3.8.2	GCCcore/9.3.0
0.6.7		gompi/2020b, gompi/2022a

Parallel-Hashmap

Parallel Hashmap is built on a modified version of Abseil's flat_hash_map. Parallel Hashmap has lower space requirements, is nearly as fast as the underlying flat_hash_map, and can be used from multiple threads with high levels of concurrency.

homepage: https://github.com/greg7mdp/parallel-hashmap

version	toolchain
1.3.12	GCCcore/12.3.0
1.33	GCCcore/10.3.0
1.36	GCCcore/11.3.0

ParallelIO

A high-level Parallel I/O Library for structured grid applications

homepage: https://github.com/NCAR/ParallelIO

version	toolchain
2.2.2a	intel/2017a
2.5.10	gompi/2022a, iimpi/2022a

parameterized

Parameterized testing with any Python test framework

homepage: https://github.com/wolever/parameterized

version	toolchain
0.8.1	GCCcore/10.3.0
0.9.0	GCCcore/11.3.0, GCCcore/12.3.0

paramiko

Paramiko is a pure-Python (3.6+) implementation of the SSHv2 protocol, providing both client and server functionality. It provides the foundation for the high-level SSH library Fabric, which is what we recommend you use for common client use-cases such as running remote shell commands or transferring files.

homepage: https://paramiko.org

version	toolchain
3.2.0	GCCcore/12.3.0

parasail

parasail is a SIMD C (C99) library containing implementations of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global pairwise sequence alignment algorithms.

homepage: https://github.com/jeffdaily/parasail

version	toolchain
2.2	intel/2018a
2.4	foss/2018b
2.4.1	GCC/8.3.0, intel/2019b
2.4.2	GCC/9.3.0, iccifort/2020.1.217
2.4.3	GCC/10.2.0, GCC/10.3.0
2.5	GCC/11.2.0
2.6	GCC/11.3.0
2.6.2	GCC/12.2.0, GCC/12.3.0

Paraver

A very powerful performance visualization and analysis tool based on traces that can be used to analyse any information that is expressed on its input trace format. Traces for parallel MPI, OpenMP and other programs can be genereated with Extrae.

homepage: https://tools.bsc.es/paraver

version	toolchain
4.8.1	foss/2019a
4.9.2	foss/2021a
4.11.1	foss/2022a

ParaView

ParaView is a scientific parallel visualizer.

homepage: https://www.paraview.org

version	versionsuffix	toolchain
4.4.0		foss/2016a, intel/2016a
4.4.0	-mpi	gimkl/2.11.5
5.1.2	-mpi	foss/2016b, intel/2016b
5.2.0	-mpi	foss/2016b, intel/2017a
5.3.0	-mpi	foss/2016b
5.4.1	-Python-2.7.16-mpi	foss/2019b
5.4.1	-mpi	foss/2017b, foss/2018a, foss/2018b, intel/2017a, intel/2017b, intel/2018a
5.5.2	-Python-2.7.15-mpi	foss/2018b
5.6.2	-Python-3.7.4-mpi	foss/2019b, intel/2019b
5.8.0	-Python-3.8.2-mpi	foss/2020a, intel/2020a
5.8.1	-mpi	foss/2020b
5.9.1	-mpi	foss/2021a, foss/2021b, intel/2021a
5.10.1	-mpi	foss/2022a
5.11.0	-mpi	foss/2022b
5.11.1		foss/2022b
5.11.1	-CUDA-12.2.0	foss/2022b
5.11.1	-mpi	foss/2022a
5.11.2		foss/2023a
5.12.0		foss/2023b

Parcels

Parcels (Probably A Really Computationally Efficient Lagrangian Simulator) is a set of Python classes and methods to create customisable particle tracking simulations using output from Ocean Circulation models. Parcels can be used to track passive and active particulates such as water, plankton, plastic and fish.

homepage: http://www.oceanparcels.org/

version	toolchain
2.4.0	foss/2022a

PARI-GP

PARI/GP is a widely used computer algebra system designed for fast computations in number theory (factorizations, algebraic number theory, elliptic curves...), but also contains a large number of other useful functions to compute with mathematical entities such as matrices, polynomials, power series, algebraic numbers etc., and a lot of transcendental functions. PARI is also available as a C library to allow for faster computations.

homepage: http://pari.math.u-bordeaux.fr

version	toolchain
2.7.6	foss/2016a
2.15.4	GCCcore/11.3.0

ParmEd

ParmEd is a general tool for aiding in investigations of biomolecular systems using popular molecular simulation packages, like Amber, CHARMM, and OpenMM written in Python.

homepage: https://parmed.github.io/ParmEd

version	versionsuffix	toolchain
2.7.3	-Python-3.6.3	intel/2017b
3.2.0	-Python-3.7.4	intel/2019b
3.2.0	-Python-3.8.2	intel/2020a

ParMETIS

ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.

homepage: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview

version	toolchain
4.0.3	foss/2016a, foss/2016b, foss/2017a, foss/2017b, foss/2018a, foss/2018b, gimkl/2.11.5, gompi/2019a, gompi/2019b, gompi/2020a, gompi/2020b, gompi/2021a, gompi/2021b, gompi/2022a, gompi/2022b, gompi/2023a, iimpi/2019a, iimpi/2019b, iimpi/2020a, iimpi/2020b, iimpi/2021a, iimpi/2021b, intel/2016a, intel/2016b, intel/2017a, intel/2017b, intel/2018a, intel/2018b

ParMGridGen

ParMGridGen is an MPI-based parallel library that is based on the serial package MGridGen, that implements (serial) algorithms for obtaining a sequence of successive coarse grids that are well-suited for geometric multigrid methods.

homepage: http://www-users.cs.umn.edu/~moulitsa/software.html

version	toolchain
1.0	gimkl/2.11.5, gompi/2019b, gompi/2020a, iimpi/2019b, iimpi/2020a, intel/2016a, intel/2017a

Parsl

Parsl extends parallelism in Python beyond a single computer. You can use Parsl just like Python's parallel executors but across multiple cores and nodes. However, the real power of Parsl is in expressing multi-step workflows of functions. Parsl lets you chain functions together and will launch each function as inputs and computing resources are available.

homepage: https://parsl-project.org/

version	toolchain
2023.7.17	GCCcore/11.3.0

PartitionFinder

PartitionFinder 2 is a Python program for simultaneously choosing partitioning schemes and models of molecular evolution for phylogenetic analyses of DNA, protein, and morphological data. You can PartitionFinder 2 before running a phylogenetic analysis, in order to decide how to divide up your sequence data into separate blocks before analysis, and to simultaneously perform model selection on each of those blocks.

homepage: https://www.robertlanfear.com/partitionfinder

version	versionsuffix	toolchain
2.1.1	-Python-2.7.16	intel/2019b
2.1.1	-Python-2.7.18	foss/2020b

PASA

PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments.

homepage: https://github.com/PASApipeline/PASApipeline

version	toolchain
2.5.3	foss/2022b

pasta

PASTA (Practical Alignment using SATe and Transitivity)

homepage: https://github.com/smirarab/pasta

version	versionsuffix	toolchain
1.8.5	-Python-3.7.2	GCC/8.2.0-2.31.1

PaStiX

PaStiX (Parallel Sparse matriX package) is a scientific library that provides a high performance parallel solver for very large sparse linear systems based on direct methods.

homepage: http://pastix.gforge.inria.fr/

version	toolchain
5.2.3	foss/2017b

pastml

Ancestor character reconstruction and visualisation for rooted phylogenetic trees

homepage: https://pastml.pasteur.fr/

version	toolchain
1.9.34	foss/2021a

patch

Patch takes a patch file containing a difference listing produced by the diff program and applies those differences to one or more original files, producing patched versions.

homepage: https://savannah.gnu.org/projects/patch

version	toolchain
2.7.6	system

patchelf

PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.

homepage: http://nixos.org/patchelf.html

version	toolchain
0.8	GNU/4.9.3-2.25
0.9	GCCcore/6.4.0, foss/2016a
0.10	GCCcore/7.2.0, GCCcore/8.3.0
0.12	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/9.3.0
0.13	GCCcore/11.2.0
0.15.0	GCCcore/11.3.0
0.17.2	GCCcore/12.2.0
0.18.0	GCCcore/12.3.0, GCCcore/13.2.0

path.py

path.py is a Python library implementing path objects as first-class entities, allowing common operations on files to be invoked on those path objects directly.

homepage: https://github.com/jaraco/path.py

version	versionsuffix	toolchain
8.2.1	-Python-2.7.11	foss/2016a
8.2.1	-Python-2.7.12	foss/2016b, intel/2016b
8.2.1	-Python-3.5.1	foss/2016a
8.2.1	-Python-3.5.2	intel/2016b
10.1	-Python-2.7.12	intel/2016b

PAUP

PAUP (Phylogenetic Analysis Using Parsimony and other methods) is a computational phylogenetics program for inferring evolutionary trees.

homepage: https://paup.phylosolutions.com/

version	versionsuffix	toolchain
4.0a166	-centos64	system
4.0a168	-centos64	system

pauvre

Tools for plotting Oxford Nanopore and other long-read data

homepage: https://github.com/conchoecia/pauvre

version	versionsuffix	toolchain
0.2.3		foss/2021a
0.1923	-Python-3.7.4	intel/2019b
0.1924		intel/2020b

pbbam

The pbbam software package provides components to create, query, & edit PacBio BAM files and associated indices.

homepage: http://pbbam.readthedocs.io/

version	toolchain
1.0.6	gompi/2019a
20170508	intel/2017a

pbcopper

The pbcopper library provides a suite of data structures, algorithms, and utilities for C++ applications.

homepage: https://github.com/PacificBiosciences/pbcopper

version	toolchain
1.3.0	gompi/2019a

pbdagcon

pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus) which is a sequence consensus algorithm based on using directed acyclic graphs to encode multiple sequence alignment.

homepage: https://github.com/PacificBiosciences/pbdagcon

version	toolchain
20170330	intel/2017a

pbipa

Improved Phased Assembler (IPA) is the official PacBio software for HiFi genome assembly. IPA was designed to utilize the accuracy of PacBio HiFi reads to produce high-quality phased genome assemblies. IPA is an end-to-end solution, starting with input reads and resulting in a polished assembly. IPA is fast, providing an easy to use local run mode or a distributed pipeline for a cluster.

homepage: https://github.com/PacificBiosciences/pbipa

version	toolchain
1.8.0	foss/2021b

pblat

When the query file format is fasta, you can specify many threads to process it. It can reduce run time linearly, and use almost equal memory as the original blat program. This is useful when you blat a big query file to a huge reference like human whole genome sequence.

homepage: https://github.com/icebert/pblat

version	toolchain
2.5.1	foss/2022b

pbmm2

A minimap2 frontend for PacBio native data formats

homepage: https://github.com/PacificBiosciences/pbmm2

version	toolchain
1.1.0	gompi/2019a

pbs_python

The pbs_python package is a wrapper class for the Torque C library. With this package you now can write utilities/extensions in Python instead of C. We developed this package because we want to replace xpbsmon by an ascii version named pbsmon. PBSQuery is also included in this package. This is a python module build on top of the pbs python module to simplify querying the batch server, eg: how many jobs, how many nodes, ...

homepage: https://oss.trac.surfsara.nl/pbs_python

version	versionsuffix	toolchain
4.6.0		system
4.6.0	-Python-2.7.11	intel/2016a
4.6.0	-Python-2.7.12	intel/2016b
4.6.0	-Python-2.7.13	intel/2017a

PBSuite

PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles.

homepage: https://sourceforge.net/p/pb-jelly/wiki/Home/

version	versionsuffix	toolchain
15.8.24	-Python-2.7.12	intel/2016b

PBZIP2

PBZIP2 is a parallel implementation of the bzip2 block-sorting file compressor that uses pthreads and achieves near-linear speedup on SMP machines. The output of this version is fully compatible with bzip2 v1.0.2 or newer (ie: anything compressed with pbzip2 can be decompressed with bzip2). PBZIP2 should work on any system that has a pthreads compatible C++ compiler (such as gcc). It has been tested on: Linux, Windows (cygwin & MinGW), Solaris, Tru64/OSF1, HP-UX, OS/2, OSX, and Irix.

homepage: http://compression.great-site.net/pbzip2

version	toolchain
1.1.13	GCCcore/12.3.0

PCAngsd

PCAngsd, which estimates the covariance matrix for low depth NGS data in an iterative procedure based on genotype likelihoods and is able to perform multiple population genetic analyses in heterogeneous populations.

homepage: http://www.popgen.dk/software/index.php/PCAngsd

version	versionsuffix	toolchain
0.97	-Python-2.7.14	foss/2018a

PCC

The compiler is based on the original Portable C Compiler by S. C. Johnson, written in the late 70's. About 50% of the frontend code and 80% of the backend code has been modified.

homepage: http://pcc.ludd.ltu.se/

version	toolchain
20131024	system

PCL

The Point Cloud Library (PCL) is a standalone, large scale, open project for 2D/3D image and point cloud processing.

homepage: http://pointclouds.org/

version	versionsuffix	toolchain
1.7.2	-Python-2.7.11	intel/2016a
1.8.1	-Python-2.7.14	intel/2017b

PCMSolver

An API for the Polarizable Continuum Model.

homepage: https://pcmsolver.readthedocs.org

version	versionsuffix	toolchain
1.1.4	-Python-2.7.11	intel/2016a
1.2.3		iimpi/2020b
1.2.3	-Python-3.6.6	foss/2018b
1.2.3	-Python-3.7.2	gompi/2019a
1.2.3	-Python-3.7.4	iimpi/2019b
20160205	-Python-2.7.11	intel/2016a

PCRaster

PCRaster Is a collection of software targeted at the development and deployment of spatio-temporal environmental models.

homepage: http://pcraster.geo.uu.nl/

version	versionsuffix	toolchain
4.1.0	-Python-2.7.14	intel/2017b

PCRE

The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.

homepage: https://www.pcre.org/

version	toolchain
8.38	foss/2016a, foss/2016b, gimkl/2.11.5, intel/2016a, intel/2016b
8.39	GCCcore/5.4.0, foss/2016b, intel/2016b
8.40	GCCcore/6.3.0, gimkl/2017a, intel/2016b, intel/2017a
8.41	GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.3.0
8.42	GCCcore/6.4.0
8.43	GCCcore/8.2.0, GCCcore/8.3.0
8.44	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/9.3.0
8.45	GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

PCRE2

The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.

homepage: https://www.pcre.org/

version	toolchain
10.21	foss/2016a
10.31	foss/2018b
10.33	GCCcore/8.2.0, GCCcore/8.3.0
10.34	GCCcore/9.3.0
10.35	GCCcore/10.2.0
10.36	GCCcore/10.3.0
10.37	GCCcore/11.2.0
10.40	GCCcore/11.3.0, GCCcore/12.2.0
10.42	GCCcore/12.3.0, GCCcore/13.2.0

PDM

A modern Python package and dependency manager supporting the latest PEP standards.

homepage: https://pdm-project.org

version	toolchain
2.12.4	GCCcore/12.3.0

pdsh

A high performance, parallel remote shell utility

homepage: https://github.com/chaos/pdsh

version	toolchain
2.34	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0

PDT

Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT implements a standard program representation, the program database (PDB), that can be accessed in a uniform way through a class library supporting common PDB operations.

homepage: https://www.cs.uoregon.edu/research/pdt/

version	toolchain
3.22	foss/2016a
3.25	GCCcore/10.2.0, GCCcore/8.2.0, GCCcore/8.3.0
3.25.1	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/9.3.0
3.25.2	GCCcore/13.2.0

peakdetect

Simple peak detection library for Python based on Billauer's work and this gist.

homepage: https://github.com/avhn/peakdetect

version	toolchain
1.2	foss/2022a

PEAR

PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.

homepage: http://sco.h-its.org/exelixis/web/software/pear/

version	toolchain
0.9.8	foss/2016b, intel/2016b
0.9.10	GCC/6.4.0-2.28, iccifort/2017.4.196-GCC-6.4.0-2.28
0.9.11	GCC/10.3.0, GCC/11.2.0, GCC/11.3.0, GCCcore/7.3.0, GCCcore/9.3.0, foss/2018a

PennCNV

A free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays.

homepage: https://penncnv.openbioinformatics.org/

version	toolchain
1.0.5	GCCcore/8.3.0

PEPT

A Python library that integrates all the tools necessary to perform research using Positron Emission Particle Tracking (PEPT). The library includes algorithms for the location, identification and tracking of particles, in addition to tools for visualisation and analysis, and utilities allowing the realistic simulation of PEPT data.

homepage: https://pept.readthedocs.io/en/latest/

version	toolchain
0.4.1	foss/2021a

Percolator

Semi-supervised learning for peptide identification from shotgun proteomics datasets

homepage: https://github.com/percolator/percolator

version	toolchain
3.4	gompi/2019a

Perl

Larry Wall's Practical Extraction and Report Language Includes a small selection of extra CPAN packages for core functionality.

homepage: https://www.perl.org/

version	versionsuffix	toolchain
5.20.1	-bare	GCC/4.8.2, GCC/4.9.2
5.20.2	-bare	GCC/4.9.2
5.20.3		foss/2016a, intel/2016a
5.22.0	-bare	GCC/4.9.2
5.22.1		foss/2016a, foss/2016b, intel/2016a
5.22.1	-bare	foss/2016a, intel/2016a
5.22.2		intel/2016a
5.24.0		GCC/5.4.0-2.26, GCCcore/4.9.3, GCCcore/5.4.0, foss/2016b, intel/2016b
5.24.0	-bare	foss/2016b
5.24.1		GCCcore/6.3.0, foss/2017a, intel/2017a
5.26.0		GCCcore/6.4.0, foss/2017b, intel/2017b, intel/2018.00, intel/2018.01
5.26.1		GCCcore/6.4.0, foss/2018a
5.26.1	-bare	foss/2018a
5.28.0		GCCcore/7.3.0
5.28.1		GCCcore/8.2.0
5.30.0		GCCcore/8.3.0
5.30.0	-minimal	GCCcore/8.3.0
5.30.2		GCCcore/9.3.0
5.30.2	-minimal	GCCcore/9.3.0
5.32.0		GCCcore/10.2.0
5.32.0	-minimal	GCCcore/10.2.0
5.32.1		FCC/4.5.0, GCCcore/10.3.0
5.32.1	-minimal	GCCcore/10.3.0
5.34.0		GCCcore/11.2.0
5.34.0	-minimal	GCCcore/11.2.0
5.34.1		GCCcore/11.3.0
5.34.1	-minimal	GCCcore/11.3.0
5.36.0		GCCcore/12.1.0, GCCcore/12.2.0
5.36.0	-minimal	GCCcore/12.2.0
5.36.1		GCCcore/12.3.0, GCCcore/13.1.0
5.38.0		GCCcore/13.2.0, system

perl-app-cpanminus

cpanm - get, unpack build and install modules from CPAN

homepage: https://github.com/miyagawa/cpanminus

version	toolchain
1.7039	system

Perl-bundle-CPAN

A set of common packages from CPAN

homepage: https://www.perl.org/

version	toolchain
5.36.1	GCCcore/12.3.0
5.38.0	GCCcore/13.2.0

Perl4-CoreLibs

Libraries historically supplied with Perl 4

homepage: https://metacpan.org/pod/Perl4::CoreLibs

version	versionsuffix	toolchain
0.003	-Perl-5.24.1	intel/2017a

Perseus

The Perseus software platform supports biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data.

homepage: https://maxquant.org/perseus

version	toolchain
2.0.7.0	GCCcore/11.2.0

PEST++

PEST++ is a software suite aimed at supporting complex numerical models in the decision-support context. Much focus has been devoted to supporting environmental models (groundwater, surface water, etc) but these tools are readily applicable to any computer model.

homepage: https://github.com/usgs/pestpp

version	toolchain
5.0.5	foss/2020a

PETSc

PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.

homepage: http://www.mcs.anl.gov/petsc

version	versionsuffix	toolchain
3.7.2	-Python-2.7.11	intel/2016a
3.7.3	-Python-2.7.11	foss/2016a
3.7.5	-downloaded-deps	intel/2016b
3.8.3	-downloaded-deps	foss/2017b
3.9.1	-downloaded-deps	foss/2018a
3.9.3		foss/2018a, intel/2018a
3.11.0	-downloaded-deps	foss/2018b
3.11.1	-Python-3.7.2	foss/2019a, intel/2019a
3.12.4	-Python-2.7.16	intel/2019b
3.12.4	-Python-3.7.4	foss/2019b, intel/2019b
3.12.4	-Python-3.8.2	foss/2020a, intel/2020a
3.14.4		foss/2020b, intel/2020b
3.15.1		foss/2021a, intel/2021a
3.17.4		foss/2022a
3.18.4		intel/2021b
3.19.2		foss/2022b
3.20.3		foss/2023a

petsc4py

petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation.

homepage: https://bitbucket.org/petsc/petsc4py

version	versionsuffix	toolchain
3.9.1	-Python-3.6.4	foss/2018a
3.12.0	-Python-3.7.4	foss/2019b
3.15.0		foss/2021a

PfamScan

PfamScan is used to search a FASTA sequence against a library of Pfam HMM.

homepage: https://www.ebi.ac.uk/seqdb/confluence/display/THD/PfamScan

version	toolchain
1.6	gompi/2022a

PFFT

PFFT is a software library for computing massively parallel, fast Fourier transformations on distributed memory architectures. PFFT can be understood as a generalization of FFTW-MPI to multidimensional data decomposition. The library is written in C and MPI. A Fortran interface is also available. Support for hybrid parallelization based on OpenMP and MPI is under development.

homepage: https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software.php.en#pfft

version	toolchain
20181230	gompi/2022a

pfind

Drop-in replacement for find, implemented for using parallel access and MPI.

homepage: https://github.com/VI4IO/pfind

version	toolchain
20220613	gompi/2021b

pftoolsV3

A suite of tools to build and search generalized profiles (protein and DNA).

homepage: https://github.com/sib-swiss/pftools3

version	toolchain
3.2.11	GCCcore/10.3.0, foss/2021a
3.2.12	GCCcore/11.2.0, GCCcore/11.3.0
20160324	foss/2016a

pFUnit

pFUnit is a unit testing framework enabling JUnit-like testing of serial and MPI-parallel software written in Fortran.

homepage: https://github.com/Goddard-Fortran-Ecosystem/pFUnit

version	toolchain
3.2.9	gompi/2018b
4.2.0	gompi/2020b, iimpi/2021a
4.7.3	gompi/2022a

PGDSpider

An automated data conversion tool for connecting population genetics and genomics programs

homepage: http://cmpg.unibe.ch/software/PGDSpider/

version	versionsuffix	toolchain
2.1.0.3	-Java-1.7.0_80	system

PGI

C, C++ and Fortran compilers from The Portland Group - PGI

homepage: https://www.pgroup.com/

version	versionsuffix	toolchain
15.7	-GNU-4.9.2-2.25	system
15.7	-GNU-4.9.3-2.25	system
15.10	-GCC-4.9.3-2.25	system
16.1	-CDK-GCC-4.9.2-2.25	system
16.3	-GCC-4.9.3-2.25	system
16.4	-GCC-5.3.0-2.26	system
16.7	-GCC-5.4.0-2.26	system
16.10	-GCC-5.4.0-2.26	system
17.1	-GCC-6.3.0-2.27	system
17.3	-GCC-6.3.0-2.28	system
17.4	-GCC-6.4.0-2.28	system
17.10	-GCC-6.4.0-2.28	system
18.1	-GCC-7.2.0-2.29	system
18.4	-GCC-6.4.0-2.28	system
18.7	-GCC-7.3.0-2.30	system
18.10	-GCC-6.4.0-2.28	system
19.1	-GCC-8.2.0-2.31.1	system
19.4	-GCC-8.2.0-2.31.1	system
19.7	-GCC-8.3.0-2.32	system
19.10	-GCC-8.3.0-2.32	system

PGPLOT

The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs. It is intended for making graphical images of publication quality with minimum effort on the part of the user. For most applications, the program can be device-independent, and the output can be directed to the appropriate device at run time.

homepage: https://sites.astro.caltech.edu/~tjp/pgplot/

version	toolchain
5.2.2	GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/13.2.0

PHANOTATE

PHANOTATE: a tool to annotate phage genomes

homepage: https://github.com/deprekate/PHANOTATE

version	toolchain
20190724	foss/2018b

Phantompeakqualtools

It computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data.

homepage: https://github.com/kundajelab/phantompeakqualtools

version	toolchain
1.2.2	foss/2021b

PHASE

The program PHASE implements a Bayesian statistical method for reconstructing haplotypes from population genotype data. Documentation: http://stephenslab.uchicago.edu/assets/software/phase/instruct2.1.pdf

homepage: http://stephenslab.uchicago.edu/phase/download.html

version	toolchain
2.1.1	system

PHAST

PHAST is a freely available software package for comparative and evolutionary genomics.

homepage: http://compgen.cshl.edu/phast/

version	toolchain
1.4	intel/2017a
1.5	GCC/6.4.0-2.28, iccifort/2017.4.196-GCC-6.4.0-2.28

Phenoflow

R package offering functionality for the advanced analysis of microbial flow cytometry data

homepage: https://github.com/rprops/Phenoflow_package

version	versionsuffix	toolchain
1.1.2-20200917	-R-4.2.1	foss/2022a

PheWAS

Provides an accessible R interface to the phenome wide association study.

homepage: https://www.vumc.org/cpm/center-precision-medicine-blog/phewas-r-package

version	versionsuffix	toolchain
0.12	-R-3.3.3	foss/2016b, intel/2016b
0.99.5-2	-R-3.6.0	foss/2019a, intel/2019a

PheWeb

A tool for building PheWAS websites from association files

homepage: https://github.com/statgen/pheweb

version	versionsuffix	toolchain
1.1.20	-Python-3.7.4	foss/2019b

Philosopher

Philosopher is a fast, easy-to-use, scalable, and versatile data analysis software for mass spectrometry-based proteomics. Philosopher is dependency-free and can analyze both traditional database searches and open searches for post-translational modification (PTM) discovery.

homepage: https://philosopher.nesvilab.org/

version	toolchain
5.0.0	GCC/11.3.0

PhiPack

The PhiPack software package implements (in C) a few tests for recombination and can produce refined incompatibility matrices as well.

homepage: http://www.maths.otago.ac.nz/~dbryant/software.html

version	toolchain
2016.06.14	iccifort/2019.1.144-GCC-8.2.0-2.31.1

PHLAT

PHLAT is a bioinformatics algorithm that offers HLA typing at four-digit resolution (or higher) using genome-wide transcriptome and exome sequencing data over a wide range of read lengths and sequencing depths.

homepage: https://sites.google.com/site/phlatfortype/

version	versionsuffix	toolchain
1.1	-Python-2.7.15	foss/2018b

phonemizer

The phonemizer allows simple phonemization of words and texts in many languages. Provides both the phonemize command-line tool and the Python function phonemizer.phonemize. It is using four backends: espeak, espeak-mbrola, festival and segments.

homepage: https://github.com/bootphon/phonemizer

version	versionsuffix	toolchain
2.2.1	-Python-3.8.2	gompi/2020a
3.2.1		gfbf/2023a

phono3py

A simulation package of phonon-phonon interaction related properties.

homepage: http://phonopy.github.io/phono3py/

version	versionsuffix	toolchain
1.12.5.35	-Python-2.7.14	intel/2017b
1.12.7.55	-Python-2.7.14	foss/2018a, intel/2018a
2.7.0		foss/2023a

phonopy

Phonopy is an open source package of phonon calculations based on the supercell approach.

homepage: https://atztogo.github.io/phonopy/

version	versionsuffix	toolchain
1.10.1	-Python-2.7.11	intel/2016a
1.12.2.20	-Python-2.7.14	intel/2017b
1.12.6.66	-Python-2.7.14	foss/2018a, intel/2018a
1.13.0.64	-Python-2.7.14	intel/2018a
1.14.2	-Python-2.7.15	intel/2018b
2.0.0	-Python-2.7.14	intel/2018a
2.2.0	-Python-3.7.2	intel/2019a
2.7.1	-Python-3.7.4	intel/2019b
2.7.1	-Python-3.8.2	intel/2020a
2.12.0		foss/2020b
2.16.3		foss/2022a
2.20.0		foss/2023a

photontorch

Photontorch is a photonic simulator for highly parallel simulation and optimization of photonic circuits in time and frequency domain. Photontorch features CUDA enabled simulation and optimization of photonic circuits. It leverages the deep learning framework PyTorch to view the photonic circuit as essentially a recurrent neural network. This enables the use of native PyTorch optimizers to optimize the (physical) parameters of the circuit.

homepage: https://docs.photontorch.com/

version	toolchain
0.4.1	foss/2020b, foss/2022a, fosscuda/2020b

phototonic

Phototonic is an image viewer and organizer

homepage: https://github.com/oferkv/phototonic

version	toolchain
2.1	GCCcore/10.3.0

PHYLIP

PHYLIP is a free package of programs for inferring phylogenies.

homepage: http://evolution.genetics.washington.edu/phylip

version	toolchain
3.696	foss/2016a, intel/2016a
3.697	GCC/12.3.0, GCC/6.4.0-2.28, GCC/9.3.0, iccifort/2017.4.196-GCC-6.4.0-2.28

PhyloBayes-MPI

A Bayesian software for phylogenetic reconstruction using mixture models

homepage: https://github.com/bayesiancook/pbmpi

version	toolchain
20161021	intel/2016b

phylokit

C++ library for high performance phylogenetics

homepage: https://github.com/pranjalv123/phylokit

version	toolchain
1.0	GCC/8.2.0-2.31.1

phylonaut

Dynamic programming for phylogenetics applications

homepage: https://github.com/pranjalv123/phylonaut

version	toolchain
20190626	gompi/2019a

PhyloPhlAn

PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method for large-scale microbial genome characterization and phylogenetic analysis at multiple levels of resolution.

homepage: https://github.com/biobakery/phylophlan

version	versionsuffix	toolchain
3.0	-Python-3.8.2	foss/2020a
3.0.2		foss/2021a
3.0.3		foss/2022a

phyluce

phyluce is a software package for working with data generated from sequence capture of UCE (ultra-conserved element) loci, as first published in [BCF2012]. Specifically, phyluce is a suite of programs to: 1) assemble raw sequence reads from Illumina platforms into contigs 2) determine which contigs represent UCE loci 3) filter potentially paralagous UCE loci 4) generate different sets of UCE loci across taxa of interest

homepage: https://github.com/faircloth-lab/phyluce

version	toolchain
1.7.3	foss/2023a

PhyML

Phylogenetic estimation using (Maximum) Likelihood

homepage: https://github.com/stephaneguindon/phyml

version	toolchain
3.3.20190321	foss/2018b
3.3.20200621	foss/2020b

phyx

phyx performs phylogenetics analyses on trees and sequences.

homepage: https://github.com/FePhyFoFum/phyx

version	toolchain
1.01	foss/2019a
1.3	foss/2022a

picard

A set of tools (in Java) for working with next generation sequencing data in the BAM format.

homepage: https://broadinstitute.github.io/picard/

version	versionsuffix	toolchain
1.39		system
1.100		system
1.109		system
1.119		system
1.119	-Java-1.7.0_80	system
1.120	-Java-1.8.0_66	system
1.141	-Java-1.8.0_74	system
2.0.1	-Java-1.8.0_66	system
2.1.0		system
2.1.0	-Java-1.8.0_74	system
2.1.1	-Java-1.8.0_112	system
2.1.1	-Java-1.8.0_74	system
2.2.4	-Java-1.8.0_92	system
2.6.0	-Java-1.8.0_131	system
2.10.1	-Java-1.8.0_131	system
2.18.5	-Java-1.8.0_162	system
2.18.11	-Java-1.8.0_162	system
2.18.14	-Java-1.8	system
2.18.17	-Java-1.8	system
2.18.27	-Java-1.8	system
2.20.6	-Java-1.8	system
2.21.1	-Java-11	system
2.21.6	-Java-11	system
2.22.1	-Java-11	system
2.25.0	-Java-11	system
2.25.1	-Java-11	system
2.25.5	-Java-13	system
2.26.10	-Java-15	system
3.0.0	-Java-17	system

PICI-LIGGGHTS

UoB Positron Imaging Centre's Improved LIGGGHTS distribution with an emphasis on the Python interface.

homepage: https://github.com/uob-positron-imaging-centre/PICI-LIGGGHTS

version	toolchain
3.8.1	foss/2022a

PICRUSt2

PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.

homepage: https://github.com/picrust/picrust2

version	toolchain
2.5.2	foss/2022a, foss/2022b

pigz

pigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries.

homepage: https://zlib.net/pigz/

version	toolchain
2.3.3	foss/2016b
2.3.4	GCCcore/6.4.0
2.4	GCCcore/10.2.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0, foss/2018a
2.6	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0
2.7	GCCcore/11.3.0, GCCcore/12.2.0
2.8	GCCcore/12.3.0

PIL

The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. This library supports many file formats, and provides powerful image processing and graphics capabilities.

homepage: http://www.pythonware.com/products/pil

version	versionsuffix	toolchain
1.1.7	-Python-2.7.11	intel/2016a
1.1.7	-Python-2.7.11-freetype-2.6.3	intel/2016a
1.1.7	-Python-2.7.12	foss/2016b, intel/2016b
1.1.7	-Python-2.7.13	intel/2017a
1.1.7	-Python-2.7.15	foss/2019a

PileOMeth

PileOMeth processes a coordinate-sorted and indexed BAM or CRAM file containing some form of BS-seq alignments. PileOMeth extracts per-base methylation metrics from them. PileOMeth requires an indexed fasta file containing the reference genome as well.

homepage: https://github.com/dpryan79/PileOMeth

version	toolchain
0.1.11	foss/2016b

Pillow

Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.

homepage: https://pillow.readthedocs.org/

version	versionsuffix	toolchain
3.2.0	-Python-2.7.11	intel/2016a
3.2.0	-Python-2.7.11-freetype-2.6.3	foss/2016a, intel/2016a
3.4.2	-Python-2.7.12	intel/2016b
3.4.2	-Python-3.5.2	foss/2016b, intel/2016b
3.4.2	-Python-3.5.2-freetype-2.6.5	intel/2016b
4.1.0	-Python-2.7.13	intel/2017a
4.1.1	-Python-3.6.1	intel/2017a
4.2.1	-Python-3.6.1	intel/2017a
4.3.0	-Python-2.7.13	intel/2017a
4.3.0	-Python-2.7.14	intel/2017b
4.3.0	-Python-3.6.3	foss/2017b
5.0.0	-Python-2.7.14	foss/2017b, intel/2017b, intel/2018a
5.0.0	-Python-3.6.3	foss/2017b, intel/2017b
5.0.0	-Python-3.6.4	foss/2018a, intel/2018a
5.3.0	-Python-2.7.15	foss/2018b
5.3.0	-Python-3.6.6	foss/2018b, fosscuda/2018b, intel/2018b
6.0.0		GCCcore/8.2.0
6.2.1		GCCcore/8.3.0
6.2.2	-Python-2.7.18	foss/2020b
7.0.0	-Python-3.8.2	GCCcore/9.3.0
8.0.1		GCCcore/10.2.0
8.2.0		GCCcore/10.3.0
8.3.1		GCCcore/11.2.0
8.3.2		GCCcore/11.2.0
9.1.0		GCCcore/10.3.0
9.1.1		GCCcore/11.2.0, GCCcore/11.3.0
9.2.0		GCCcore/10.2.0
9.4.0		GCCcore/12.2.0
10.0.0		GCCcore/12.3.0
10.2.0		GCCcore/13.2.0

Pillow-SIMD

Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.

homepage: https://github.com/uploadcare/pillow-simd

version	versionsuffix	toolchain
5.0.0	-Python-3.6.4	foss/2018a, intel/2018a
5.3.0.post0	-Python-3.6.6	foss/2018b, fosscuda/2018b, intel/2018b
6.0.x.post0		GCCcore/8.2.0, GCCcore/8.3.0
7.1.2		GCCcore/10.2.0
7.1.2	-Python-3.8.2	GCCcore/9.3.0
8.2.0		GCCcore/10.3.0
8.3.1		GCCcore/11.2.0
8.3.2		GCCcore/11.2.0
9.2.0		GCCcore/11.3.0
9.5.0		GCCcore/12.2.0, GCCcore/12.3.0

Pilon

Pilon is an automated genome assembly improvement and variant detection tool

homepage: https://github.com/broadinstitute/pilon

version	versionsuffix	toolchain
1.22	-Java-1.8	system
1.22	-Java-1.8.0_162	system
1.23	-Java-1.8	system
1.23	-Java-11	system

PIMS

PIMS is a lazy-loading interface to sequential data with numpy-like slicing.

homepage: https://soft-matter.github.io/pims

version	versionsuffix	toolchain
0.4.1	-Python-2.7.14	intel/2017b

Pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

homepage: http://gmt.genome.wustl.edu/packages/pindel/

version	toolchain
0.2.5b8	foss/2016b
0.2.5b9-20170508	GCC/11.2.0, GCC/11.3.0, GCC/6.4.0-2.28

Pingouin

Pingouin is an open-source statistical package written in Python 3 and based mostly on Pandas and NumPy.

homepage: https://pingouin-stats.org/

version	versionsuffix	toolchain
0.3.8	-Python-3.7.4	foss/2019b

Pint

Pint is a Python package to define, operate and manipulate physical quantities: the product of a numerical value and a unit of measurement. It allows arithmetic operations between them and conversions from and to different units.

homepage: https://github.com/hgrecco/pint

version	versionsuffix	toolchain
0.14	-Python-3.7.4	GCCcore/8.3.0
0.19.2		GCCcore/11.2.0
0.20.1		GCCcore/10.3.0
0.22		GCCcore/11.3.0
0.23		GCCcore/12.3.0

pip

The PyPA recommended tool for installing Python packages.

homepage: https://pip.pypa.io

version	versionsuffix	toolchain
8.0.2	-Python-2.7.11	intel/2016a
8.1.2	-Python-2.7.11	foss/2016a
8.1.2	-Python-2.7.12	foss/2016b, intel/2016b

PIPITS

An automated pipeline for analyses of fungal internal transcribed spacer (ITS) sequences from the Illumina sequencing platform.

homepage: https://github.com/hsgweon/pipits

version	versionsuffix	toolchain
2.7	-Python-3.8.2	foss/2020a
2.8		foss/2021a
3.0		foss/2021a, foss/2022a

PIRATE

A toolbox for pangenome analysis and threshold evaluation.

homepage: https://github.com/SionBayliss/PIRATE

version	versionsuffix	toolchain
1.0.5	-R-4.2.1	foss/2022a

pIRS

pIRS (profile based Illumina pair-end Reads Simulator) is a program for simulating paired-end reads from a reference genome. It is optimized for simulating reads similar to those generated from the Illumina platform.

homepage: https://github.com/galaxy001/pirs

version	toolchain
2.0.2	gompi/2019b

Pisces

Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.

homepage: https://github.com/Illumina/Pisces

version	toolchain
5.2.7.47	GCCcore/6.4.0

piSvM

piSvM is a parallel implementation of the Support Vector Machine (SVM) algorithm that allows efficient training and testing on a multiprocessor system.

homepage: http://pisvm.sourceforge.net/

version	toolchain
1.3	intel/2017b

piSvM-JSC

piSvM is a parallel implementation of the Support Vector Machine (SVM) algorithm that allows efficient training and testing on a multiprocessor system. This version is a fork of the original PiSvM to increase scalability.

homepage: https://github.com/mricherzhagen/pisvm

version	toolchain
1.2-20150622	intel/2017b

pixman

Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.

homepage: http://www.pixman.org/

version	toolchain
0.34.0	GCCcore/5.4.0, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.3.0, foss/2016a, foss/2016b, intel/2016a, intel/2016b
0.38.0	GCCcore/8.2.0
0.38.4	GCCcore/8.3.0, GCCcore/9.3.0
0.40.0	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0
0.42.2	GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

pizzly

Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples.

homepage: https://github.com/pmelsted/pizzly

version	toolchain
0.37.3	foss/2018b

pkg-config

pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c pkg-config --libs --cflags glib-2.0 for instance, rather than hard-coding values on where to find glib (or other libraries).

homepage: http://www.freedesktop.org/wiki/Software/pkg-config/

version	toolchain
0.28	GCC/4.8.2, GCC/4.9.2, GNU/4.9.3-2.25
0.29	foss/2016a, gimkl/2.11.5, intel/2016a
0.29.1	GCCcore/4.9.3, GCCcore/5.4.0, GCCcore/6.3.0, foss/2016a, foss/2016b, foss/2017a, gimkl/2017a, intel/2016a, intel/2016b, intel/2017a
0.29.2	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0, intel/2017a, system

pkgconf

pkgconf is a program which helps to configure compiler and linker flags for development libraries. It is similar to pkg-config from freedesktop.org.

homepage: https://github.com/pkgconf/pkgconf

version	toolchain
1.8.0	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, system
1.9.3	GCCcore/12.2.0
1.9.4	GCCcore/13.1.0
1.9.5	GCCcore/12.3.0
2.0.3	GCCcore/13.2.0

pkgconfig

pkgconfig is a Python module to interface with the pkg-config command line tool

homepage: https://github.com/matze/pkgconfig

version	versionsuffix	toolchain
1.1.0	-Python-2.7.11	foss/2016a, intel/2016a
1.1.0	-Python-2.7.12	foss/2016b, intel/2016b
1.1.0	-Python-3.5.1	foss/2016a
1.1.0	-Python-3.5.2	foss/2016b, intel/2016b
1.2.2	-Python-2.7.13	foss/2017a, intel/2017a
1.2.2	-Python-2.7.14	foss/2017b, fosscuda/2017b, intel/2017b
1.2.2	-Python-3.6.1	foss/2017a, intel/2017a
1.2.2	-Python-3.6.3	foss/2017b, fosscuda/2017b, intel/2017b
1.3.1	-Python-2.7.14	foss/2018a, intel/2018a
1.3.1	-Python-2.7.15	foss/2018b, fosscuda/2018b, intel/2018b
1.3.1	-Python-3.6.4	foss/2018a, intel/2018a
1.3.1	-Python-3.6.6	foss/2018b, fosscuda/2018b, intel/2018b
1.5.1	-Python-3.7.4	GCCcore/8.3.0
1.5.1	-Python-3.8.2	GCCcore/9.3.0
1.5.1	-python	GCCcore/10.2.0, GCCcore/8.2.0
1.5.4	-python	GCCcore/10.3.0
1.5.5	-python	GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

PLAMS

The Python Library for Automating Molecular Simulation (PLAMS) is powerful and flexible Python tool interfaced to the Amsterdam Modeling Suite engines ADF, BAND, DFTB, MOPAC, ReaxFF, and UFF.

homepage: https://www.scm.com/product/plams

version	toolchain
1.5.1	intel/2022a

plantcv

PlantCV: Plant phenotyping using computer vision.

homepage: https://pypi.org/project/plantcv/

version	versionsuffix	toolchain
3.8.0	-Python-3.8.2	foss/2020a

PlaScope

Plasmid exploration of bacterial genomes

homepage: https://github.com/GuilhemRoyer/PlaScope

version	toolchain
1.3.1	foss/2018b

PlasmaPy

Open source Python ecosystem for plasma research and education

homepage: https://www.plasmapy.org

version	versionsuffix	toolchain
0.3.1	-Python-3.8.2	foss/2020a

PLAST

PLAST is a parallel alignment search tool for comparing large protein banks

homepage: http://www.irisa.fr/symbiose/projects/plast/

version	versionsuffix	toolchain
2.3.1	-Java-1.8.0_92	foss/2016a

Platanus

PLATform for Assembling NUcleotide Sequences

homepage: http://platanus.bio.titech.ac.jp/

version	versionsuffix	toolchain
1.2.1	-linux-x86_64	system
1.2.4		foss/2017a

Platypus

Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data.

homepage: http://www.well.ox.ac.uk/platypus

version	versionsuffix	toolchain
0.8.1	-Python-2.7.11	intel/2016a

Platypus-Opt

Platypus is a framework for evolutionary computing in Python with a focus on multiobjective evolutionary algorithms (MOEAs).

homepage: https://github.com/Project-Platypus/Platypus

version	toolchain
1.1.0	foss/2022a

plc

plc is the public Planck Likelihood Code. It provides C and Fortran libraries that allow users to compute the log likelihoods of the temperature, polarization, and lensing maps. Optionally, it also provides a python version of this library, as well as tools to modify the predetermined options for some likelihoods (e.g. changing the high-ell and low-ell lmin and lmax values of the temperature).

homepage: http://pla.esac.esa.int/pla/#home

version	versionsuffix	toolchain
3.0.1	-Python-2.7.15	foss/2019a, intel/2018b
3.0.1	-Python-3.7.4	foss/2019b

PLINK

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

homepage: https://www.cog-genomics.org/plink/2.0/

version	toolchain
1.07	foss/2016a, foss/2016b
1.07-x86_64	system
1.9b5	golf/2020a
1.9b_4.1-x86_64	system
1.9b_6.17-x86_64	system
1.9b_6.21-x86_64	system
2.00-alpha1-x86_64	system
2.00-alpha2-x86_64	system
2.00-alpha2-x86_64_avx2	system
2.00a2.3	GCC/10.3.0, GCC/11.2.0
2.00a2.3_x86_64	system
2.00a3.1	GCC/11.2.0
2.00a3.6	GCC/11.3.0
2.00a3.7	foss/2022a, gfbf/2023a

plinkliftover

PLINKLiftOver is a utility enabling liftOver to work on genomics files from PLINK, allowing one to update the coordinates from one genome reference version to another.

homepage: https://github.com/milescsmith/plinkliftover

version	toolchain
0.3.0	foss/2022b

plinkQC

plinkQC is a R/CRAN package for genotype quality control in genetic association studies. It makes PLINK basic statistics (e.g.missing genotyping rates per individual, allele frequencies per genetic marker) and relationship functions easily accessible from within R and allows for automatic evaluation of the results.

homepage: https://meyer-lab-cshl.github.io/plinkQC/

version	versionsuffix	toolchain
0.3.3	-R-4.0.0	foss/2020a

PLINKSEQ

PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing and genotyping projects, particularly whole-exome and whole-genome studies. It is independent of (but designed to be complementary to) the existing PLINK package.

homepage: https://atgu.mgh.harvard.edu/plinkseq/

version	toolchain
0.10	GCC/6.4.0-2.28, iccifort/2017.4.196-GCC-6.4.0-2.28

plot1cell

plot1cell: a package for advanced single cell data visualization

homepage: https://github.com/HaojiaWu/plot1cell

version	versionsuffix	toolchain
0.0.1	-R-4.2.1	foss/2022a
0.0.1	-R-4.2.2	foss/2022b

Ploticus

Ploticus is a free GPL software utility that can produce various types of plots and graphs

homepage: http://ploticus.sourceforge.net/doc/welcome.html

version	toolchain
2.42	GCCcore/7.3.0

plotly

Easily translate 'ggplot2' graphs to an interactive web-based version and/or create custom web-based visualizations directly from R.

homepage: https://cran.r-project.org/web/packages/plotly

version	versionsuffix	toolchain
4.7.1	-R-3.4.0	intel/2017a
4.8.0	-R-3.4.4	intel/2018a

plotly-orca

Orca is an Electron app that generates images and reports of Plotly things like plotly.js graphs, dash apps, dashboards from the command line.

homepage: https://github.com/plotly/orca

version	toolchain
1.3.0	GCCcore/8.3.0
1.3.1	GCCcore/10.2.0, GCCcore/9.3.0

plotly.py

An open-source, interactive graphing library for Python

homepage: https://plot.ly/python

version	toolchain
4.1.0	intel/2019a
4.4.1	intel/2019b
4.8.1	GCCcore/9.3.0
4.14.3	GCCcore/10.2.0, GCCcore/10.3.0
5.1.0	GCCcore/10.3.0
5.4.0	GCCcore/11.2.0
5.12.0	GCCcore/11.3.0
5.13.1	GCCcore/12.2.0
5.16.0	GCCcore/12.3.0
5.18.0	GCCcore/13.2.0

plotutils

The GNU plotutils package contains software for both programmers and technical users. Its centerpiece is libplot, a powerful C/C++ function library for exporting 2-D vector graphics in many file formats, both vector and bitmap. On the X Window System, it can also do 2-D vector graphics animations. libplot is device-independent, in the sense that its API (application programming interface) does not depend on the type of graphics file to be exported. A Postscript-like API is used both for file export and for graphics animations. A libplot programmer needs to learn only one API: not the details of many graphics file formats.

homepage: https://www.gnu.org/software/plotutils/

version	toolchain
2.6	GCC/11.3.0

PLplot

PLplot is a cross-platform software package for creating scientific plots whose (UTF-8) plot symbols and text are limited in practice only by what Unicode-aware system fonts are installed on a user's computer.

homepage: http://plplot.sourceforge.net

version	versionsuffix	toolchain
5.11.1	-Java-1.7.0_80-Python-2.7.11	foss/2016a
5.11.1	-Java-1.7.0_80-Python-2.7.12	intel/2016b

PLUMED

PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.

homepage: https://www.plumed.org

version	versionsuffix	toolchain
2.2.2		intel/2016a
2.2.3		foss/2016b, intel/2016b
2.3.0		foss/2016b, foss/2017a, intel/2016b
2.3.4		intel/2017b
2.4.0		foss/2018a, intel/2017b, intel/2018a
2.4.0	-PathCV	intel/2018a
2.4.1		iomkl/2018a
2.4.2		foss/2018b, intel/2018b
2.5.0		intel/2018b
2.5.0	-Python-2.7.15	foss/2018b, fosscuda/2018b
2.5.1		foss/2019a, intel/2018b
2.5.1	-PathCV	intel/2018b
2.5.2	-Python-3.7.2	intel/2019a
2.5.3	-Python-3.7.4	foss/2019b, intel/2019b
2.5.4	-Python-3.7.4	foss/2019b, fosscuda/2019b
2.5b	-Python-2.7.14	intel/2018a
2.6.0	-Python-3.8.2	foss/2020a, intel/2020a
2.6.2		foss/2020b, intel/2020b
2.7.0		foss/2020b
2.7.2		foss/2021a, intel/2021a
2.7.3		foss/2021b
2.8.0		foss/2021b
2.8.1		foss/2022a
2.9.0		foss/2022b, foss/2023a

PLY

PLY is yet another implementation of lex and yacc for Python.

homepage: http://www.dabeaz.com/ply/

version	versionsuffix	toolchain
3.11		GCCcore/12.2.0, GCCcore/12.3.0
3.11	-Python-3.6.4	foss/2018a
3.11	-Python-3.7.4	GCCcore/8.3.0

PMIx

Process Management for Exascale Environments PMI Exascale (PMIx) represents an attempt to provide an extended version of the PMI standard specifically designed to support clusters up to and including exascale sizes. The overall objective of the project is not to branch the existing pseudo-standard definitions - in fact, PMIx fully supports both of the existing PMI-1 and PMI-2 APIs - but rather to (a) augment and extend those APIs to eliminate some current restrictions that impact scalability, and (b) provide a reference implementation of the PMI-server that demonstrates the desired level of scalability.

homepage: https://pmix.org/

version	toolchain
1.2.5	GCCcore/6.4.0
2.1.3	GCCcore/7.2.0, GCCcore/7.3.0
2.2.1	GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/8.2.0
2.2.3	GCCcore/7.2.0, GCCcore/7.3.0
3.0.1	GCCcore/6.4.0, GCCcore/7.3.0
3.0.2	GCCcore/8.2.0, GCCcore/8.3.0
3.1.1	GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0
3.1.4	GCCcore/8.3.0
3.1.5	GCCcore/10.2.0, GCCcore/9.3.0
3.2.3	GCCcore/10.3.0
4.1.0	GCCcore/11.2.0
4.1.2	GCCcore/11.3.0
4.2.2	GCCcore/12.2.0
4.2.4	GCCcore/12.3.0
4.2.6	GCCcore/13.2.0

pmt

PMT is a high-level software library capable of collecting power consumption measurements on various hardware.

homepage: https://git.astron.nl/RD/pmt

version	versionsuffix	toolchain
1.1.0		GCCcore/11.3.0
1.2.0		GCCcore/11.3.0, GCCcore/12.3.0
1.2.0	-CUDA-11.7.0	GCCcore/11.3.0
1.2.0	-CUDA-12.1.1	GCCcore/12.3.0

pmx

pmx (formerly pymacs) is a small bunch of classes to read structure files such as pdb or gro and trajectory data in gromacs xtc format. Over the years it has been extended towards a versatile (bio-) molecular structure manipulation package with some additional functionalities, e.g. gromacs file parsers and scripts for setup and analysis of free energy calculations.

homepage: https://github.com/deGrootLab/pmx

version	versionsuffix	toolchain
2.0	-Python-2.7.18	foss/2020b

PnetCDF

Parallel netCDF: A Parallel I/O Library for NetCDF File Access

homepage: https://trac.mcs.anl.gov/projects/parallel-netcdf

version	toolchain
1.8.1	intel/2017a
1.9.0	intel/2018a
1.10.0	foss/2018b, intel/2018b
1.12.1	gompi/2019b, gompi/2020a, gompic/2019b, gompic/2020a, iimpi/2020a
1.12.2	gompi/2020b, gompi/2021a, gompic/2020b, iimpi/2021a
1.12.3	gompi/2021b, gompi/2022a, gompi/2023a, iimpi/2022a

pocl

PoCL is a portable open source (MIT-licensed) implementation of the OpenCL standard (1.2 with some 2.0 features supported).

homepage: http://portablecl.org

version	versionsuffix	toolchain
1.2		GCC/7.3.0-2.30
1.3		GCC/8.2.0-2.31.1, gcccuda/2019a
1.4		GCC/8.3.0, gcccuda/2019b
1.5		GCC/9.3.0
1.6		GCC/10.2.0, gcccuda/2020b, iccifort/2020.4.304
1.8		GCC/10.3.0, GCC/11.2.0, GCC/11.3.0
1.8	-CUDA-11.7.0	GCC/11.3.0
4.0		GCC/12.3.0
4.0	-CUDA-12.1.1	GCC/12.3.0

pod5-file-format

POD5 is a file format for storing nanopore dna data in an easily accessible way. The format is able to be written in a streaming manner which allows a sequencing instrument to directly write the format.

homepage: https://github.com/nanoporetech/pod5-file-format

version	toolchain
0.1.8	foss/2022a

poetry

Python packaging and dependency management made easy. Poetry helps you declare, manage and install dependencies of Python projects, ensuring you have the right stack everywhere.

homepage: https://python-poetry.org

version	versionsuffix	toolchain
1.0.9	-Python-3.8.2	GCCcore/9.3.0
1.2.2		GCCcore/11.3.0
1.5.1		GCCcore/12.3.0
1.6.1		GCCcore/13.2.0
1.7.1		GCCcore/12.3.0

polars

Lightning-fast DataFrame library for Rust and Python.

homepage: https://pola.rs/

version	toolchain
0.15.6	foss/2022a

polymake

polymake is open source software for research in polyhedral geometry. It deals with polytopes, polyhedra and fans as well as simplicial complexes, matroids, graphs, tropical hypersurfaces, and other objects.

homepage: https://polymake.org

version	toolchain
4.0r1	foss/2019b
4.8	foss/2021b, gfbf/2022a

pomkl

Toolchain with PGI C, C++ and Fortran compilers, alongside Intel MKL & OpenMPI.

homepage: http://www.pgroup.com/index.htm

version	toolchain
2016.03	system
2016.04	system
2016.09	system

pompi

Toolchain with PGI C, C++ and Fortran compilers, alongside OpenMPI.

homepage: http://www.pgroup.com/index.htm

version	toolchain
2016.03	system
2016.04	system
2016.09	system

poppler

Poppler is a PDF rendering library

homepage: https://poppler.freedesktop.org

version	toolchain
0.70.1	foss/2018b
0.90.1	GCCcore/8.3.0
21.06.1	GCC/10.2.0, GCC/10.3.0
22.01.0	GCC/11.2.0
22.12.0	GCC/11.3.0
23.09.0	GCC/12.3.0

poppunk

PopPUNK is a tool for clustering genomes. We refer to the clusters as variable-length-k-mer clusters, or VLKCs. Biologically, these clusters typically represent distinct strains. We refer to subclusters of strains as lineages.

homepage: https://poppunk.readthedocs.io

version	toolchain
2.6.0	foss/2022a

popscle

A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools

homepage: https://github.com/statgen/popscle

version	toolchain
0.1-beta	foss/2019b
0.1-beta-20210505	GCC/11.3.0

popt

Popt is a C library for parsing command line parameters.

homepage: http://freecode.com/projects/popt

version	toolchain
1.14	GCC/4.8.2
1.16	GCC/10.2.0, GCC/4.9.2, system

Porechop

Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity

homepage: https://github.com/rrwick/Porechop

version	versionsuffix	toolchain
0.2.3	-Python-3.5.2	foss/2016b
0.2.4		GCCcore/10.3.0, GCCcore/11.2.0
0.2.4	-Python-3.6.6	foss/2018b
0.2.4	-Python-3.7.4	intel/2019b

porefoam

Direct pore-scale simulation of single- and two-phase flow through confined media

homepage: https://github.com/ImperialCollegeLondon/porefoam

version	toolchain
2021-09-21	foss/2020a

poretools

A toolkit for working with nanopore sequencing data from Oxford Nanopore.

homepage: https://poretools.readthedocs.io/en/latest/

version	versionsuffix	toolchain
0.6.0	-Python-2.7.14	intel/2018a

Portcullis

Portcullis stands for PORTable CULLing of Invalid Splice junctions from pre-aligned RNA-seq data. It is known that RNAseq mapping tools generate many invalid junction predictions, particularly in deep datasets with high coverage over splice sites. In order to address this, instead for creating a new RNAseq mapper, with a focus on SJ accuracy we created a tool that takes in a BAM file generated by an RNAseq mapper of the user's own choice (e.g. Tophat2, Gsnap, STAR2 or HISAT2) as input (i.e. it's portable). It then, analyses and quantifies all splice junctions in the file before, filtering (culling) those which are unlikely to be genuine. Portcullis output's junctions in a variety of formats making it suitable for downstream analysis (such as differential splicing analysis and gene modelling) without additional work. Portcullis can also filter the original BAM file removing alignments associated with bad junctions.

homepage: https://github.com/maplesond/portcullis

version	versionsuffix	toolchain
1.2.2	-Python-3.7.4	foss/2019b

PortMidi

PortMidi is a library for software developers. It supports real-time input and output of MIDI data using a system-independent interface. PortMidi runs on Windows (using MME), Macintosh (using CoreMIDI), and Linux (using ALSA).

homepage: https://github.com/PortMidi/portmidi

version	toolchain
2.0.4	GCCcore/11.3.0

Postgres-XL

Postgres-XL is a horizontally scalable open source SQL database cluster, flexible enough to handle varying database workloads:

homepage: http://www.postgres-xl.org

version	versionsuffix	toolchain
9.5r1	-Python-2.7.11	intel/2016a

PostgreSQL

PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.

homepage: https://www.postgresql.org/

version	versionsuffix	toolchain
9.4.7	-Python-2.7.11	intel/2016a
9.5.2	-Python-2.7.11	intel/2016a
9.6.0	-Python-2.7.12	intel/2016b
9.6.2	-Python-2.7.12	foss/2016b, intel/2016b
10.2	-Python-2.7.14	intel/2018a
10.3		foss/2018b
10.3	-Python-2.7.14	foss/2017b, foss/2018a, intel/2017b, intel/2018a
11.3	-Python-2.7.15	GCCcore/8.2.0
11.3	-Python-3.7.2	GCCcore/8.2.0
12.4		GCCcore/9.3.0
13.2		GCCcore/10.2.0
13.3		GCCcore/10.3.0
13.4		GCCcore/11.2.0
14.4		GCCcore/11.3.0
15.2		GCCcore/12.2.0
16.1		GCCcore/12.3.0, GCCcore/13.2.0

POT

POT (Python Optimal Transport) is a Python library provide several solvers for optimization problems related to Optimal Transport for signal, image processing and machine learning.

homepage: https://github.com/rflamary/POT

version	versionsuffix	toolchain
0.5.1	-Python-3.6.6	intel/2018b
0.9.0		foss/2022a

POV-Ray

The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning three-dimensional graphics. The source code is available for those wanting to do their own ports.

homepage: https://www.povray.org/

version	toolchain
3.7.0.0	intel/2016b
3.7.0.7	foss/2017b, foss/2018b, intel/2017b, intel/2018a, intel/2018b
3.7.0.8	GCC/10.2.0, iccifort/2020.4.304
3.7.0.10	GCC/11.3.0

powerlaw

powerlaw: A Python Package for Analysis of Heavy-Tailed Distributions

homepage: http://www.github.com/jeffalstott/powerlaw

version	toolchain
1.5	foss/2022a

pp-sketchlib

Library of sketching functions used by PopPUNK

homepage: https://github.com/bacpop/pp-sketchlib

version	toolchain
2.1.1	foss/2022a

PPanGGOLiN

PPanGGOLiN is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed to scale up to tens of thousands of genomes. It has the specificity to partition the pangenome using a statistical approach rather than using fixed thresholds which gives it the ability to work with low-quality data such as Metagenomic Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) thus taking advantage of large scale environmental studies and letting users study the pangenome of uncultivable species.

homepage: https://github.com/labgem/PPanGGOLiN

version	toolchain
1.1.136	foss/2021b

PPfold

PPfold is a new implementation of pfold, written in Java 6.0. It can predict the consensus secondary structure of RNA alignments through a stochastic context-free grammar coupled to an evolutionary model. It can also use data from chemical probing experiments to predict RNA secondary structure. PPfold is multithreaded, and can solve the structure of much longer alignments than pfold.

homepage:

version	versionsuffix	toolchain
3.1.1	-Java-1.8.0_66	system

ppl

The Parma Polyhedra Library (PPL) provides numerical abstractions especially targeted at applications in the field of analysis and verification of complex systems.

homepage: https://www.bugseng.com/parma-polyhedra-library

version	toolchain
1.2	GCCcore/11.3.0, GCCcore/6.4.0

pplacer

Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.

homepage: http://matsen.fhcrc.org/pplacer/

version	toolchain
1.1.alpha19	system

pplpy

This Python package provides a wrapper to the C++ Parma Polyhedra Library (PPL).

homepage: https://pypi.org/project/pplpy/

version	versionsuffix	toolchain
0.8.4	-Python-2.7.14	foss/2017b, intel/2017b
0.8.4	-Python-3.6.3	foss/2017b, intel/2017b
0.8.9		GCC/11.3.0

PRANK

PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events.

homepage: http://wasabiapp.org/software/prank/

version	toolchain
170427	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/11.3.0, GCC/12.3.0, GCC/9.3.0, intel/2018a

PRC

PRC is a stand-alone program for aligning and scoring two profile hidden Markov models. This can be used to detect remote relationships between profiles more effectively than by doing simple profile-sequence comparisons. PRC takes into account all transition and emission probabilities in both hidden Markov models.

homepage:

version	toolchain
1.5.6	intel/2018a

preCICE

preCICE (Precise Code Interaction Coupling Environment) is a coupling library for partitioned multi-physics simulations, including, but not restricted to fluid-structure interaction and conjugate heat transfer simulations. Partitioned means that preCICE couples existing programs (solvers) capable of simulating a subpart of the complete physics involved in a simulation. This allows for the high flexibility that is needed to keep a decent time-to-solution for complex multi-physics scenarios.

homepage: https://www.precice.org/

version	versionsuffix	toolchain
2.1.1	-Python-3.8.2	foss/2020a
2.2.0	-Python-3.8.2	foss/2020a, intel/2020a
2.5.0		foss/2022a

PREQUAL

A program to identify and mask regions with non-homologous adjacent characters in FASTA files.

homepage: https://github.com/simonwhelan/prequal

version	toolchain
1.02	GCCcore/11.2.0

preseq

Software for predicting library complexity and genome coverage in high-throughput sequencing.

homepage: https://smithlabresearch.org/software/preseq

version	toolchain
2.0.2	foss/2016b
2.0.3	foss/2018b, intel/2018a
3.1.2	GCC/10.3.0, GCC/11.2.0
3.2.0	GCC/11.3.0

presto

Presto performs a fast Wilcoxon rank sum test and auROC analysis.

homepage: https://github.com/immunogenomics/presto

version	versionsuffix	toolchain
1.0.0-20200718	-R-4.1.2	foss/2021b
1.0.0-20230113	-R-4.2.1	foss/2022a
1.0.0-20230501	-R-4.3.2	foss/2023a

pretty-yaml

PyYAML-based python module to produce pretty and readable YAML-serialized data. This module is for serialization only, see ruamel.yaml module for literate YAML parsing (keeping track of comments, spacing, line/column numbers of values, etc).

homepage: https://github.com/mk-fg/pretty-yaml

version	toolchain
19.12.0	GCCcore/8.3.0
20.4.0	GCCcore/9.3.0
21.10.1	GCCcore/10.3.0
23.9.5	GCCcore/11.3.0

primecount

primecount is a command-line program and C/C++ library that counts the number of primes ≤ x (maximum 1031) using highly optimized implementations of the combinatorial prime counting algorithms.

homepage: https://github.com/kimwalisch/primecount

version	toolchain
7.9	GCCcore/11.3.0

primecountpy

This is a Cython interface to the C++ library primecount.

homepage: https://pypi.org/project/primecountpy

version	toolchain
0.1.0	GCCcore/11.3.0

Primer3

Primer3 is a widely used program for designing PCR primers (PCR = 'Polymerase Chain Reaction'). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.

homepage: https://primer3.org/

version	toolchain
2.3.7	intel/2017b
2.4.0	iccifort/2019.1.144-GCC-8.2.0-2.31.1, intel/2018b
2.5.0	GCC/9.3.0

PRINSEQ

A bioinformatics tool to PRe-process and show INformation of SEQuence data.

homepage: http://prinseq.sourceforge.net

version	versionsuffix	toolchain
0.20.4	-Perl-5.28.0	foss/2018b
0.20.4	-Perl-5.32.0	foss/2020b
0.20.4	-Perl-5.34.0	foss/2021b

printproto

X.org PrintProto protocol headers.

homepage: http://xorg.freedesktop.org/

version	toolchain
1.0.5	intel/2016a

PRISMS-PF

PRISMS-PF is a powerful, massively parallel finite element code for conducting phase field and other related simulations of microstructural evolution.

homepage: https://prisms-center.github.io/phaseField

version	toolchain
2.1.1	foss/2019a, intel/2019a
2.2	foss/2021a

ProbABEL

Tool for genome-wide association analysis of imputed genetic data.

homepage: http://www.genabel.org/packages/ProbABEL

version	toolchain
0.5.0	GCCcore/9.3.0, system

ProBiS

ProBiS algorithm aligns and superimposes complete protein surfaces, surface motifs, or protein binding sites.

homepage: http://insilab.org/probis-algorithm

version	toolchain
20230403	gompi/2022b

prodigal

Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.

homepage: https://github.com/hyattpd/Prodigal/

version	toolchain
2.6.2	GCC/4.9.3-binutils-2.25
2.6.3	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0

ProFit

ProFit (pronounced Pro-Fit, not profit!) is designed to be the ultimate program for performing least squares fits of two or more protein structures. It performs a very simple and basic function, but allows as much flexibility as possible in performing this procedure. Thus one can specify subsets of atoms to be considered, specify zones to be fitted by number, sequence, or by sequence alignment.

homepage: http://www.bioinf.org.uk/software/profit

version	toolchain
3.3	GCC/10.3.0

PROJ

Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates

homepage: https://proj.org

version	toolchain
4.9.2	foss/2016a, foss/2016b, intel/2016a, intel/2016b
4.9.3	foss/2016b, foss/2017b, intel/2016b, intel/2017a, intel/2017b
5.0.0	foss/2018a, foss/2018b, intel/2018a, intel/2018b, iomkl/2018a
6.0.0	GCCcore/8.2.0
6.2.1	GCCcore/8.3.0
6.3.1	GCCcore/10.3.0
7.0.0	GCCcore/9.3.0
7.2.1	GCCcore/10.2.0
8.0.1	GCCcore/10.3.0
8.1.0	GCCcore/11.2.0
9.0.0	GCCcore/11.3.0
9.1.1	GCCcore/12.2.0
9.2.0	GCCcore/12.3.0
9.3.1	GCCcore/13.2.0

ProjectQ

An open source software framework for quantum computing

homepage: https://projectq.ch

version	versionsuffix	toolchain
0.4.2	-Python-3.6.6	intel/2018b

prokka

Prokka is a software tool for the rapid annotation of prokaryotic genomes.

homepage: https://www.vicbioinformatics.com/software.prokka.shtml

version	versionsuffix	toolchain
1.11	-BioPerl-1.7.0	foss/2016b
1.13	-BioPerl-1.7.2	intel/2018a
1.13.4		foss/2018b
1.13.7		gompi/2019a
1.14.5		gompi/2019a, gompi/2019b, gompi/2020b, gompi/2021a, gompi/2021b, gompi/2022a, gompi/2022b

prompt-toolkit

prompt_toolkit is a Python library for building powerful interactive command lines and terminal applications.

homepage: https://github.com/jonathanslenders/python-prompt-toolkit

version	versionsuffix	toolchain
1.0.3	-Python-2.7.11	foss/2016a
1.0.3	-Python-3.5.1	foss/2016a
1.0.6	-Python-2.7.12	foss/2016b, intel/2016b
1.0.6	-Python-3.5.2	intel/2016b
1.0.13	-Python-2.7.12	intel/2016b
3.0.36		GCCcore/12.2.0, GCCcore/13.2.0

proovread

PacBio hybrid error correction through iterative short read consensus

homepage: https://github.com/BioInf-Wuerzburg/proovread

version	toolchain
2.14.1	intel/2017b

propy

Propy is a protein description software. It allows analyzing sequence-derived structural and physicochemical features, which are very useful in representing and distinguishing proteins or peptides of different structural, functional and interaction properties. These have been widely used in developing methods and software for predicting protein structural and functional classes, protein-protein interactions, drug-target interactions, protein substrates, among others.

homepage: https://code.google.com/archive/p/protpy

version	versionsuffix	toolchain
1.0	-Python-2.7.13	foss/2017a

Proteinortho

Proteinortho is a tool to detect orthologous genes within different species.

homepage: https://www.bioinf.uni-leipzig.de/Software/proteinortho

version	versionsuffix	toolchain
5.16b	-Python-3.6.4-Perl-5.26.1	foss/2018a
6.2.3		gompi/2021b

ProtHint

ProtHint is a pipeline for predicting and scoring hints (in the form of introns, start and stop codons) in the genome of interest by mapping and spliced aligning predicted genes to a database of reference protein sequences.

homepage: https://github.com/gatech-genemark/ProtHint

version	versionsuffix	toolchain
2.4.0	-Python-3.7.2	iccifort/2019.1.144-GCC-8.2.0-2.31.1
2.4.0	-Python-3.7.4	iccifort/2019.5.281

protobuf

Google Protocol Buffers

homepage: https://github.com/google/protobuf/

version	toolchain
2.5.0	GCCcore/10.2.0, GCCcore/7.3.0, GCCcore/8.3.0, system
2.6.1	system
3.0.2	foss/2016a
3.2.0	foss/2016b, intel/2016b
3.3.0	foss/2016b, intel/2017a
3.4.0	GCCcore/6.4.0, intel/2017a, intel/2017b
3.5.1	intel/2017b
3.6.0	GCCcore/7.3.0
3.6.1	GCCcore/7.3.0
3.6.1.2	GCCcore/8.2.0
3.7.1	GCCcore/8.2.0, GCCcore/8.3.0
3.10.0	GCCcore/8.3.0, GCCcore/9.3.0
3.13.0	GCCcore/9.3.0
3.14.0	GCCcore/10.2.0
3.17.3	GCCcore/10.3.0, GCCcore/11.2.0
3.19.4	GCCcore/11.3.0
3.21.9	GCCcore/10.3.0
23.0	GCCcore/12.2.0
24.0	GCCcore/12.3.0
25.3	GCCcore/13.2.0

protobuf-python

Python Protocol Buffers runtime library.

homepage: https://github.com/google/protobuf/

version	versionsuffix	toolchain
3.0.2	-Python-2.7.11	foss/2016a
3.0.2	-Python-3.5.1	foss/2016a
3.2.0	-Python-2.7.12	foss/2016b, intel/2016b
3.2.0	-Python-3.5.2	foss/2016b, intel/2016b
3.3.0	-Python-2.7.13	intel/2017a
3.3.0	-Python-3.5.2	foss/2016b
3.3.0	-Python-3.6.1	intel/2017a
3.4.0	-Python-2.7.13	intel/2017a
3.4.0	-Python-2.7.14	intel/2017b
3.4.0	-Python-3.6.1	intel/2017a
3.4.0	-Python-3.6.3	intel/2017b
3.6.0	-Python-2.7.15	fosscuda/2018b
3.6.0	-Python-3.6.6	foss/2018b, fosscuda/2018b
3.10.0	-Python-3.7.4	foss/2019b, fosscuda/2019b
3.13.0	-Python-3.8.2	foss/2020a, fosscuda/2020a
3.14.0		GCCcore/10.2.0
3.17.3		GCCcore/10.3.0, GCCcore/11.2.0
3.19.4		GCCcore/11.3.0
4.23.0		GCCcore/12.2.0
4.24.0		GCCcore/12.3.0
4.25.3		GCCcore/13.2.0

protozero

Minimalistic protocol buffer decoder and encoder in C++.

homepage: https://github.com/mapbox/protozero

version	toolchain
1.6.8	GCCcore/7.3.0
1.7.0	GCCcore/8.3.0

PRSice

PRSice (pronounced 'precise') is a Polygenic Risk Score software for calculating, applying, evaluating and plotting the results of polygenic risk scores (PRS) analyses.

homepage: https://www.prsice.info/

version	toolchain
2.2.12	GCCcore/8.3.0
2.3.1	GCCcore/9.3.0
2.3.3	GCCcore/10.3.0, GCCcore/9.3.0
2.3.5	GCCcore/11.3.0, GCCcore/12.3.0

PSASS

PSASS (Pooled Sequencing Analysis for Sex Signal) is a software to compare pooled sequencing datasets from two groups (usually two sexes). Results from PSASS can be easily visualized using the sgtr R package. PSASS is integrated in a Snakemake workflow to perform all required steps starting from a genome and reads files.

homepage: https://github.com/SexGenomicsToolkit/PSASS

version	toolchain
3.1.0	GCC/12.3.0

pscom

ParaStation is a robust and efficient cluster middleware, consisting of a high-performance communication layer (MPI) and a sophisticated management layer.

homepage: http://www.par-tec.com

version	toolchain
5.0.43	GCC/4.8.2
5.0.44-1	GCC/4.9.2
5.0.48-1	system

PSI

PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform computations with more than 2500 basis functions running serially or in parallel.

homepage: http://www.psicode.org/

version	versionsuffix	toolchain
4.0b6-20160201	-mt-Python-2.7.11	intel/2016a

PSI4

PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform computations with more than 2500 basis functions running serially or in parallel.

homepage: https://www.psicode.org/

version	versionsuffix	toolchain
1.0	-Python-2.7.11	intel/2016a
1.0	-mt-Python-2.7.11	intel/2016a
1.2.1	-Python-2.7.15	intel/2018b
1.2.1	-Python-2.7.15-maxam8	intel/2018b
1.3.1	-Python-3.7.2	foss/2019a
1.3.2	-Python-3.7.4	intel/2019b
1.7		foss/2021b

PsiCLASS

PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.

homepage: https://github.com/splicebox/PsiCLASS

version	toolchain
1.0.3	GCC/11.2.0

PSIPRED

Accurate protein secondary structure prediction

homepage: http://bioinf.cs.ucl.ac.uk

version	toolchain
4.02	GCC/8.3.0

psmc

This software package infers population size history from a diploid sequence using the Pairwise Sequentially Markovian Coalescent (PSMC) model.

homepage: https://github.com/lh3/psmc

version	toolchain
0.6.5	foss/2016a, foss/2018a
0.6.5_20221121	GCC/12.3.0

psmpi

ParaStation MPI is an open source high-performance MPI 3.0 implementation, based on MPICH v3. It provides extra low level communication libraries and integration with various batch systems for tighter process control.

homepage: https://github.com/ParaStation/psmpi2

version	versionsuffix	toolchain
5.1.0-1		GCC/4.9.2
5.1.5-1		GCC/4.9.3
5.1.5-1	-mt	GCC/4.9.3

psmpi2

ParaStation is a robust and efficient cluster middleware, consisting of a high-performance communication layer (MPI) and a sophisticated management layer.

homepage: http://www.par-tec.com

version	versionsuffix	toolchain
5.0.29		GCC/4.8.2
5.0.29	-mt	GCC/4.8.2

PSolver

Interpolating scaling function Poisson Solver Library

homepage: http://bigdft.org/devel-doc/d1/d81/group__PSOLVER.html

version	toolchain
1.7.6	foss/2017b, foss/2018a, foss/2018b, intel/2017b, intel/2018a, intel/2018b
1.8.3	foss/2020b, foss/2021a, foss/2021b, intel/2020b, intel/2021a, intel/2021b

PSORTb

PSORTb v3.0.4 is the most precise bacterial localization prediction tool available.

homepage: http://psort.org/psortb/index.html

version	versionsuffix	toolchain
3.0.4	-Perl-5.22.1	foss/2016a

psrecord

psrecord is a small utility that uses the psutil library to record the CPU and memory activity of a process.

homepage: https://github.com/astrofrog/psrecord

version	versionsuffix	toolchain
1.1	-Python-2.7.14	intel/2018a
1.1	-Python-2.7.15	intel/2018b
1.1	-Python-3.6.4	intel/2018a
1.1	-Python-3.6.6	intel/2018b

pstoedit

pstoedit translates PostScript and PDF graphics into other vector formats

homepage: http://pstoedit.net/

version	toolchain
3.70	GCCcore/6.3.0, GCCcore/6.4.0
3.78	GCC/11.3.0

psutil

A cross-platform process and system utilities module for Python

homepage: https://github.com/giampaolo/psutil

version	versionsuffix	toolchain
4.2.0	-Python-2.7.11	intel/2016a
4.3.0	-Python-2.7.11	foss/2016a, intel/2016a
5.4.3	-Python-2.7.14	intel/2017b
5.4.7	-Python-2.7.15	foss/2018b
5.4.7	-Python-3.6.6	foss/2018b
5.6.1	-Python-2.7.15	fosscuda/2018b
5.6.3		GCCcore/8.2.0
5.9.3		GCCcore/10.2.0, GCCcore/11.3.0
5.9.4		GCCcore/11.2.0
5.9.5		GCCcore/12.2.0

psycopg

Psycopg is the most popular PostgreSQL adapter for the Python programming language.

homepage: https://psycopg.org/

version	toolchain
3.1.18	GCCcore/12.2.0, GCCcore/13.2.0

psycopg2

Psycopg is the most popular PostgreSQL adapter for the Python programming language.

homepage: https://psycopg.org/

version	versionsuffix	toolchain
2.7	-Python-2.7.12	foss/2016b, intel/2016b
2.8.3	-Python-3.7.2	foss/2019a
2.8.6	-Python-3.8.2	GCCcore/9.3.0
2.9.5		GCCcore/11.2.0
2.9.6		GCCcore/11.3.0
2.9.9		GCCcore/12.3.0

ptemcee

ptemcee, pronounced "tem-cee", is fork of Daniel Foreman-Mackey's wonderful emcee to implement parallel tempering more robustly. If you're trying to characterise awkward, multi-model probability distributions, then ptemcee is your friend.

homepage: https://github.com/willvousden/ptemcee

version	toolchain
1.0.0	foss/2019a

PTESFinder

Post-Transcriptional Exon Shuffling (PTES) Identification Pipeline

homepage: https://sourceforge.net/projects/ptesfinder-v1/

version	toolchain
1	intel/2017b

pubtcrs

This repository contains C++ source code for the TCR clustering and correlation analyses described in the manuscript "Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity" by William S DeWitt III, Anajane Smith, Gary Schoch, John A Hansen, Frederick A Matsen IV and Philip Bradley, available on bioRxiv.

homepage: https://github.com/phbradley/pubtcrs

version	toolchain
20180622	intel/2019a

pugixml

pugixml is a light-weight C++ XML processing library

homepage: https://pugixml.org/

version	toolchain
1.11.4	GCCcore/10.3.0
1.12.1	GCCcore/11.2.0, GCCcore/11.3.0

pullseq

Utility program for extracting sequences from a fasta/fastq file

homepage: https://github.com/bcthomas/pullseq

version	toolchain
1.0.2	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/7.3.0

PuLP

PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and call GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI, MOSEK, XPRESS, CHOCO, MIPCL, SCIP to solve linear problems.

homepage: https://github.com/coin-or/pulp

version	toolchain
2.5.1	foss/2021a
2.7.0	foss/2022b
2.8.0	foss/2023a

purge_dups

purge haplotigs and overlaps in an assembly based on read depth

homepage: https://github.com/dfguan/purge_dups

version	toolchain
1.2.5	foss/2021b

pv

Pipe Viewer - monitor the progress of data through a pipe

homepage: https://www.ivarch.com/programs/pv.shtml

version	toolchain
1.7.24	GCCcore/12.3.0

py

library with cross-python path, ini-parsing, io, code, log facilities

homepage: < https://pylib.readthedocs.org/>

version	versionsuffix	toolchain
1.4.31	-Python-2.7.11	foss/2016a
1.4.31	-Python-3.5.1	foss/2016a

py-aiger

A python library for manipulating sequential and combinatorial circuits. This module provides the py-aiger extensions: aiger_bv, aiger_cnf, aiger_ptltl, aiger_coins, aiger_gridworld, aiger_dfa

homepage: https://github.com/mvcisback/py-aiger

version	versionsuffix	toolchain
6.1.1	-Python-3.8.2	GCCcore/9.3.0
6.1.14		GCCcore/10.2.0

py-aiger-bdd

Aiger to BDD bridge.

homepage: https://github.com/mvcisback/py-aiger-bdd

version	versionsuffix	toolchain
3.0.0	-Python-3.8.2	foss/2020a

py-c3d

This is a small library for reading and writing C3D binary files. C3D files are a standard format for recording 3-dimensional time sequence data, especially data recorded by a 3D motion tracking apparatus.

homepage: https://github.com/EmbodiedCognition/py-c3d

version	toolchain
0.5.2	foss/2022a

py-cpuinfo

py-cpuinfo gets CPU info with pure Python.

homepage: https://github.com/workhorsy/py-cpuinfo

version	toolchain
5.0.0	system
8.0.0	GCCcore/11.2.0
9.0.0	GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

py3Dmol

A simple IPython/Jupyter widget to embed an interactive 3Dmol.js viewer in a notebook.

homepage: https://github.com/3dmol/3Dmol.js/tree/master/py3Dmol

version	toolchain
2.0.1.post1	GCCcore/11.3.0

pyABC

Massively parallel, distributed and scalable ABC-SMC (Approximate Bayesian Computation - Sequential Monte Carlo) for parameter estimation of complex stochastic models. Implemented in Python with support of the R language.

homepage: https://github.com/icb-dcm/pyabc

version	versionsuffix	toolchain
0.10.4	-Python-3.7.4	foss/2019b

PyAMG

PyAMG is a library of Algebraic Multigrid (AMG) solvers with a convenient Python interface.

homepage: https://pyamg.github.io

version	versionsuffix	toolchain
3.0.1	-Python-2.7.11	intel/2016a
4.0.0		foss/2020b, intel/2020b
4.2.3		foss/2021a

PyAPS3

Python 3 Atmospheric Phase Screen

homepage: https://github.com/AngeliqueBenoit/pyaps3

version	versionsuffix	toolchain
20190407	-Python-3.7.2	foss/2019a

PyAV

PyAV is a Pythonic binding for FFmpeg. We aim to provide all of the power and control of the underlying library, but manage the gritty details as much as possible.

homepage: https://pyav.org

version	toolchain
10.0.0	GCCcore/11.3.0

pybedtools

pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python.

homepage: https://daler.github.io/pybedtools

version	versionsuffix	toolchain
0.7.10	-Python-2.7.14	intel/2017b, intel/2018a
0.7.10	-Python-3.6.6	foss/2018b
0.8.0		foss/2019a, intel/2019a
0.8.1		foss/2019b
0.8.2		GCC/10.2.0, GCC/11.2.0, iccifort/2020.4.304
0.8.2	-Python-2.7.18	GCC/10.2.0, GCC/11.2.0
0.9.0		GCC/11.3.0, GCC/12.2.0

PyBerny

PyBerny is an optimizer of molecular geometries with respect to the total energy, using nuclear gradient information.

homepage: https://github.com/jhrmnn/pyberny

version	versionsuffix	toolchain
0.6.2	-Python-3.8.2	intel/2020a
0.6.3		foss/2022a, foss/2022b

pyBigWig

A python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files.

homepage: https://github.com/deeptools/pyBigWig

version	versionsuffix	toolchain
0.3.13	-Python-3.6.6	foss/2018b
0.3.17		GCCcore/8.2.0, GCCcore/9.3.0
0.3.18		GCCcore/10.2.0, foss/2021a, foss/2021b, foss/2022a
0.3.22		foss/2022b

pybind11

pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code.

homepage: https://pybind11.readthedocs.io

version	versionsuffix	toolchain
2.2.4	-Python-3.6.4	foss/2018a
2.2.4	-Python-3.6.6	intel/2018b
2.4.3	-Python-3.7.4	GCCcore/8.3.0
2.4.3	-Python-3.8.2	GCCcore/9.3.0
2.6.0		GCCcore/10.2.0
2.6.2		GCCcore/10.3.0
2.7.1		GCCcore/11.2.0
2.7.1	-Python-2.7.18	GCCcore/11.2.0
2.9.2		GCCcore/11.3.0
2.10.3		GCCcore/12.2.0
2.11.1		GCCcore/12.3.0, GCCcore/13.2.0

pybinding

Pybinding is a Python package for numerical tight-binding calculations in solid state physics.

homepage: https://github.com/dean0x7d/pybinding

version	toolchain
0.9.5	foss/2022a

PyBioLib

PyBioLib is a Python package for running BioLib applications from Python scripts and the command line. BioLib is a library of biological data science applications. Applications on BioLib range from small bioinformatics utilities to state-of-the-art machine learning algorithms for predicting characteristics of biological molecules.

homepage: https://biolib.com/

version	toolchain
1.1.988	GCCcore/11.3.0

PyCairo

Python bindings for the cairo library

homepage: https://pycairo.readthedocs.io/

version	versionsuffix	toolchain
1.10.0	-Python-2.7.11	intel/2016a
1.16.1	-Python-3.6.3	foss/2017b
1.16.2	-Python-2.7.14	intel/2017b
1.18.0	-Python-2.7.14	intel/2018a
1.18.0	-Python-2.7.15	foss/2018b
1.18.0	-Python-3.6.6	foss/2018b
1.18.0	-Python-3.7.2	GCCcore/8.2.0
1.18.2		GCCcore/8.3.0, GCCcore/9.3.0
1.20.0		GCCcore/10.2.0
1.20.1		GCCcore/10.3.0, GCCcore/11.2.0
1.21.0		GCCcore/11.3.0
1.24.0		GCCcore/12.2.0
1.25.0		GCCcore/12.3.0
1.25.1		GCCcore/13.2.0

PyCalib

Python library for classifier calibration

homepage: https://github.com/classifier-calibration/PyCalib

version	toolchain
0.1.0.dev0	foss/2021b
20230531	gfbf/2022b

pyccel

Python extension language using accelerators

homepage: https://github.com/pyccel/pyccel

version	toolchain
1.7.0	foss/2022a

PyCharm

PyCharm Community Edition: Python IDE for Professional Developers

homepage: https://www.jetbrains.com/pycharm/

version	toolchain
2017.2.3	system
2019.3.1	system
2021.1.1	system
2022.2.2	system
2022.3.2	system

PyCheMPS2

PyCheMPS2 is a python interface to CheMPS2, for compilation without MPI. CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry.

homepage: https://sebwouters.github.io/CheMPS2

version	toolchain
1.8.12	foss/2022a, foss/2022b

Pychopper

A tool to identify, orient, trim and rescue full length cDNA reads.

homepage: https://github.com/nanoporetech/pychopper

version	versionsuffix	toolchain
2.3.1	-Python-3.7.4	intel/2019b

PyCifRW

PyCIFRW provides support for reading and writing CIF (Crystallographic Information Format) files using Python.

homepage: https://bitbucket.org/jamesrhester/pycifrw/src/development

version	toolchain
4.4.2	GCCcore/8.3.0

PyClone

PyClone is a Python package that wraps rclone and provides a threaded interface for an installation at the host or container level.

homepage: https://gitlab.com/ltgiv/pyclone

version	toolchain
2020.9b2	GCCcore/10.2.0

pycma

A stochastic numerical optimization algorithm for difficult (non-convex, ill-conditioned, multi-modal, rugged, noisy) optimization problems in continuous search spaces, implemented in Python.

homepage: https://github.com/CMA-ES/pycma

version	toolchain
2.7.0	intel/2019a

pycocotools

Official APIs for the MS-COCO dataset

homepage: https://pypi.org/project/pycocotools

version	versionsuffix	toolchain
2.0.0	-Python-3.7.4	foss/2019b, fosscuda/2019b
2.0.1	-Python-3.7.4	foss/2019b, fosscuda/2019b
2.0.2	-Python-3.8.2	foss/2020a, fosscuda/2020a
2.0.4		foss/2021a
2.0.6		foss/2022a

pycodestyle

pycodestyle is a tool to check your Python code against some of the style conventions in PEP 8.

homepage: https://pycodestyle.readthedocs.io

version	versionsuffix	toolchain
2.5.0	-Python-3.6.4	intel/2018a
2.11.1		foss/2022a

PyCogent

PyCogent is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for: controlling third-party applications; devising workflows; querying databases; conducting novel probabilistic analyses of biological sequence evolution; and generating publication quality graphics.

homepage: http://pycogent.org

version	versionsuffix	toolchain
1.5.3	-Python-2.7.12	intel/2016b
1.9	-Python-2.7.12	foss/2016b, intel/2016b
1.9	-Python-2.7.15	foss/2018b

pycoQC

PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.

homepage: https://tleonardi.github.io/pycoQC

version	toolchain
2.5.2	foss/2021a

pycubescd

Charge-displacement analysis via natural orbitals for chemical valence in the four-component relativistic framework

homepage: https://github.com/BERTHA-4c-DKS/pycubescd

version	toolchain
20220704	foss/2022a

PyCUDA

PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python.

homepage: https://mathema.tician.de/software/pycuda

version	versionsuffix	toolchain
2016.1.2	-Python-2.7.12	intel/2016b
2017.1.1	-CUDA-9.0.176-Python-2.7.14	foss/2017b
2017.1.1	-Python-2.7.14	intel/2018a
2018.1	-Python-3.6.4-CUDA-9.1.85	intel/2018a
2019.1.2	-Python-3.7.4	fosscuda/2019b, intelcuda/2019b
2020.1		fosscuda/2020b

PycURL

PycURL is a Python interface to libcurl. PycURL can be used to fetch objects identified by a URL from a Python program, similar to the urllib Python module. PycURL is mature, very fast, and supports a lot of features.

homepage: http://pycurl.io/

version	versionsuffix	toolchain
7.43.0.5	-Python-3.7.4	GCCcore/8.3.0
7.45.2		GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0

PyDamage

Pydamage, is a Python software to automate the process of contig damage identification and estimation. After modelling the ancient DNA damage using the C to T transitions, Pydamage uses a likelihood ratio test to discriminate between truly ancient, and modern contigs originating from sample contamination.

homepage: https://github.com/maxibor/pydamage

version	toolchain
0.70	foss/2021a

pydantic

Data validation and settings management using Python type hinting.

homepage: https://github.com/samuelcolvin/pydantic

version	versionsuffix	toolchain
1.6.1	-Python-3.7.4	GCCcore/8.3.0
1.10.2		GCCcore/11.2.0
1.10.4		GCCcore/11.3.0
1.10.13		GCCcore/12.3.0
2.5.3		GCCcore/12.2.0, GCCcore/12.3.0
2.6.4		GCCcore/13.2.0

PyDatastream

Lightweight SOAP client

homepage: https://pypi.python.org/pypi/suds-py3

version	versionsuffix	toolchain
0.5.1	-Python-3.6.4	intel/2018a

pydicom

Pure python package for DICOM medical file reading and writing.

homepage: https://pydicom.github.io/

version	versionsuffix	toolchain
0.9.9	-Python-2.7.11	intel/2016a
1.2.2		GCCcore/8.2.0
1.4.2		GCCcore/8.3.0
2.1.2		GCCcore/10.2.0
2.1.2	-Python-3.8.2	GCCcore/9.3.0
2.2.2		GCCcore/10.3.0, GCCcore/11.2.0
2.3.0		GCCcore/11.3.0
2.4.4		GCCcore/12.3.0

pydicom-seg

Reading and writing of DICOM-SEG medical image segmentation storage files using pydicom as DICOM serialization/deserialization library.

homepage: https://github.com/razorx89/pydicom-seg

version	toolchain
0.4.1	foss/2022a

pydlpoly

Pydlpoly is a molecular dynamics simulation package which is a modified version of DL-POLY with a Python language interface.

homepage: http://cmc.aci.ruhr-uni-bochum.de/cmc/

version	versionsuffix	toolchain
20150225	-Python-2.7.12	intel/2016b
20150225	-Python-2.7.13	intel/2017a

pydot

Python interface to Graphviz's Dot language.

homepage: https://github.com/pydot/pydot

version	toolchain
1.4.1	GCCcore/9.3.0, foss/2019b
1.4.2	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0
2.0.0	GCCcore/12.3.0

pyEGA3

A basic Python-based EGA download client

homepage: https://github.com/EGA-archive/ega-download-client

version	versionsuffix	toolchain
3.0.33	-Python-3.7.2	GCCcore/8.2.0
3.4.0	-Python-3.7.4	GCCcore/8.3.0
3.4.0	-Python-3.8.2	GCCcore/9.3.0
4.0.0		GCCcore/11.2.0
5.0.2		GCCcore/12.3.0

pyenchant

PyEnchant is a spellchecking library for Python, based on the excellent Enchant library.

homepage: https://pythonhosted.org/pyenchant/

version	versionsuffix	toolchain
1.6.8	-Python-2.7.13	intel/2017a

PyEVTK

EVTK (Export VTK) package allows exporting data to binary VTK files for visualization and data analysis with any of the visualization packages that support VTK files

homepage: https://github.com/paulo-herrera/PyEVTK

version	toolchain
1.4.1	foss/2021b
2.0.0	foss/2021b

pyFAI

Python implementation of fast azimuthal integration.

homepage: https://github.com/silx-kit/pyFAI

version	versionsuffix	toolchain
0.19.0	-Python-3.7.4	foss/2019b, fosscuda/2019b
0.20.0		foss/2020b, fosscuda/2020b
0.21.3		foss/2021b

pyfaidx

pyfaidx: efficient pythonic random access to fasta subsequences

homepage: https://pypi.python.org/pypi/pyfaidx

version	versionsuffix	toolchain
0.5.9.5		GCCcore/10.2.0
0.5.9.5	-Python-3.7.4	GCCcore/8.3.0
0.6.3.1		GCCcore/10.3.0
0.7.0		GCCcore/11.2.0
0.7.1		GCCcore/11.3.0
0.7.2.1		GCCcore/12.2.0
0.8.1.1		GCCcore/12.3.0, GCCcore/13.2.0

pyfasta

fast, memory-efficient, pythonic (and command-line) access to fasta sequence files

homepage: https://pypi.org/project/pyfasta/

version	toolchain
0.5.2	foss/2020b

PyFFmpeg

Python FFmpeg wrapper

homepage: https://github.com/mhaller/pyffmpeg

version	versionsuffix	toolchain
2.1beta	-Python-2.7.10	gimkl/2.11.5
2.1beta	-Python-2.7.11	intel/2016a

pyFFTW

A pythonic wrapper around FFTW, the FFT library, presenting a unified interface for all the supported transforms.

homepage: https://github.com/pyFFTW/pyFFTW

version	versionsuffix	toolchain
0.11.1		intel/2019a
0.11.1	-Python-3.6.6	foss/2018b
0.12.0		foss/2020b, fosscuda/2020b
0.13.1		foss/2022a

pyfits

The PyFITS module is a Python library providing access to FITS (Flexible Image Transport System)

homepage: https://pythonhosted.org/pyfits/

version	versionsuffix	toolchain
3.5	-Python-2.7.15	intel/2018b

PyFMI

PyFMI is a package for loading and interacting with Functional Mock-Up Units (FMUs), which are compiled dynamic models compliant with the Functional Mock-Up Interface (FMI)

homepage: https://pypi.org/project/PyFMI/

version	versionsuffix	toolchain
2.4.0	-Python-2.7.15	intel/2018b

PyFoam

A Python library to control OpenFOAM-runs and manipulate OpenFOAM-data.

homepage: http://openfoamwiki.net/index.php/Contrib/PyFoam

version	toolchain
2020.5	foss/2020b

PyFR

PyFR is an open-source Python based framework for solving advection-diffusion type problems on streaming architectures using the Flux Reconstruction approach of Huynh. The framework is designed to solve a range of governing systems on mixed unstructured grids containing various element types. It is also designed to target a range of hardware platforms via use of an in-built domain specific language derived from the Mako templating engine.

homepage: http://www.pyfr.org

version	versionsuffix	toolchain
1.7.6	-Python-3.6.4-CUDA-9.1.85	intel/2018a
1.9.0	-Python-3.7.4	intelcuda/2019b

PyFrag

The PyFrag program is specially designed to facilitate the analysis of reaction mechanism in a more efficient and user-friendly way. PyFrag resolves three main challenges associated with the automatized computational exploration of reaction mechanisms: 1) the management of multiple parallel calculations to automatically find a reaction path; 2) the monitoring of the entire computational process along with the extraction and plotting of relevant information from large amounts of data; and 3) the analysis and presentation of these data in a clear and informative way. This module provides the Activation Strain Analysis (ASA) Module of PyFrag 2023

homepage: https://pyfragdocument.readthedocs.io/en/latest/includeme.html

version	versionsuffix	toolchain
2019-20220216	-ASA	intel/2020b
2023-dev.20240220	-ASA	intel/2022a

pygame

Pygame is a set of Python modules designed for writing video games. Pygame adds functionality on top of the excellent SDL library. This allows you to create fully featured games and multimedia programs in the python language.

homepage: https://www.pygame.org

version	toolchain
2.1.0	GCCcore/11.3.0

pygccxml

Python package for easy C++ declarations navigation.

homepage: https://pypi.python.org/pypi/pygccxml

version	versionsuffix	toolchain
20160706	-Python-2.7.11	foss/2016a
20160706	-Python-3.5.1	foss/2016a

pyGenomeTracks

pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable.

homepage: https://pygenometracks.readthedocs.io

version	toolchain
3.7	foss/2021b
3.8	foss/2022a

PyGEOS

PyGEOS is a C/Python library with vectorized geometry functions. The geometry operations are done in the open-source geometry library GEOS. PyGEOS wraps these operations in NumPy ufuncs providing a performance improvement when operating on arrays of geometries.

homepage: https://pygeos.readthedocs.io

version	versionsuffix	toolchain
0.7.1	-Python-3.7.4	foss/2019b
0.8	-Python-3.8.2	foss/2020a
0.10.2		intel/2020b
0.14		gfbf/2022b

pyGIMLi

pyGIMLi is an open-source multi-method library for solving inverse and forward tasks related to geophysical problems. Written in C++ and Python, it offers both efficiency and flexibility allowing you to quickly build your own robust inversion applications for the geophysical problem at hand.

homepage: http://www.pygimli.org/

version	versionsuffix	toolchain
20160803	-Python-2.7.11	foss/2016a
20160803	-Python-3.5.1	foss/2016a

Pygments

Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications that need to prettify source code.

homepage: https://pygments.org/

version	versionsuffix	toolchain
2.1.3	-Python-2.7.11	foss/2016a
2.1.3	-Python-3.5.1	foss/2016a

pygmo

pygmo is a scientific Python library for massively parallel optimization.

homepage: https://esa.github.io/pygmo2

version	toolchain
2.16.1	foss/2020b
2.18.0	foss/2021a, foss/2021b, foss/2022a

PyGObject

PyGObject is a Python package which provides bindings for GObject based libraries such as GTK, GStreamer, WebKitGTK, GLib, GIO and many more.

homepage: https://pygobject.readthedocs.io/

version	versionsuffix	toolchain
2.28.6	-Python-2.7.11	intel/2016a
2.28.6	-Python-2.7.14	intel/2017b
2.28.7	-Python-2.7.14	intel/2018a
2.28.7	-Python-2.7.15	foss/2018b
3.34.0	-Python-2.7.16	GCCcore/8.3.0
3.34.0	-Python-3.7.2	GCCcore/8.2.0
3.34.0	-Python-3.7.4	GCCcore/8.3.0
3.42.1		GCCcore/11.3.0
3.44.1		GCCcore/12.2.0
3.46.0		GCCcore/12.3.0, GCCcore/13.2.0

pygraphviz

PyGraphviz is a Python interface to the Graphviz graph layout and visualization package. With PyGraphviz you can create, edit, read, write, and draw graphs using Python to access the Graphviz graph data structure and layout algorithms.

homepage: https://pygraphviz.github.io/

version	toolchain
1.5	foss/2019b
1.7	foss/2020b, foss/2021a
1.10	GCCcore/11.3.0
1.11	GCCcore/12.3.0

pygrib

Python interface for reading and writing GRIB data

homepage: https://jswhit.github.io/pygrib

version	toolchain
2.0.4	foss/2019a

PyGTK

PyGTK lets you to easily create programs with a graphical user interface using the Python programming language.

homepage: http://www.pygtk.org/

version	versionsuffix	toolchain
2.24.0	-Python-2.7.11	intel/2016a
2.24.0	-Python-2.7.14	intel/2017b, intel/2018a
2.24.0	-Python-2.7.15	foss/2018b

PyGTS

PyGTS is a python package used to construct, manipulate, and perform computations on triangulated surfaces. It is a hand-crafted and pythonic binding for the GNU Triangulated Surface (GTS) Library.

homepage: https://sourceforge.net/projects/pygts/

version	versionsuffix	toolchain
0.3.1	-Python-2.7.11	foss/2016a, intel/2016a
0.3.1	-Python-2.7.12	foss/2016b, intel/2016b
0.3.1	-Python-2.7.14	intel/2018a

PyGWAS

PyGWAS is a library for running Genome Wide Association studies.

homepage: https://github.com/timeu/pygwas

version	versionsuffix	toolchain
1.2.0	-Python-2.7.11	foss/2016a
1.3.1	-Python-2.7.11	foss/2016a
1.4.0	-Python-2.7.11	foss/2016a
1.5.0	-Python-2.7.11	foss/2016a
1.6.1	-Python-2.7.11	foss/2016a, intel/2016a
1.7.1	-Python-2.7.13	foss/2017a

pyhdf

Python wrapper around the NCSA HDF version 4 library

homepage: https://github.com/fhs/pyhdf

version	toolchain
0.10.1	foss/2019a

PyImageJ

PyImageJ provides a set of wrapper functions for integration between ImageJ2 and Python. It also supports the original ImageJ API and data structures. A major advantage of this approach is the ability to combine ImageJ and ImageJ2 with other tools available from the Python software ecosystem, including NumPy, SciPy, scikit-image, CellProfiler, OpenCV, ITK and many more.

homepage: https://pyimagej.readthedocs.io/

version	toolchain
1.3.1	foss/2021a

PyInstaller

PyInstaller bundles a Python application and all its dependencies into a single package. The user can run the packaged app without installing a Python interpreter or any modules.

homepage: https://pyinstaller.org/en/stable/

version	toolchain
6.3.0	GCCcore/12.3.0

pyiron

An integrated development environment (IDE) for computational materials science.

homepage: https://github.com/pyiron/pyiron

version	versionsuffix	toolchain
0.2.5	-Python-3.7.2	intel/2019a
0.3.0	-Python-3.8.2	intel/2020a

Pyke3

Pyke introduces a form of Logic Programming (inspired by Prolog) to the Python community by providing a knowledge-based inference engine (expert system) written in 100% Python.

homepage: http://sourceforge.net/projects/pyke/

version	versionsuffix	toolchain
1.1.1	-Python-3.6.6	intel/2018b

pylift

pylift is an uplift library that provides, primarily: (1) Fast uplift modeling implementations and (2) Evaluation tools (UpliftEval class).

homepage: https://github.com/df-foundation/pylift

version	versionsuffix	toolchain
0.1.5	-Python-3.7.4	foss/2019b
0.1.5	-Python-3.8.2	foss/2020a

Pylint

Pylint is a tool that checks for errors in Python code, tries to enforce a coding standard and looks for code smells. It can also look for certain type errors, it can recommend suggestions about how particular blocks can be refactored and can offer you details about the code's complexity.

homepage: https://www.pylint.org/

version	versionsuffix	toolchain
1.9.3	-Python-2.7.15	foss/2018b, intel/2018b, iomkl/2018b
1.9.5	-Python-2.7.15	GCCcore/8.2.0
1.9.5	-Python-2.7.16	GCCcore/8.3.0
2.7.4		GCCcore/10.2.0
2.17.4		GCCcore/12.2.0

pylipid

PyLipID is a python package for analyzing lipid interactions with membrane proteins from Molecular Dynamics Simulations.

homepage: https://github.com/wlsong/PyLipID

version	toolchain
1.5.14	foss/2021b

pyMannKendall

A python package for non parametric Mann Kendall family of trend tests.

homepage: https://github.com/mmhs013/pymannkendall

version	toolchain
1.4.3	foss/2022a

pymatgen

Python Materials Genomics is a robust materials analysis code that defines core object representations for structures and molecules with support for many electronic structure codes.

homepage: https://pypi.python.org/pypi/pymatgen

version	versionsuffix	toolchain
3.5.0	-Python-2.7.11	intel/2016.02-GCC-4.9
4.1.1	-Python-2.7.12	intel/2016b
4.3.2	-Python-2.7.12	intel/2016b
4.7.3	-Python-2.7.13	intel/2017a
2017.10.16	-Python-2.7.14	intel/2017b
2017.10.16	-Python-3.6.3	intel/2017b
2022.0.4		foss/2020b
2023.3.10		foss/2022a
2023.12.18		foss/2023a

pymatgen-db

Pymatgen-db is a database add-on for the Python Materials Genomics (pymatgen) materials analysis library.

homepage: https://pypi.python.org/pypi/pymatgen-db

version	versionsuffix	toolchain
0.6.5	-Python-2.7.13	intel/2017a

pymbar

The pymbar package contains the pymbar suite of tools for the analysis of simulated and experimental data with the multistate Bennett acceptance ratio (MBAR) estimator.

homepage: http://pymbar.readthedocs.io/en/master/

version	versionsuffix	toolchain
3.0.3	-Python-3.6.3	intel/2017b
3.0.3	-Python-3.8.2	intel/2020a

PyMC

PyMC is a probabilistic programming library for Python that allows users to build Bayesian models with a simple Python API and fit them using Markov chain Monte Carlo (MCMC) methods.

homepage: https://www.pymc.io

version	toolchain
5.9.0	foss/2023a

PyMC3

Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning with Theano

homepage: https://docs.pymc.io/

version	versionsuffix	toolchain
3.8	-Python-3.7.4	foss/2019b, intel/2019b
3.11.1		foss/2021b, fosscuda/2020b, intel/2020b, intel/2021b

pymca

The PyMca X-Ray Fluorescence Toolkit, including PyMca5 and fisx.

homepage: https://github.com/vasole/pymca

version	versionsuffix	toolchain
5.6.3		foss/2020b, fosscuda/2020b
5.6.3	-Python-3.7.4	foss/2019b, fosscuda/2019b
5.7.6		foss/2021b

pymemcache

A comprehensive, fast, pure-Python memcached client.

homepage: https://github.com/pinterest/pymemcache

version	versionsuffix	toolchain
2.1.1	-Python-3.6.4	foss/2018a, intel/2018a

PyMOL

PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is free to everyone!

homepage: https://github.com/schrodinger/pymol-open-source

version	toolchain
2.5.0	foss/2020b

PyNAST

PyNAST is a reimplementation of the NAST sequence aligner, which has become a popular tool for adding new 16s rRNA sequences to existing 16s rRNA alignments. This reimplementation is more flexible, faster, and easier to install and maintain than the original NAST implementation.

homepage: https://biocore.github.io/pynast

version	versionsuffix	toolchain
1.2.2	-Python-2.7.12	foss/2016b, intel/2016b
1.2.2	-Python-2.7.15	foss/2018b

pyobjcryst

Python bindings to ObjCryst++, the Object-Oriented Crystallographic Library.

homepage: https://github.com/diffpy/pyobjcryst

version	versionsuffix	toolchain
2.1.0.post2	-Python-3.8.2	intel/2020a
2.2.1		foss/2021b

PyOD

PyOD is a comprehensive and scalable Python toolkit for detecting outlying objects in multivariate data.

homepage: https://pyod.readthedocs.io

version	toolchain
0.8.7	foss/2020b, intel/2020b

pyodbc

pyodbc is an open source Python module that makes accessing ODBC databases simple. It implements the DB API 2.0 specification but is packed with even more Pythonic convenience.

homepage: https://github.com/mkleehammer/pyodbc

version	toolchain
4.0.39	foss/2022b

Pyomo

Pyomo is a Python-based open-source software package that supports a diverse set of optimization capabilities for formulating and analyzing optimization models.

homepage: https://www.pyomo.org/

version	versionsuffix	toolchain
5.5.0	-Python-2.7.15	foss/2018b
5.5.0	-Python-3.6.6	foss/2018b
6.0.1		foss/2020b, foss/2021a
6.4.2		foss/2022a
6.5.0		foss/2022b

PyOpenCL

PyOpenCL lets you access GPUs and other massively parallel compute devices from Python.

homepage: https://mathema.tician.de/software/pyopencl/

version	versionsuffix	toolchain
2020.2.2	-Python-3.7.4	fosscuda/2019b
2021.1.2		foss/2020b, fosscuda/2020b, intel/2020b
2021.2.13		foss/2021b
2021.2.13	-CUDA-11.4.1	foss/2021b
2023.1.4		foss/2022a, foss/2023a
2023.1.4	-CUDA-11.7.0	foss/2022a
2023.1.4	-CUDA-12.1.1	foss/2023a

PyOpenGL

PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs.

homepage: http://pyopengl.sourceforge.net

version	versionsuffix	toolchain
3.1.1a1		GCCcore/8.2.0
3.1.1a1	-Python-2.7.11	intel/2016a
3.1.1a1	-Python-2.7.12	foss/2016b
3.1.1a1	-Python-2.7.14	foss/2018a, intel/2017b
3.1.3b2	-Python-2.7.14	intel/2018a
3.1.3b2	-Python-2.7.15	foss/2018b
3.1.5		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/8.3.0
3.1.6		GCCcore/11.2.0, GCCcore/11.3.0
3.1.7		GCCcore/12.3.0

pyparsing

The pyparsing module is an alternative approach to creating and executing simple grammars, vs. the traditional lex/yacc approach, or the use of regular expressions. The pyparsing module provides a library of classes that client code uses to construct the grammar directly in Python code.

homepage: https://github.com/pyparsing/pyparsing

version	versionsuffix	toolchain
2.4.6	-Python-2.7.16	GCCcore/8.3.0
3.0.9		GCCcore/11.3.0
3.1.1		GCCcore/12.3.0

pyperf

The Python pyperf module is a toolkit to write, run and analyze benchmarks

homepage: https://github.com/psf/pyperf

version	toolchain
2.5.0	GCCcore/11.3.0
2.6.0	GCCcore/12.2.0

pyplusplus

Py++ is a code generator for Boost.Python that simplifies writing Python bindings of a C/C++ library The tool is implemented as a Python module which is controlled by a user script.

homepage: https://bitbucket.org/ompl/pyplusplus

version	versionsuffix	toolchain
20160707	-Python-2.7.11	foss/2016a
20160707	-Python-3.5.1	foss/2016a

pypmt

PMT is a high-level software library capable of collecting power consumption measurements on various hardware.

homepage: https://git.astron.nl/RD/pmt

version	toolchain
1.1.0	foss/2022a, gfbf/2023a
1.2.0	foss/2022a, gfbf/2023a

PYPOWER

PYPOWER is a power flow and Optimal Power Flow (OPF) solver. It is a port of MATPOWER to the Python programming language.

homepage: https://github.com/rwl/PYPOWER

version	toolchain
5.1.15	foss/2020b

pyproj

Python interface to PROJ4 library for cartographic transformations

homepage: https://pyproj4.github.io/pyproj

version	versionsuffix	toolchain
2.1.3		GCCcore/8.2.0
2.4.2	-Python-3.7.4	GCCcore/8.3.0
2.6.1.post1	-Python-3.8.2	GCCcore/9.3.0
3.0.1		GCCcore/10.2.0
3.1.0		GCCcore/10.3.0
3.3.1		GCCcore/11.2.0, GCCcore/11.3.0
3.4.0		GCCcore/11.3.0
3.5.0		GCCcore/12.2.0
3.6.0		GCCcore/12.3.0

PyPSA

PyPSA is an open source toolbox for simulating and optimising modern power systems that include features such as conventional generators with unit commitment, variable wind and solar generation, storage units, coupling to other energy sectors, and mixed alternating and direct current networks. PyPSA is designed to scale well with large networks and long time series.

homepage: https://pypsa.readthedocs.io/

version	toolchain
0.17.1	foss/2020b

PyPy

A fast, compliant alternative implementation of Python

homepage: https://www.pypy.org

version	versionsuffix	toolchain
7.3.12	-3.10	system

pyqstem

QSTEM is a program for quantitative image simulation in electron microscopy, including TEM, STEM and CBED image simulation. This project interfaces the QSTEM code with Python and the Atomic Simulation Environment (ASE) to provide a single environment for building models, simulating and analysing images.

homepage: https://github.com/jacobjma/PyQSTEM

version	versionsuffix	toolchain
1.0.3	-ASE-3.22.0	foss/2020b, fosscuda/2020b
1.0.3	-Python-3.6.6	foss/2018b, intel/2018b

PyQt

PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.

homepage: http://www.riverbankcomputing.co.uk/software/pyqt

version	versionsuffix	toolchain
4.11.4	-Python-2.7.11	intel/2016a
4.11.4	-Python-2.7.12	intel/2016b
4.12	-Python-2.7.12	foss/2016b, intel/2016b
4.12	-Python-2.7.13	intel/2017a
4.12.1	-Python-2.7.14	foss/2018a
4.12.3	-Python-2.7.15	fosscuda/2018b

PyQt-builder

PyQt-builder is the PEP 517 compliant build system for PyQt and projects that extend PyQt. It extends the SIP build system and uses Qt’s qmake to perform the actual compilation and installation of extension modules.

homepage: http://www.example.com

version	toolchain
1.15.4	GCCcore/12.3.0

PyQt5

PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company.

homepage: http://www.riverbankcomputing.co.uk/software/pyqt

version	versionsuffix	toolchain
5.7	-Python-2.7.11	foss/2016a
5.7.1	-Python-2.7.12	intel/2016b
5.8.2	-Python-2.7.13	intel/2017a
5.9.2	-Python-2.7.14	foss/2017b, intel/2017b, intel/2018a
5.9.2	-Python-3.6.4	foss/2018a, intel/2018a
5.11.3	-Python-3.6.6	foss/2018b, intel/2018b
5.12.1	-Python-2.7.15	GCCcore/8.2.0
5.12.1	-Python-3.7.2	GCCcore/8.2.0
5.13.2	-Python-3.7.4	GCCcore/8.3.0
5.15.1		GCCcore/10.2.0
5.15.1	-Python-3.8.2	GCCcore/9.3.0
5.15.4		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0
5.15.5		GCCcore/11.3.0
5.15.7		GCCcore/12.2.0
5.15.10		GCCcore/12.3.0

PyQtGraph

PyQtGraph is a pure-python graphics and GUI library built on PyQt5/PySide2 and numpy.

homepage: http://www.pyqtgraph.org/

version	versionsuffix	toolchain
0.10.0	-Python-3.6.4	intel/2018a
0.10.0	-Python-3.6.6	foss/2018b, intel/2018b
0.10.0	-Python-3.7.2	intel/2019a
0.11.0	-Python-3.7.4	foss/2019b
0.11.1		foss/2020b, fosscuda/2020b
0.12.3		foss/2021a
0.13.3		foss/2022a

pyradiomics

Open-source python package for the extraction of Radiomics features from 2D and 3D images and binary masks.

homepage: https://pyradiomics.readthedocs.io/

version	versionsuffix	toolchain
3.0.1		foss/2021a
3.0.1	-Python-3.7.4	foss/2019b

PyRe

PyRe (Python Reliability) is a Python module for structural reliability analysis.

homepage: https://hackl.science/pyre

version	versionsuffix	toolchain
5.0.3-20190221	-Python-3.7.4	foss/2019b, intel/2019b

PyRETIS

PyRETIS is a Python library for rare event molecular simulations with emphasis on methods based on transition interface sampling and replica exchange transition interface sampling.

homepage: http://www.pyretis.org

version	versionsuffix	toolchain
2.1.0	-Python-3.6.6	intel/2018b
2.5.0		foss/2020b, intel/2020b
2.5.0	-Python-3.8.2	foss/2020a, intel/2020a

pyringe

Debugger capable of attaching to and injecting code into python processes.

homepage: https://github.com/google/pyringe

version	versionsuffix	toolchain
1.0.2	-Python-2.7.11	intel/2016a

pyro-api

Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch.

homepage: https://github.com/pyro-ppl/pyro-api

version	toolchain
0.1.2	fosscuda/2020b

pyro-ppl

Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch.

homepage: https://github.com/pyro-ppl/pyro

version	versionsuffix	toolchain
1.5.2		fosscuda/2020b
1.8.0	-CUDA-11.3.1	foss/2021a
1.8.4		foss/2022a
1.8.4	-CUDA-11.7.0	foss/2022a

Pyro4

Pyro means PYthon Remote Objects. It is a library that enables you to build applications in which objects can talk to eachother over the network, with minimal programming effort.

homepage: https://pypi.python.org/pypi/Pyro4

version	versionsuffix	toolchain
4.47	-Python-2.7.11	foss/2016a

PyRosetta

PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions.

homepage: https://www.pyrosetta.org/

version	versionsuffix	toolchain
4.release-292	-Python-3.7.4	GCCcore/8.3.0

Pysam

Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.

homepage: https://github.com/pysam-developers/pysam

version	versionsuffix	toolchain
0.8.4	-Python-2.7.12	intel/2016b
0.9.1.4	-Python-2.7.12	foss/2016b
0.10.0	-Python-2.7.12	foss/2016b, intel/2016b
0.12.0.1	-Python-2.7.13	intel/2017a
0.12.0.1	-Python-2.7.14	intel/2017b
0.12.0.1	-Python-3.6.3	intel/2017b
0.13	-Python-2.7.14	intel/2017b
0.13.0	-Python-3.6.3	intel/2017b
0.14	-Python-2.7.14	foss/2017b, intel/2017b
0.14	-Python-3.6.3	foss/2017b, intel/2017b
0.14	-Python-3.6.4	intel/2018a
0.14.1	-Python-2.7.14	foss/2018a, intel/2018a
0.14.1	-Python-3.6.4	foss/2018a, intel/2018a
0.15.1	-Python-2.7.15	foss/2018b, intel/2018b
0.15.1	-Python-3.6.6	foss/2018b, intel/2018b
0.15.2		GCC/8.2.0-2.31.1, iccifort/2019.1.144-GCC-8.2.0-2.31.1
0.15.3		GCC/8.3.0, iccifort/2019.5.281
0.16.0.1		GCC/10.2.0, GCC/10.3.0, GCC/8.3.0, GCC/9.3.0, iccifort/2020.1.217, iccifort/2020.4.304
0.16.0.1	-Python-2.7.18	GCC/10.2.0
0.17.0		GCC/11.2.0
0.17.0	-Python-2.7.18	GCC/11.2.0
0.18.0		GCC/11.2.0
0.19.1		GCC/11.3.0
0.20.0		GCC/11.3.0
0.21.0		GCC/12.2.0
0.22.0		GCC/12.3.0

pysamstats

A Python utility for calculating statistics against genome positions based on sequence alignments from a SAM or BAM file.

homepage: https://github.com/alimanfoo/pysamstats

version	toolchain
1.1.2	foss/2020b

PySAT

PySAT is a Python toolkit, which aims at providing a simple and unified interface to a number of state-of-art Boolean satisfiability (SAT) solvers as well as to a variety of cardinality and pseudo-Boolean encodings.

homepage: https://pysathq.github.io/

version	versionsuffix	toolchain
0.1.6.dev11	-Python-3.8.2	GCC/9.3.0
0.1.7.dev1		GCC/10.2.0

pyScaf

pyScaf orders contigs from genome assemblies utilising several types of information

homepage: https://github.com/lpryszcz/pyScaf

version	versionsuffix	toolchain
0.12a4	-Python-2.7.14	intel/2017b

pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

homepage: https://github.com/aertslab/pySCENIC

version	versionsuffix	toolchain
0.10.3	-Python-3.8.2	foss/2020a, intel/2020a
0.12.1		foss/2022a
0.12.1-20240311		foss/2023a

PySCF

PySCF is an open-source collection of electronic structure modules powered by Python.

homepage: http://www.pyscf.org

version	versionsuffix	toolchain
1.6.3	-Python-3.7.2	foss/2019a
1.7.6		foss/2020b, foss/2021a, gomkl/2021a
2.1.1		foss/2022a
2.4.0		foss/2022b

pysheds

Simple and fast watershed delineation in python.

homepage: https://mattbartos.com/pysheds/

version	toolchain
0.2.7.1	foss/2020b

pyshp

Pure Python read/write support for ESRI Shapefile format

homepage: https://github.com/GeospatialPython/pyshp

version	versionsuffix	toolchain
1.2.12	-Python-3.6.2	foss/2017b
2.1.3		GCCcore/10.2.0

PySide2

PySide2 is the official Python module from the Qt for Python project, which provides access to the complete Qt 5.12+ framework.

homepage: https://pypi.python.org/pypi/PySide2

version	toolchain
5.14.2.3	GCCcore/10.2.0

PySINDy

" PySINDy is a sparse regression package with several implementations for the Sparse Identification of Nonlinear Dynamical systems (SINDy) method introduced in Brunton et al. (2016a), including the unified optimization approach of Champion et al. (2019), SINDy with control from Brunton et al. (2016b), Trapping SINDy from Kaptanoglu et al. (2021), SINDy-PI from Kaheman et al. (2020), PDE-FIND from Rudy et al. (2017), and so on. A comprehensive literature review is given in de Silva et al. (2020) and Kaptanoglu, de Silva et al. (2021).

homepage: https://pysindy.readthedocs.io/en/latest/

version	toolchain
1.7.3	foss/2022a

pyslim

A Python API for reading and modifying tskit tree sequence files produced by SLiM, or modifying files produced by other programs (e.g., msprime, fwdpy11, and tsinfer) for use in SLiM.

homepage: https://tskit.dev/pyslim/docs/stable/introduction.html

version	toolchain
1.0.1	foss/2021b, foss/2022a

pysndfx

A lightweight Python wrapper for SoX - Sound eXchange. Supported effects range from EQ and compression to phasers, reverb and pitch shifters.

homepage: https://github.com/carlthome/python-audio-effects

version	versionsuffix	toolchain
0.3.6	-Python-3.7.4	foss/2019b

Pysolar

Pysolar is a collection of Python libraries for simulating the irradiation of any point on earth by the sun.

homepage: https://pysolar.org/

version	versionsuffix	toolchain
0.7	-Python-3.6.3	intel/2017b
0.7	-Python-3.6.4	intel/2018a
0.8	-Python-3.6.6	intel/2018b
0.8	-Python-3.7.2	GCCcore/8.2.0

pyspoa

Python bindings to spoa.

homepage: https://github.com/nanoporetech/pyspoa

version	versionsuffix	toolchain
0.0.4	-Python-3.7.4	GCC/8.3.0
0.0.8		GCC/10.2.0, GCC/10.3.0, GCC/11.2.0
0.0.9		GCC/11.3.0, GCC/12.2.0
0.2.1		GCC/12.3.0

pysqlite

pysqlite is an interface to the SQLite 3.x embedded relational database engine. It is almost fully compliant with the Python database API version 2.0 also exposes the unique features of SQLite.

homepage: https://pypi.python.org/pypi/pysqlite

version	versionsuffix	toolchain
2.8.2	-Python-2.7.11	foss/2016a

PyStan

Python interface to Stan, a package for Bayesian inference using the No-U-Turn sampler, a variant of Hamiltonian Monte Carlo.

homepage: https://github.com/stan-dev/pystan

version	versionsuffix	toolchain
2.19.0.0	-Python-3.6.4	intel/2018a
2.19.1.1		foss/2020b, intel/2020b
3.5.0		foss/2021b

pysteps

Pysteps is an open-source and community-driven Python library for probabilistic precipitation nowcasting, i.e. short-term ensemble prediction systems.

homepage: https://pysteps.github.io/

version	toolchain
1.7.1	foss/2022a

pystran

Toolset of dynamical model STRucture ANalysis algorithms

homepage: https://stijnvanhoey.github.io/pystran/

version	versionsuffix	toolchain
2017.04.20	-Python-2.7.14	intel/2017b

PyTables

PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browsing, processing and searching very large amounts of data. One important feature of PyTables is that it optimizes memory and disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as relational or object oriented databases.

homepage: https://www.pytables.org

version	versionsuffix	toolchain
3.2.2	-Python-2.7.12	foss/2016b
3.2.3.1	-Python-2.7.12	intel/2016b
3.3.0	-Python-2.7.12	foss/2016b, intel/2016b
3.3.0	-Python-3.5.2	intel/2016b
3.4.2	-Python-2.7.13	foss/2017a
3.4.2	-Python-3.6.1	intel/2017a
3.4.2	-Python-3.6.3	intel/2017b
3.4.2	-Python-3.6.4	foss/2018a, intel/2018a
3.4.4	-Python-2.7.15	foss/2018b
3.4.4	-Python-3.5.1	foss/2016a
3.4.4	-Python-3.6.6	foss/2018b, fosscuda/2018b, intel/2018b
3.5.2		intel/2019a
3.5.2	-Python-2.7.14	intel/2018a
3.5.2	-Python-2.7.16	intel/2019b
3.5.2	-Python-2.7.18	foss/2020b
3.6.1		foss/2020b, foss/2021a, foss/2021b, fosscuda/2020b, intel/2020b
3.6.1	-Python-3.7.4	foss/2019b, fosscuda/2019b
3.6.1	-Python-3.8.2	foss/2020a, intel/2020a
3.8.0		foss/2022a, foss/2022b
3.9.2		foss/2023b

PyTensor

Optimizing compiler for evaluating mathematical expressions on CPUs and GPUs

homepage: https://github.com/pymc-devs/pytensor

version	toolchain
2.17.1	gfbf/2023a

pytesseract

Python-tesseract is an optical character recognition (OCR) tool for python. That is, it will recognize and "read" the text embedded in images. Python-tesseract is a wrapper for Google's Tesseract-OCR Engine. It is also useful as a stand-alone invocation script to tesseract, as it can read all image types supported by the Pillow and Leptonica imaging libraries, including jpeg, png, gif, bmp, tiff, and others. Additionally, if used as a script, Python-tesseract will print the recognized text instead of writing it to a file.

homepage: https://github.com/madmaze/pytesseract

version	toolchain
0.3.10	GCCcore/11.3.0

pytest

The pytest framework makes it easy to write small, readable tests, and can scale to support complex functional testing for applications and libraries.

homepage: https://docs.pytest.org/en/latest/

version	versionsuffix	toolchain
3.0.1	-Python-2.7.11	foss/2016a
3.0.1	-Python-3.5.1	foss/2016a
3.8.0	-Python-3.6.4	foss/2018a, intel/2018a
3.8.2	-Python-2.7.14	foss/2017b, intel/2017b
3.8.2	-Python-2.7.15	intel/2018b
3.8.2	-Python-3.6.3	foss/2017b, intel/2017b
3.8.2	-Python-3.6.6	foss/2018b, intel/2018b
4.3.0	-Python-3.6.6	foss/2018b, intel/2018b
4.4.0	-Python-2.7.15	foss/2018b, intel/2018b
4.4.0	-Python-3.6.6	foss/2018b, intel/2018b
6.0.1	-Python-3.7.4	GCCcore/8.3.0
7.1.3		GCCcore/11.2.0
7.2.2		GCCcore/11.2.0
7.4.2		GCCcore/12.3.0

pytest-benchmark

A pytest fixture for benchmarking code.

homepage: https://github.com/ionelmc/pytest-benchmark

version	toolchain
3.4.1	GCCcore/10.2.0

pytest-cpp

Use pytest runner to discover and execute C++ tests.

homepage: http://github.com/pytest-dev/pytest-cpp

version	toolchain
2.3.0	GCCcore/11.3.0

pytest-flakefinder

Runs tests multiple times to expose flakiness.

homepage: https://github.com/dropbox/pytest-flakefinder

version	toolchain
1.1.0	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

pytest-rerunfailures

pytest plugin to re-run tests to eliminate flaky failures.

homepage: https://github.com/pytest-dev/pytest-rerunfailures

version	toolchain
11.1	GCCcore/11.3.0
12.0	GCCcore/12.2.0, GCCcore/12.3.0
14.0	GCCcore/13.2.0

pytest-shard

pytest plugin to support parallelism across multiple machines. Shards tests based on a hash of their test name enabling easy parallelism across machines, suitable for a wide variety of continuous integration services. Tests are split at the finest level of granularity, individual test cases, enabling parallelism even if all of your tests are in a single file (or even single parameterized test method).

homepage: https://github.com/AdamGleave/pytest-shard

version	toolchain
0.1.2	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

pytest-workflow

Configure workflow/pipeline tests using yaml files. pytest-workflow is a workflow-system agnostic testing framework that aims to make pipeline/workflow testing easy by using YAML files for the test configuration. Whether you write your pipelines in WDL, snakemake, nextflow, bash or any other workflow framework, pytest-workflow makes testing easy. pytest-workflow is build on top of the pytest test framework.

homepage: https://github.com/LUMC/pytest-workflow

version	toolchain
2.0.1	GCCcore/12.2.0
2.1.0	GCCcore/13.2.0

pytest-xdist

xdist: pytest distributed testing plugin The pytest-xdist plugin extends pytest with some unique test execution modes: * test run parallelization: if you have multiple CPUs or hosts you can use those for a combined test run. This allows to speed up development or to use special resources of remote machines. * --looponfail: run your tests repeatedly in a subprocess. After each run pytest waits until a file in your project changes and then re-runs the previously failing tests. This is repeated until all tests pass after which again a full run is performed. * Multi-Platform coverage: you can specify different Python interpreters or different platforms and run tests in parallel on all of them. Before running tests remotely, pytest efficiently “rsyncs” your program source code to the remote place. All test results are reported back and displayed to your local terminal. You may specify different Python versions and interpreters.

homepage: https://github.com/pytest-dev/pytest-xdist

version	toolchain
2.1.0	GCCcore/10.2.0
2.3.0	GCCcore/10.2.0, GCCcore/10.3.0
2.5.0	GCCcore/11.2.0, GCCcore/11.3.0
3.3.1	GCCcore/12.3.0

pythermalcomfort

Package to calculate several thermal comfort indices (e.g. PMV, PPD, SET, adaptive) and convert physical variables.

homepage: https://github.com/CenterForTheBuiltEnvironment/pythermalcomfort

version	toolchain
2.8.10	foss/2022a

PYTHIA

PYTHIA is a program for the generation of high-energy physics collision events, i.e. for the description of collisions at high energies between electrons, protons, photons and heavy nuclei. It contains theory and models for a number of physics aspects, including hard and soft interactions, parton distributions, initial- and final-state parton showers, multiparton interactions, fragmentation and decay. It is largely based on original research, but also borrows many formulae and other knowledge from the literature. As such it is categorized as a general purpose Monte Carlo event generator.

homepage: https://www.pythia.org

version	versionsuffix	toolchain
8.226	-Python-2.7.13	intel/2017a
8.309		foss/2022b

Python

Python is a programming language that lets you work more quickly and integrate your systems more effectively.

homepage: https://python.org/

version	versionsuffix	toolchain
2.7.9	-bare	GCC/4.8.4, GCC/4.9.2
2.7.10		gimkl/2.11.5
2.7.10	-bare	GCC/4.9.3-2.25, GNU/4.9.3-2.25
2.7.11		foss/2016a, gimkl/2.11.5, intel/2016.02-GCC-4.9, intel/2016a, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25
2.7.11	-bare	GCC/4.9.3-2.25
2.7.11	-libX11-1.6.3	intel/2016a
2.7.12		foss/2016b, intel/2016b, iomkl/2017a
2.7.12	-bare	GCC/5.4.0-2.26, GCCcore/4.9.3, iccifort/2016.3.210-GCC-5.4.0-2.26
2.7.13		foss/2017a, intel/2017a
2.7.13	-bare	GCCcore/6.3.0
2.7.14		foss/2017b, foss/2018a, fosscuda/2017b, fosscuda/2018a, intel/2017b, intel/2018.01, intel/2018a, intelcuda/2017b, iomkl/2018a
2.7.14	-bare	GCCcore/6.4.0
2.7.15		GCCcore/8.2.0, foss/2018b, fosscuda/2018b, intel/2018b, iomkl/2018b
2.7.15	-bare	GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/8.2.0
2.7.16		GCCcore/8.3.0
2.7.16	-bare	GCCcore/8.3.0
2.7.18		GCCcore/10.2.0, GCCcore/11.2.0, GCCcore/12.3.0, GCCcore/9.3.0
2.7.18	-bare	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/9.3.0
3.5.1		foss/2016a, intel/2016a
3.5.2		foss/2016.04, foss/2016b, intel/2016b
3.5.2	-bare	GCC/5.4.0-2.26, iccifort/2016.3.210-GCC-5.4.0-2.26
3.6.1		foss/2017a, intel/2017a
3.6.2		foss/2017b, intel/2017b, intel/2018.00
3.6.3		foss/2017b, fosscuda/2017b, intel/2017b, intel/2018.01, intelcuda/2017b
3.6.4		foss/2017a, foss/2018a, fosscuda/2018a, golf/2018a, iimkl/2018a, intel/2018a, iomkl/2018.02, iomkl/2018a
3.6.6		foss/2018b, fosscuda/2018b, intel/2018b, iomkl/2018b
3.7.0		foss/2018b, intel/2018b, iomkl/2018b
3.7.2		GCCcore/8.2.0
3.7.4		GCCcore/8.3.0
3.8.2		GCCcore/9.3.0
3.8.6		GCCcore/10.2.0
3.9.5		GCCcore/10.3.0
3.9.5	-bare	GCCcore/10.3.0
3.9.6		GCCcore/11.2.0
3.9.6	-bare	GCCcore/11.2.0
3.10.4		GCCcore/11.3.0
3.10.4	-bare	GCCcore/11.3.0
3.10.8		GCCcore/12.2.0
3.10.8	-bare	GCCcore/12.2.0
3.11.2	-bare	GCCcore/12.2.0
3.11.3		GCCcore/12.3.0
3.11.5		GCCcore/13.2.0

Python-bundle

Python distribution with a number of widely used extensions incl. NumPy, SciPy, Matplotlib, JupyterLab, MPI4PY, ...

homepage: https://easybuild.io/

version	toolchain
3.10.4	foss/2022a

Python-bundle-PyPI

Bundle of Python packages from PyPI

homepage: https://python.org/

version	toolchain
2023.06	GCCcore/12.3.0
2023.10	GCCcore/13.2.0

python-casacore

Python-casacore is a set of Python bindings for casacore, a c++ library used in radio astronomy. Python-casacore replaces the old pyrap.

homepage: https://casacore.github.io/python-casacore/#

version	toolchain
3.5.2	foss/2023b

python-docx

python-docx is a Python library for creating and updating Microsoft Word (.docx) files

homepage: https://python-docx.readthedocs.io/en/latest/

version	toolchain
0.8.11	GCCcore/10.2.0, GCCcore/12.2.0

python-hl7

A simple library for parsing messages of Health Level 7 (HL7) version 2.x into Python objects.

homepage: https://github.com/johnpaulett/python-hl7

version	versionsuffix	toolchain
0.3.4	-Python-3.7.4	GCCcore/8.3.0

python-igraph

Python interface to the igraph high performance graph library, primarily aimed at complex network research and analysis.

homepage: https://igraph.org/python

version	versionsuffix	toolchain
0.7.1.post6	-Python-2.7.14	intel/2017b
0.7.1.post6	-Python-3.6.6	foss/2018b
0.8.0		foss/2019b, foss/2020a
0.9.0		foss/2020b, fosscuda/2020b
0.9.6		foss/2021a
0.9.8		foss/2021b
0.10.3		foss/2022a
0.10.6		foss/2022b
0.11.4		foss/2023a

python-irodsclient

A python API for iRODS

homepage: https://github.com/irods/python-irodsclient

version	toolchain
1.1.4	GCCcore/10.3.0, GCCcore/11.2.0
2.0.0	GCCcore/12.3.0

python-isal

Faster zlib and gzip compatible compression and decompression by providing python bindings for the isa-l library.

homepage: https://github.com/pycompression/python-isal

version	toolchain
0.11.0	GCCcore/10.3.0
0.11.1	GCCcore/10.2.0, GCCcore/11.2.0
1.1.0	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0
1.6.1	GCCcore/13.2.0

python-Levenshtein

Python extension for computing string edit distances and similarities.

homepage: https://pypi.org/project/python-Levenshtein/

version	versionsuffix	toolchain
0.12.0	-Python-3.6.6	foss/2018b
0.12.0	-Python-3.7.4	foss/2019b
0.12.1		foss/2020b

python-libsbml

LibSBML Python API.

homepage: https://sbml.org/

version	toolchain
5.19.7	foss/2021a
5.20.2	foss/2023b

python-louvain

Louvain algorithm for community detection

homepage: https://pypi.org/project/python-louvain

version	toolchain
0.15	foss/2021b
0.16	foss/2022a

python-mujoco

This package is the canonical Python bindings for the MuJoCo physics engine. The mujoco package provides direct access to raw MuJoCo C API functions, structs, constants, and enumerations. Structs are provided as Python classes, with Pythonic initialization and deletion semantics.

homepage: https://www.mujoco.org

version	toolchain
2.2.2	foss/2022a

python-parasail

Python Bindings for the Parasail C Library

homepage: https://github.com/jeffdaily/parasail-python

version	versionsuffix	toolchain
1.1.12	-Python-2.7.14	intel/2018a
1.1.16	-Python-3.6.6	foss/2018b
1.2	-Python-3.7.4	foss/2019b, fosscuda/2019b, intel/2019b
1.2.2	-Python-3.8.2	intel/2020a
1.2.3	-Python-3.8.2	foss/2020a
1.2.4		foss/2020b, foss/2021a, foss/2021b, fosscuda/2020b
1.3.3		foss/2022a
1.3.4		foss/2022b, foss/2023a

python-telegram-bot

This library provides a pure Python, asynchronous interface for the Telegram Bot API. It's compatible with Python versions 3.7+.

homepage: https://python-telegram-bot.org/

version	toolchain
20.0a0	GCCcore/10.2.0

python-weka-wrapper3

Python3 wrapper for the Weka Machine Learning Workbench

homepage: https://github.com/fracpete/python-weka-wrapper3

version	versionsuffix	toolchain
0.1.11	-Python-3.7.4	foss/2019b

python-xxhash

xxhash is a Python binding for the xxHash library by Yann Collet.

homepage: https://github.com/ifduyue/python-xxhash

version	toolchain
2.0.2	GCCcore/10.2.0
3.1.0	GCCcore/11.3.0
3.2.0	GCCcore/12.2.0
3.4.1	GCCcore/12.3.0

pythran

Pythran is an ahead of time compiler for a subset of the Python language, with a focus on scientific computing. It takes a Python module annotated with a few interface description and turns it into a native Python module with the same interface, but (hopefully) faster.

homepage: https://pythran.readthedocs.io

version	versionsuffix	toolchain
0.9.4.post1	-Python-3.7.4	foss/2019b

PyTorch

Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first.

homepage: https://pytorch.org/

version	versionsuffix	toolchain
0.3.1	-Python-2.7.14	fosscuda/2017b
0.3.1	-Python-3.6.3	fosscuda/2017b
0.3.1	-Python-3.6.4	intel/2018a
0.3.1	-Python-3.6.4-CUDA-9.1.85	foss/2018a
0.4.1	-Python-3.6.4	intel/2018a
1.0.1	-Python-3.6.6	foss/2018b, fosscuda/2018b
1.1.0	-Python-3.7.2	foss/2019a
1.2.0	-Python-3.7.2	foss/2019a, fosscuda/2019a
1.3.1		fosscuda/2020b
1.3.1	-Python-3.7.4	foss/2019b, fosscuda/2019b
1.4.0	-Python-3.7.4	foss/2019b, fosscuda/2019b
1.6.0	-Python-3.7.4	foss/2019b, fosscuda/2019b
1.6.0	-Python-3.7.4-imkl	fosscuda/2019b
1.7.1		foss/2020b, fosscuda/2020b
1.7.1	-Python-3.7.4	fosscuda/2019b
1.7.1	-Python-3.8.2	fosscuda/2020a
1.8.1		foss/2020b, fosscuda/2020b
1.8.1	-Python-3.7.4	fosscuda/2019b
1.9.0		foss/2020b, fosscuda/2020b
1.9.0	-imkl	fosscuda/2020b
1.10.0		foss/2021a, fosscuda/2020b
1.10.0	-CUDA-11.3.1	foss/2021a
1.11.0	-CUDA-11.3.1	foss/2021a
1.12.0		foss/2022a
1.12.0	-CUDA-11.7.0	foss/2022a
1.12.1		foss/2021a, foss/2021b, foss/2022a
1.12.1	-CUDA-11.3.1	foss/2021a
1.12.1	-CUDA-11.5.2	foss/2021b
1.12.1	-CUDA-11.7.0	foss/2022a
1.13.1		foss/2022a, foss/2022b
1.13.1	-CUDA-11.7.0	foss/2022a
2.0.1		foss/2022a, foss/2022b
2.1.2		foss/2022a, foss/2022b, foss/2023a, foss/2023b
2.1.2	-CUDA-12.1.1	foss/2023a

pytorch-3dunet

PyTorch implementation of 3D U-Net and its variants: - UNet3D: Standard 3D U-Net based on 3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation - ResidualUNet3D: Residual 3D U-Net based on Superhuman Accuracy on the SNEMI3D Connectomics Challenge - ResidualUNetSE3D: Similar to ResidualUNet3D with the addition of Squeeze and Excitation blocks based on Deep Learning Semantic Segmentation for High- Resolution Medical Volumes. Original squeeze and excite paper: Squeeze-and- Excitation Networks The code allows for training the U-Net for both: semantic segmentation (binary and multi-class) and regression problems (e.g. de-noising, learning deconvolutions).

homepage: https://github.com/wolny/pytorch-3dunet

version	versionsuffix	toolchain
1.6.0	-CUDA-11.7.0	foss/2022a

PyTorch-bundle

PyTorch with compatible versions of official Torch extensions.

homepage: https://pytorch.org/

version	versionsuffix	toolchain
1.12.1	-CUDA-11.7.0	foss/2022a
1.13.1	-CUDA-11.7.0	foss/2022a

pytorch-CycleGAN-pix2pix

PyTorch implementations for both unpaired and paired image-to-image translation.

homepage: https://github.com/junyanz/pytorch-CycleGAN-and-pix2pix

version	versionsuffix	toolchain
20230314	-CUDA-11.7.0	foss/2022a

PyTorch-Geometric

PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch.

homepage: https://github.com/rusty1s/pytorch_geometric

version	versionsuffix	toolchain
1.3.2	-Python-3.7.4	foss/2019b
1.4.2	-Python-3.7.4-PyTorch-1.4.0	foss/2019b
1.6.3		foss/2020b, fosscuda/2020b
1.6.3	-Python-3.7.4-PyTorch-1.8.1	fosscuda/2019b
2.0.1	-PyTorch-1.9.0	fosscuda/2020b
2.1.0	-PyTorch-1.12.0	foss/2022a
2.1.0	-PyTorch-1.12.0-CUDA-11.7.0	foss/2022a
2.1.0	-PyTorch-1.12.1-CUDA-11.3.1	foss/2021a

PyTorch-Ignite

Ignite is a high-level library to help with training and evaluating neural networks in PyTorch flexibly and transparently.

homepage: https://pytorch-ignite.ai/

version	versionsuffix	toolchain
0.4.9	-CUDA-11.3.1	foss/2021a
0.4.12		foss/2022a
0.4.12	-CUDA-11.7.0	foss/2022a
0.4.13		foss/2023a

PyTorch-Image-Models

PyTorch Image Models (timm) is a collection of image models, layers, utilities, optimizers, schedulers, data-loaders / augmentations, and reference training / validation scripts that aim to pull together a wide variety of SOTA models with ability to reproduce ImageNet training results.

homepage: https://huggingface.co/docs/timm

version	versionsuffix	toolchain
0.9.2		foss/2022a
0.9.2	-CUDA-11.7.0	foss/2022a

PyTorch-Lightning

PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers.

homepage: https://pytorchlightning.ai

version	versionsuffix	toolchain
1.5.9		foss/2021a
1.5.9	-CUDA-11.3.1	foss/2021a
1.7.7		foss/2022a
1.7.7	-CUDA-11.7.0	foss/2022a
1.8.4		foss/2022a
1.8.4	-CUDA-11.7.0	foss/2022a
2.1.2		foss/2022b
2.2.1		foss/2023a
2.2.1	-CUDA-12.1.1	foss/2023a

PyTorch3D

PyTorch3D is FAIR's library of reusable components for deep learning with 3D data.

homepage: https://pytorch3d.org/

version	versionsuffix	toolchain
0.4.0	-PyTorch-1.7.1	fosscuda/2020b

PyTorchVideo

PyTorchVideo is a deeplearning library with a focus on video understanding work. PytorchVideo provides reusable, modular and efficient components needed to accelerate the video understanding research. PyTorchVideo is developed using PyTorch and supports different deeplearning video components like video models, video datasets, and video-specific transforms.

homepage: https://pytorchvideo.org/

version	versionsuffix	toolchain
0.1.5	-PyTorch-1.12.0	foss/2022a
0.1.5	-PyTorch-1.12.0-CUDA-11.7.0	foss/2022a

PyVCF

A Variant Call Format reader for Python.

homepage: https://github.com/jamescasbon/PyVCF

version	versionsuffix	toolchain
0.6.8	-Python-2.7.16	GCC/8.3.0

PyVCF3

A VCFv4.0 and 4.1 parser for Python. The intent of this module is to mimic the csv module in the Python stdlib, as opposed to more flexible serialization formats like JSON or YAML. vcf will attempt to parse the content of each record based on the data types specified in the meta-information lines -- specifically the ##INFO and ##FORMAT lines. If these lines are missing or incomplete, it will check against the reserved types mentioned in the spec. Failing that, it will just return strings. PyVCF3 has been created because the Official PyVCF repository is no longer maintained and do not accept any pull requests. This fork is for python 3 only and has been published on pyPI as PyVCF3.

homepage: https://github.com/dridk/PyVCF3

version	toolchain
1.0.3	GCCcore/11.3.0

pyWannier90

A Wannier90 Python interface for VASP and PySCF

homepage: https://github.com/hungpham2017/pyWannier90

version	toolchain
2021-12-07	foss/2021a, gomkl/2021a

PyWavelets

PyWavelets is open source wavelet transform software for Python.

homepage: https://pywavelets.readthedocs.io

version	versionsuffix	toolchain
1.1.1		intelcuda/2020b
1.1.1	-Python-3.7.4	intel/2019b

PyWBGT

Cython source code for estimating wet bulb globe temperature (WBGT) from datasets of standard meterological measurements using models developed by Liljegren et al (2008)

homepage: https://github.com/QINQINKONG/PyWBGT

version	toolchain
1.0.0	foss/2021b, foss/2022a

pyXDF

Python package for working with XDF files.

homepage: https://github.com/xdf-modules/pyxdf

version	toolchain
1.16.3	foss/2021a
1.16.5	gfbf/2023a

PyYAML

PyYAML is a YAML parser and emitter for the Python programming language.

homepage: https://github.com/yaml/pyyaml

version	versionsuffix	toolchain
3.11	-Python-2.7.11	intel/2016a
3.12		system
3.12	-Python-2.7.12	foss/2016b, intel/2016b
3.12	-Python-2.7.13	intel/2017a
3.12	-Python-2.7.14	foss/2017b, foss/2018a, fosscuda/2017b, intel/2017b, intel/2018a
3.12	-Python-3.5.2	intel/2016b
3.12	-Python-3.6.1	intel/2017a
3.12	-Python-3.6.3	foss/2017b, fosscuda/2017b, intel/2017b
3.12	-Python-3.6.4	foss/2018a, intel/2018a
3.13		system
3.13	-Python-2.7.15	fosscuda/2018b, intel/2018b
3.13	-Python-3.6.6	foss/2018b, fosscuda/2018b, intel/2018b
5.1		GCCcore/8.2.0
5.1.2		GCCcore/8.3.0
5.3		GCCcore/9.3.0
5.3.1		GCCcore/10.2.0
5.4.1		GCCcore/10.3.0, GCCcore/11.2.0
5.4.1	-Python-2.7.18	GCCcore/11.2.0
6.0		GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0
6.0.1		GCCcore/13.2.0

PyZMQ

Python bindings for ZeroMQ

homepage: https://www.zeromq.org/bindings:python

version	versionsuffix	toolchain
15.2.0	-Python-2.7.11-zmq4	foss/2016a, intel/2016a
15.2.0	-Python-3.5.1-zmq4	intel/2016a
15.3.0	-Python-2.7.11-zmq4	foss/2016a
15.3.0	-Python-3.5.1-zmq4	foss/2016a
15.4.0	-Python-2.7.12-zmq4	intel/2016b
15.4.0	-Python-3.5.2-zmq4	intel/2016b
16.0.2	-Python-2.7.12-zmq4	foss/2016b, intel/2016b
16.0.2	-Python-2.7.13-zmq4	foss/2017a, intel/2017a
16.0.2	-Python-3.5.2-zmq4	foss/2016b, intel/2016b
16.0.3	-Python-2.7.14-zmq4	intel/2017b
17.0.0	-Python-2.7.14-zmq4	foss/2018a
17.0.0	-Python-3.6.4-zmq4	foss/2018a
18.1.1	-Python-3.7.4	GCCcore/8.3.0
22.3.0		GCCcore/10.3.0
24.0.1		GCCcore/11.3.0
25.1.0		GCCcore/12.2.0
25.1.1		GCCcore/12.3.0
25.1.2		GCCcore/13.2.0

Q

q2-krona - Q6 - QCA - qcat - QCG-PilotJob - qcint - QCxMS - QD - QDD - QEMU - qforce - QGIS - Qhull - QIIME - QIIME2 - Qiskit - QJson - QML - qnorm - qpth - qrupdate - QScintilla - Qt - Qt5 - Qt5Webkit - Qt6 - Qtconsole - QtKeychain - QTLtools - qtop - QtPy - Qualimap - Quandl - QuantumESPRESSO - QUAST - QuaZIP - QuickFF - QuickPIC - QuickTree - Quip - Quorum - QuPath - QuTiP - Qwt - QwtPolar

q2-krona

QIIME2 plugin for creating Krona plots

homepage: https://library.qiime2.org/plugins/q2-krona/39/

version	toolchain
20220124	GCCcore/11.3.0

Q6

EVB, FEP and LIE simulator.

homepage: https://github.com/qusers/Q6

version	toolchain
20180205	gompi/2019a

QCA

Taking a hint from the similarly-named Java Cryptography Architecture, QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as Providers. The advantage of this model is to allow applications to avoid linking to or explicitly depending on any particular cryptographic library. This allows one to easily change or upgrade crypto implementations without even needing to recompile the application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX.

homepage: https://userbase.kde.org/QCA

version	toolchain
2.1.0	foss/2016a, intel/2016b
2.1.3	GCCcore/8.2.0, foss/2016b, intel/2016b
2.3.5	GCCcore/11.2.0

qcat

qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files

homepage: https://github.com/nanoporetech/qcat/releases

version	versionsuffix	toolchain
1.1.0		foss/2022b
1.1.0	-Python-3.7.4	foss/2019b, intel/2019b
1.1.0	-Python-3.8.2	intel/2020a

QCG-PilotJob

A python service for easy execution of many tasks inside a single allocation.

homepage: https://qcg-pilotjob.readthedocs.org

version	toolchain
0.12.3	foss/2021a
0.13.1	foss/2022a, gfbf/2022b, gfbf/2023b

qcint

libcint is an open source library for analytical Gaussian integrals. qcint is an optimized libcint branch for the x86-64 platform.

homepage: http://wiki.sunqm.net/libcint

version	toolchain
3.0.18	foss/2019a

QCxMS

QCxMS is a quantum chemical based program to calculate electron ionization (EI) and collision induced dissociation (CID) mass spectra using Born-Oppenheimer Molecular Dynamics (BO-MD). It is the successor of the QCEIMS program, in which the EI part is exchanged to x to account for the greater general applicibility of the program.

homepage: https://xtb-docs.readthedocs.io/en/latest/qcxms_doc/qcxms.html

version	toolchain
5.0.3	system

QD

Quad Double computation package

homepage: https://github.com/scibuilder/QD

version	versionsuffix	toolchain
0.8.9		foss/2021a
2.3.17	-20160110	NVHPC/21.2

QDD

A user-friendly program to select microsatellite markers and design primers from large sequencing projects.

homepage: http://net.imbe.fr/~emeglecz/qdd.html

version	versionsuffix	toolchain
3.1.2	-Perl-5.28.0	intel/2018b

QEMU

QEMU is a generic and open source machine emulator and virtualizer.

homepage: https://www.qemu.org/

version	toolchain
2.10.1	intel/2017b

qforce

Quantum Mechanically augmented molecular force fields. Q-Force is a software package for deriving all-atom force fields from quantum mechanical calculations in an automated manner.

homepage: https://github.com/selimsami/qforce

version	toolchain
0.6.11	foss/2022a

QGIS

QGIS is a user friendly Open Source Geographic Information System (GIS)

homepage: http://www.qgis.org/

version	versionsuffix	toolchain
2.14.12	-Python-2.7.12	intel/2016b
2.18.4	-Python-2.7.12	foss/2016b
3.4.12	-Python-3.7.2	foss/2019a
3.28.1		foss/2021b

Qhull

Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull.

homepage: http://www.qhull.org

version	toolchain
2015.2	GCCcore/5.4.0, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.3.0, foss/2016a, foss/2016b, foss/2017b, intel/2016a, intel/2016b, intel/2017a
2019.1	GCCcore/8.2.0, GCCcore/8.3.0
2020.2	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

QIIME

QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.

homepage: http://qiime.org/

version	toolchain
1.9.1	system

QIIME2

QIIME 2 is a powerful, extensible, and decentralized microbiome bioinformatics platform that is free, open source, and community developed.

homepage: https://qiime2.org

version	toolchain
2017.10	system
2018.2	system
2019.4	system
2019.7	system
2020.8	system
2020.11	system
2021.8	system
2022.8	system
2022.11	system
2023.5.1	foss/2022a
2023.7.0	foss/2022a

Qiskit

Qiskit is an open-source framework for working with noisy quantum computers at the level of pulses, circuits, and algorithms.

homepage: https://qiskit.org

version	versionsuffix	toolchain
0.11.1	-Python-3.7.2	foss/2019a
0.12.0	-Python-3.7.2	foss/2019a
0.31.0		foss/2021a

QJson

QJson is a Qt-based library that maps JSON data to QVariant objects and vice versa.

homepage: http://qjson.sourceforge.net/

version	toolchain
0.9.0	GCCcore/10.2.0, GCCcore/8.2.0, foss/2016b, intel/2016b

QML

QML is a Python2/3-compatible toolkit for representation learning of properties of molecules and solids.

homepage: https://www.qmlcode.org

version	versionsuffix	toolchain
0.2.10	-Python-2.7.13	intel/2017a

qnorm

Fast-ish (and correct!) quantile normalization in Python

homepage: https://github.com/Maarten-vd-Sande/qnorm

version	toolchain
0.8.1	foss/2022a

qpth

A fast and differentiable QP solver for PyTorch.

homepage: https://locuslab.github.io/qpth/

version	versionsuffix	toolchain
0.0.13-20190626	-Python-3.7.2	foss/2019a

qrupdate

qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.

homepage: https://sourceforge.net/projects/qrupdate/

version	toolchain
1.1.2	GCC/5.4.0-2.26, GCC/8.2.0-2.31.1, GCCcore/10.2.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/6.4.0, GCCcore/8.3.0, foss/2016a, foss/2018a, foss/2018b, intel/2016a, intel/2016b, intel/2017a

QScintilla

QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control

homepage: https://www.riverbankcomputing.com/software/qscintilla

version	versionsuffix	toolchain
2.9.4	-Python-2.7.12	foss/2016b, intel/2016b
2.10	-Python-2.7.12	foss/2016b, intel/2016b
2.11.2	-Python-3.7.2	GCCcore/8.2.0
2.11.6		GCCcore/11.2.0

Qt

Qt is a comprehensive cross-platform C++ application framework.

homepage: http://qt.io/

version	versionsuffix	toolchain
3.3.8		intel/2016a
4.8.6		system
4.8.7		GCCcore/8.2.0, foss/2016a, foss/2016b, foss/2017a, foss/2017b, foss/2018a, foss/2018b, fosscuda/2018b, gimkl/2.11.5, intel/2016a, intel/2016b, intel/2017a, intel/2017b, intel/2018a
4.8.7	-GLib-2.48.0	foss/2016a, intel/2016a

Qt5

Qt is a comprehensive cross-platform C++ application framework.

homepage: https://qt.io/

version	toolchain
5.6.0	foss/2016a, intel/2016a
5.7.0	foss/2016a, foss/2016b, intel/2016a, intel/2016b
5.7.1	intel/2016b
5.8.0	foss/2017a, foss/2017b, intel/2016b, intel/2017a, intel/2017b
5.9.3	foss/2017b
5.9.8	fosscuda/2018b
5.10.1	foss/2018a, foss/2018b, fosscuda/2018b, intel/2018a, intel/2018b
5.11.2	foss/2018b
5.12.3	GCCcore/8.2.0
5.13.1	GCCcore/8.3.0
5.14.1	GCCcore/9.3.0
5.14.2	GCCcore/10.2.0
5.15.2	GCCcore/10.3.0, GCCcore/11.2.0
5.15.5	GCCcore/11.3.0
5.15.7	GCCcore/12.2.0
5.15.10	GCCcore/12.3.0
5.15.13	GCCcore/13.2.0

Qt5Webkit

Qt Port of WebKit. WebKit is an open source web browser engine.

homepage: https://github.com/qt/qtwebkit

version	toolchain
5.212.0-alpha3	GCCcore/8.2.0
5.212.0-alpha4	GCCcore/10.2.0, GCCcore/11.2.0, GCCcore/11.3.0

Qt6

Qt is a comprehensive cross-platform C++ application framework.

homepage: https://qt.io/

version	toolchain
6.5.2	GCCcore/12.3.0
6.6.3	GCCcore/13.2.0

Qtconsole

A rich Qt-based console for working with Jupyter kernels, supporting rich media output, session export, and more. The Qtconsole is a very lightweight application that largely feels like a terminal, but provides a number of enhancements only possible in a GUI, such as inline figures, proper multiline editing with syntax highlighting, graphical calltips, and more.

homepage: https://jupyter.org/

version	versionsuffix	toolchain
4.7.7	-Python-3.7.4	foss/2019b, fosscuda/2019b
5.0.2		GCCcore/10.2.0
5.3.2		GCCcore/11.2.0
5.4.0		GCCcore/11.3.0
5.5.1		GCCcore/12.3.0

QtKeychain

Platform-independent Qt API for storing passwords securely.

homepage: https://github.com/frankosterfeld/qtkeychain

version	toolchain
0.9.1	GCCcore/8.2.0, foss/2018b
0.13.2	GCCcore/11.2.0

QTLtools

QTLtools is a tool set for molecular QTL discovery and analysis. It allows to go from the raw sequence data to collection of molecular Quantitative Trait Loci (QTLs) in few easy-to-perform steps.

homepage: https://qtltools.github.io/qtltools/

version	toolchain
1.1	intel/2016b
1.3.1	foss/2020b

qtop

qtop is a nifty command-line tool for monitoring queueing systems, esp. PBS/torque. It tries to fit as much information as possible in your screen's real estate, by stitching together the output of commands like pbsnodes -a, qstat & qstat -q. It is possible to write wrappers for other platforms -people have done so for SGE, OAR etc- or, even examine traces offline and present the sampled information.

homepage: http://cern.ch/fotis/QTOP/

version	versionsuffix	toolchain
53	-1	system

QtPy

QtPy is a small abstraction layer that lets you write applications using a single API call to either PyQt or PySide. It provides support for PyQt5, PyQt4, PySide2 and PySide.

homepage: https://github.com/spyder-ide/qtpy

version	versionsuffix	toolchain
1.9.0		GCCcore/10.2.0
1.9.0	-Python-3.7.4	GCCcore/8.3.0
2.2.1		GCCcore/11.2.0
2.3.0		GCCcore/11.3.0
2.4.1		GCCcore/12.3.0

Qualimap

Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.

homepage: http://qualimap.bioinfo.cipf.es/

version	versionsuffix	toolchain
2.2.1	-R-3.6.0	foss/2019a
2.2.1	-R-4.0.3	foss/2020b
2.2.1	-R-4.1.2	foss/2021b

Quandl

A Python library for Quandl’s RESTful API.

homepage: https://pypi.python.org/pypi/Quandl

version	versionsuffix	toolchain
3.4.2	-Python-3.6.4	intel/2018a
3.4.8		foss/2019a
3.6.1		foss/2020b, foss/2021a

QuantumESPRESSO

Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).

homepage: https://www.quantum-espresso.org

version	versionsuffix	toolchain
5.3.0		intel/2016.02-GCC-4.9
5.4.0		intel/2016.02-GCC-4.9
5.4.0	-hybrid	foss/2016b
6.0		intel/2016b
6.1		intel/2017a
6.2		intel/2017b
6.2.1		iomkl/2017b
6.3		foss/2018b, intel/2018b
6.4.1		intel/2019a
6.5		intel/2019a, intel/2019b
6.6		foss/2019b, foss/2020a, foss/2020b, intel/2019b, intel/2020a
6.7		foss/2019b, foss/2020b, foss/2021a, intel/2019b, intel/2021a, iomkl/2019b
6.8		foss/2021a, foss/2021b, intel/2021a
7.0		foss/2021b, intel/2021b
7.1		foss/2022a, intel/2022a
7.2		foss/2022b, foss/2023a, intel/2022b
7.3		foss/2023a, intel/2023a

QUAST

QUAST evaluates genome assemblies by computing various metrics. It works both with and without reference genomes. The tool accepts multiple assemblies, thus is suitable for comparison.

homepage: https://github.com/ablab/quast

version	versionsuffix	toolchain
4.6.0	-Python-3.5.2	foss/2016b
4.6.3	-Python-3.6.4	foss/2018a
5.0.2		foss/2020b, foss/2021a, foss/2021b
5.0.2	-Python-2.7.15	foss/2018b, foss/2019a
5.0.2	-Python-2.7.18	foss/2020b
5.0.2	-Python-3.7.2	foss/2019a
5.0.2	-Python-3.8.2	foss/2020a
5.2.0		foss/2022a

QuaZIP

QuaZIP is the C++ wrapper for Gilles Vollant's ZIP/UNZIP package (AKA Minizip) using Trolltech's Qt library.

homepage: https://stachenov.github.io/quazip

version	toolchain
0.8.1	GCCcore/8.2.0

QuickFF

QuickFF is a Python package developed at the Center for Molecular Modeling (CMM) to quickly derive accurate force fields from ab initio calculations.

homepage: https://molmod.github.io/QuickFF/

version	versionsuffix	toolchain
2.1.4	-Python-2.7.12	intel/2016b
2.2.0	-Python-2.7.14	intel/2017b
2.2.4	-Python-3.7.2	intel/2019a
2.2.4	-Python-3.8.2	intel/2020a
2.2.7	-Python-3.8.2	intel/2020a

QuickPIC

QuickPIC is a 3D parallel (MPI & OpenMP Hybrid) Quasi-Static PIC code, which is developed based on the framework UPIC. QuickPIC can efficiently simulate plasma based accelerator problems. This is the UCLA Plasma Simulation Group's official open-source repository for QuickPIC.

homepage: https://github.com/UCLA-Plasma-Simulation-Group/QuickPIC-OpenSource

version	toolchain
20210224	gompi/2021b

QuickTree

QuickTree is an efficient implementation of the Neighbor-Joining algorithm (PMID: 3447015), capable of reconstructing phylogenies from huge alignments in time less than the age of the universe.

homepage: https://github.com/khowe/quicktree

version	toolchain
2.5	GCC/12.2.0

Quip

Quip compresses next-generation sequencing data with extreme prejudice. It supports input and output in the FASTQ and SAM/BAM formats, compressing large datasets to as little as 15% of their original size.

homepage: http://homes.cs.washington.edu/~dcjones/quip

version	toolchain
1.1.8	GCC/4.8.2

Quorum

QuorUM is an error corrector for Illumina reads

homepage: http://www.genome.umd.edu/quorum.html

version	toolchain
1.1.1	intel/2017a

QuPath

QuPath is open source software for bioimage analysis. QuPath is often used for digital pathology applications because it offers a powerful set of tools for working with whole slide images - but it can be applied to lots of other kinds of image as well.

homepage: https://qupath.github.io

version	versionsuffix	toolchain
0.5.0	-Java-17	GCCcore/12.3.0

QuTiP

QuTiP is open-source software for simulating the dynamics of open quantum systems.

homepage: http://qutip.org

version	versionsuffix	toolchain
4.1.0	-Python-2.7.12	intel/2016b
4.3.1	-Python-3.6.6	foss/2018b, intel/2018b

Qwt

The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background.

homepage: https://qwt.sourceforge.io/

version	toolchain
6.1.2	intel/2016a
6.1.3	foss/2016b, intel/2016b
6.1.4	GCCcore/8.2.0, GCCcore/8.3.0, foss/2018b
6.1.5	GCCcore/10.2.0, GCCcore/9.3.0
6.2.0	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/12.2.0

QwtPolar

The QwtPolar library contains classes for displaying values on a polar coordinate system.

homepage: http://qwtpolar.sourceforge.net/

version	toolchain
1.1.1	GCCcore/10.2.0, GCCcore/8.2.0, foss/2016b, intel/2016b

R

R - R-bundle-Bioconductor - R-bundle-CRAN - R-INLA - R-keras - R-MXM - R-opencv - R-tesseract - R-transport - R2jags - Racon - radeontop - radian - RaGOO - Ragout - RagTag - rampart - randfold - randrproto - rapidcsv - RapidJSON - rapidNJ - rapidtide - RAPSearch2 - Raptor - Rascaf - RASPA2 - rasterio - rasterstats - Ratatosk - Raven - RAxML - RAxML-NG - Ray-assembler - Ray-project - Raysect - RBFOpt - RCall - rclone - Rcorrector - RcppGSL - rCUDA - RDFlib - RDKit - RDP-Classifier - RE2 - re2c - Reads2snp - Reapr - ReaxFF - RECON - Red - Redis - redis-py - Redundans - ReFrame - regionmask - RegTools - Relate - RELION - remake - ReMatCh - REMORA - renderproto - RepastHPC - RepeatMasker - RepeatModeler - RepeatScout - request - requests - RERconverge - ResistanceGA - resolos - Restrander - rethinking - retworkx - RevBayes - RFdiffusion - rgdal - rgeos - Rgurobi - rhdf5 - RHEIA - RheoTool - Rhodium - rickflow - RInChI - rioxarray - ripunzip - rising - Rivet - rjags - RLCard - rmarkdown - Rmath - rMATS-turbo - RMBlast - RNA-Bloom - RNA-SeQC - RNAclust - RNAcode - RNAIndel - RNAmmer - rnaQUAST - RNAz - RnBeads - Roary - ROCm - rocm-cmake - ROCm-CompilerSupport - rocm-smi - rocminfo - ROCR-Runtime - ROCT-Thunk-Interface - ROI_PAC - ROME - ROOT - root_numpy - rootpy - Rosetta - rpmrebuild - RPostgreSQL - rpy2 - RQGIS3 - RSEM - RSeQC - RStan - rstanarm - RStudio-Server - RTG-Tools - Rtree - ruamel.yaml - Ruby - Ruby-Tk - ruffus - ruptures - Rust - rustworkx

R

R is a free software environment for statistical computing and graphics.

homepage: https://www.r-project.org/

version	versionsuffix	toolchain
3.2.3		foss/2016a, foss/2016b, intel/2016a
3.2.3	-bare	foss/2016a, intel/2016a
3.2.3	-libX11-1.6.3	intel/2016a
3.3.1		foss/2016a, foss/2016b, intel/2016b
3.3.3	-X11-20160819	foss/2016b, intel/2016b
3.3.3	-X11-20170314	intel/2017a
3.4.0	-X11-20170314	intel/2017a
3.4.1	-X11-20160819	foss/2016b
3.4.3	-X11-20171023	foss/2017b, intel/2017b
3.4.3	-X11-20171023-HDF5-1.8.19	intel/2017b
3.4.4	-X11-20180131	foss/2018a, intel/2018a, iomkl/2018a
3.5.0	-X11-20180131	iomkl/2018a
3.5.1		foss/2018b, intel/2018b
3.5.1	-Python-2.7.15	foss/2018b
3.5.1	-bare	foss/2018b
3.6.0		foss/2019a, fosscuda/2019a, intel/2019a
3.6.2		foss/2019b, fosscuda/2019b, intel/2019b
3.6.3		foss/2020a
4.0.0		foss/2020a, fosscuda/2020a
4.0.3		foss/2020b, fosscuda/2020b
4.0.4		foss/2020b, fosscuda/2020b
4.0.5		foss/2020b, fosscuda/2020b
4.1.0		foss/2021a
4.1.2		foss/2021b
4.2.0		foss/2021b
4.2.1		foss/2022a
4.2.2		foss/2022b
4.3.2		gfbf/2023a
4.3.3		gfbf/2023b

R-bundle-Bioconductor

Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data.

homepage: https://bioconductor.org

version	versionsuffix	toolchain
3.2	-R-3.2.3	foss/2016a, intel/2016a
3.3	-R-3.3.1	intel/2016b
3.5	-R-3.4.0	intel/2017a
3.6	-R-3.4.3	foss/2017b, intel/2017b
3.6	-R-3.4.4	intel/2018a
3.7	-R-3.5.0	iomkl/2018a
3.7	-R-3.5.1	foss/2018b
3.8	-R-3.5.1	foss/2018b
3.9	-R-3.6.0	foss/2019a
3.10		foss/2019b
3.11	-R-4.0.0	foss/2020a
3.12	-R-4.0.3	foss/2020b
3.13	-R-4.1.0	foss/2021a
3.14	-R-4.1.2	foss/2021b
3.15	-R-4.2.0	foss/2021b
3.15	-R-4.2.1	foss/2022a
3.16	-R-4.2.2	foss/2022b
3.18	-R-4.3.2	foss/2023a

R-bundle-CRAN

Bundle of R packages from CRAN

homepage: https://www.r-project.org/

version	toolchain
2023.12	foss/2023a

R-INLA

R-INLA is a package in R that do approximate Bayesian inference for Latent Gaussian Models.

homepage: https://www.r-inla.org

version	versionsuffix	toolchain
21.05.02	-R-4.0.4	foss/2020b

R-keras

Interface to 'Keras' https://keras.io, a high-level neural networks 'API'.

homepage: https://cran.r-project.org/web/packages/keras

version	versionsuffix	toolchain
2.1.6	-R-3.4.4	foss/2018a
2.2.5.0	-Python-3.7.2-R-3.6.0	foss/2019a, fosscuda/2019a
2.2.5.0	-Python-3.7.4-R-3.6.2	foss/2019b, fosscuda/2019b
2.4.0	-R-4.0.4	foss/2020b, fosscuda/2020b

R-MXM

MXM: Feature Selection (Including Multiple Solutions) and Bayesian Networks

homepage: https://cran.r-project.org/package=MXM

version	toolchain
1.5.5	foss/2021b

R-opencv

Experimenting with computer vision and machine learning in R. This package exposes some of the available OpenCV algorithms, such as edge, body or face detection. These can either be applied to analyze static images, or to filter live video footage from a camera device.

homepage: https://cran.r-project.org/web/packages/opencv/

version	versionsuffix	toolchain
0.2.0	-R-4.0.0	foss/2020a

R-tesseract

The R extension for using tesseract

homepage: https://cran.r-project.org/package=tesseract

version	versionsuffix	toolchain
4.0	-R-3.5.1	foss/2018b
5.1.0	-R-4.2.1	foss/2022a

R-transport

transport: Computation of Optimal Transport Plans and Wasserstein Distances

homepage: https://cran.r-project.org/package=transport

version	toolchain
0.13-0	foss/2021b

R2jags

Providing wrapper functions to implement Bayesian analysis in JAGS.

homepage: https://cran.r-project.org/web/packages/R2jags

version	versionsuffix	toolchain
0.7-1	-R-4.2.1	foss/2022a

Racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.

homepage: https://github.com/lbcb-sci/racon

version	toolchain
1.3.2	GCCcore/8.2.0
1.4.7	GCCcore/8.2.0, gcccuda/2019b
1.4.10	GCC/7.3.0-2.30
1.4.13	GCCcore/8.3.0, GCCcore/9.3.0
1.4.21	GCCcore/10.2.0, GCCcore/10.3.0
1.5.0	GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0

radeontop

View your GPU utilization, both for the total activity percent and individual blocks.

homepage: https://github.com/clbr/radeontop

version	toolchain
1.3	GCCcore/10.3.0

radian

radian is an alternative console for the R program with multiline editing and rich syntax highlight.

homepage: https://github.com/randy3k/radian

version	toolchain
0.6.9	foss/2022b

RaGOO

A tool to order and orient genome assembly contigs via Minimap2 alignments to a reference genome

homepage: https://github.com/malonge/RaGOO

version	versionsuffix	toolchain
1.11	-Python-3.6.6	foss/2018b

Ragout

Ragout (Reference-Assisted Genome Ordering UTility) is a tool for chromosome-level scaffolding using multiple references. Given initial assembly fragments (contigs/scaffolds) and one or multiple related references (complete or draft), it produces a chromosome-scale assembly (as a set of scaffolds).

homepage: https://github.com/fenderglass/Ragout

version	versionsuffix	toolchain
2.0	-Python-2.7.12	foss/2016b
2.3		foss/2020b

RagTag

RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include: homology-based misassembly correction, homology-based assembly scaffolding and patching, and scaffold merging. RagTag also provides command line utilities for working with common genome assembly file formats.

homepage: https://github.com/malonge/RagTag

version	toolchain
2.0.1	foss/2020b
2.1.0	foss/2022a

rampart

Read Assignment, Mapping, and Phylogenetic Analysis in Real Time.

homepage: https://github.com/artic-network/rampart/

version	versionsuffix	toolchain
1.2.0		foss/2020b
1.2.0rc3	-Python-3.6.6	foss/2018b

randfold

Minimum free energy of folding randomization test software

homepage: http://bioinformatics.psb.ugent.be/software/details/Randfold

version	toolchain
2.0.1	foss/2018b, intel/2016b

randrproto

Xrandr protocol and ancillary headers

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.5.0	foss/2016a, intel/2016a

rapidcsv

Rapidcsv is a C++ header-only library for CSV parsing. While the name admittedly was inspired by the rapidjson project, the objectives are not the same. The goal of rapidcsv is to be an easy-to-use CSV library enabling rapid development. For optimal performance (be it CPU or memory usage) a CSV parser implemented for the specific use-case is likely to be more performant.

homepage: https://github.com/d99kris/rapidcsv

version	toolchain
8.62	GCCcore/11.2.0
8.64	GCCcore/11.3.0

RapidJSON

A fast JSON parser/generator for C++ with both SAX/DOM style API

homepage: https://rapidjson.org

version	toolchain
1.1.0	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
1.1.0-20230928	GCCcore/12.3.0

rapidNJ

RapidNJ is an algorithmic engineered implementation of canonical neighbour-joining. It uses an efficient search heuristic to speed-up the core computations of the neighbour-joining method that enables RapidNJ to outperform other state-of-the-art neighbour-joining implementations.

homepage: https://github.com/somme89/rapidNJ

version	toolchain
2.3.3	GCCcore/11.3.0

rapidtide

Rapidtide is a suite of python programs used to perform time delay analysis on functional imaging data to find time lagged correlations between the voxelwise time series and other time series.

homepage: https://rapidtide.readthedocs.io

version	versionsuffix	toolchain
1.8.0	-Python-3.7.2	intel/2019a

RAPSearch2

RAPSearch stands for Reduced Alphabet based Protein similarity Search

homepage: https://omics.informatics.indiana.edu/mg/RAPSearch2

version	toolchain
2.24	GCC/9.3.0

Raptor

Set of parsers and serializers that generate Resource Description Framework (RDF) triples by parsing syntaxes or serialize the triples into a syntax.

homepage: https://librdf.org/raptor/

version	toolchain
2.0.16	GCCcore/10.3.0

Rascaf

Rascaf (RnA-seq SCAFfolder) uses continuity and order information from paired-end RNA-seq reads to improve a draft assembly, particularly in the gene regions.

homepage: https://github.com/mourisl/Rascaf

version	toolchain
1.0.2	intel/2017a

RASPA2

RASPA is a software package for simulating adsorption and diffusion of molecules in flexible nanoporous materials.

homepage: https://iraspa.org/raspa/

version	versionsuffix	toolchain
2.0.3	-Python-2.7.12	intel/2016b
2.0.41		foss/2020b
2.0.47		foss/2022a

rasterio

Rasterio reads and writes geospatial raster data.

homepage: https://github.com/mapbox/rasterio

version	versionsuffix	toolchain
1.1.7	-Python-3.8.2	foss/2020a
1.2.3		foss/2020b
1.2.10		foss/2021b
1.3.4		foss/2022a
1.3.8		foss/2022b
1.3.9		foss/2023a

rasterstats

rasterstats is a Python module for summarizing geospatial raster datasets based on vector geometries.

homepage: https://github.com/perrygeo/python-rasterstats

version	versionsuffix	toolchain
0.15.0	-Python-3.8.2	foss/2020a
0.19.0		foss/2022a

Ratatosk

Phased hybrid error correction of long reads using colored de Bruijn graphs

homepage: https://github.com/DecodeGenetics/Ratatosk

version	toolchain
0.4	GCC/10.2.0

Raven

Raven is a de novo genome assembler for long uncorrected reads.

homepage: https://github.com/lbcb-sci/raven

version	toolchain
1.8.1	GCC/11.2.0

RAxML

RAxML search algorithm for maximum likelihood based inference of phylogenetic trees.

homepage: https://github.com/stamatak/standard-RAxML

version	versionsuffix	toolchain
8.2.4	-hybrid-avx2	foss/2016a
8.2.9	-hybrid-avx2	foss/2016a
8.2.10	-hybrid-avx2	intel/2017a
8.2.11	-hybrid-avx	foss/2017b, intel/2017b
8.2.11	-hybrid-avx2	foss/2017b, intel/2017b, intel/2018a
8.2.11	-hybrid-sse3	foss/2017b, intel/2017b
8.2.12	-hybrid-avx2	gompi/2020a, gompi/2020b, gompi/2021a, gompi/2021b, iimpi/2019b, intel/2018b, intel/2019a
8.2.12	-pthreads-avx2	GCC/10.2.0

RAxML-NG

RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree.

homepage: https://github.com/amkozlov/raxml-ng

version	toolchain
0.9.0	GCC/8.3.0, gompi/2019b
1.0.1	gompi/2019b
1.0.2	gompi/2020b
1.0.3	GCC/10.2.0
1.1.0	GCC/11.2.0
1.2.0	GCC/12.3.0

Ray-assembler

Parallel genome assemblies for parallel DNA sequencing

homepage: http://denovoassembler.sourceforge.net/

version	toolchain
2.3.1	iimpi/2019a

Ray-project

Ray is a fast and simple framework for building and running distributed applications.

homepage: https://docs.ray.io/en/latest/

version	versionsuffix	toolchain
0.8.4	-Python-3.7.4	foss/2019b
1.0.1	-Python-3.7.4	fosscuda/2019b
1.9.2		foss/2021b
1.13.0		foss/2021a, foss/2021b
2.2.0		foss/2022a

Raysect

Raysect is an OOP ray-tracing framework for Python

homepage: https://raysect.org

version	versionsuffix	toolchain
0.6.0	-Python-3.6.6	intel/2018b
0.7.1		foss/2020b, intel/2020b

RBFOpt

RBFOpt is a Python library for black-box optimization (also known as derivative-free optimization).

homepage: https://github.com/coin-or/rbfopt

version	versionsuffix	toolchain
4.1.1		intel/2019a
4.1.1	-Python-3.6.6	intel/2018b

RCall

This package facilitates communication between R and Julia and allows the user to call R packages from within Julia, providing the best of both worlds.

homepage: https://github.com/JuliaInterop/RCall.jl

version	versionsuffix	toolchain
0.13.17	-R-4.2.1-Julia-1.9.2	foss/2022a

rclone

Rclone is a command line program to sync files and directories to and from a variety of online storage services

homepage: https://rclone.org

version	versionsuffix	toolchain
1.42	-amd64	system
1.54.1	-amd64	system
1.56.0	-amd64	system
1.57.0		system
1.63.1	-amd64	system
1.65.2		system
1.66.0		system

Rcorrector

Rcorrector(RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.

homepage: https://github.com/mourisl/Rcorrector

version	toolchain
1.0.2	intel/2017a

RcppGSL

The 'RcppGSL' package provides an easy-to-use interface between 'GSL' data structures and R using concepts from 'Rcpp' which is itself a package that eases the interfaces between R and C++.

homepage: https://cran.r-project.org/web/packages/RcppGSL

version	versionsuffix	toolchain
0.3.8	-R-4.0.4	foss/2020b

rCUDA

The rCUDA Framework enables the concurrent usage of CUDA-compatible devices remotely.

homepage: http://www.rcuda.net/

version	versionsuffix	toolchain
4.0.1	_linux_64_Ubuntu10.04	system
5.0	_linux_64_scientificLinux6	system

RDFlib

RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information.

homepage: https://github.com/RDFLib/rdflib

version	toolchain
4.2.2	GCCcore/8.3.0, foss/2019a
5.0.0	GCCcore/10.2.0
6.2.0	GCCcore/10.3.0, GCCcore/11.3.0
7.0.0	GCCcore/12.3.0

RDKit

RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.

homepage: https://www.rdkit.org

version	versionsuffix	toolchain
2018.09.3	-Python-3.6.6	intel/2018b
2019.09.3	-Python-3.7.4	foss/2019b
2020.03.3	-Python-3.8.2	foss/2020a, intel/2020a
2020.09.3	-Python-3.7.4	foss/2019b
2021.03.4		foss/2021a
2022.03.5		foss/2021b
2022.09.4		foss/2022a
2023.03.3		foss/2021a

RDP-Classifier

The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment.

homepage: http://sourceforge.net/projects/rdp-classifier

version	versionsuffix	toolchain
2.7	-Java-1.7.0_60	system
2.12	-Java-1.8	system
2.13	-Java-11	system
2.13	-Java-17	system

RE2

RE2 is a fast, safe, thread-friendly alternative to backtracking regular expression engines like those used in PCRE, Perl, and Python. It is a C++ library.

homepage: https://github.com/google/re2

version	toolchain
2020-07-01	GCCcore/8.3.0
2021-06-01	GCCcore/10.2.0
2022-02-01	GCCcore/10.3.0, GCCcore/11.2.0
2022-06-01	GCCcore/11.3.0
2023-03-01	GCCcore/12.2.0
2023-08-01	GCCcore/12.3.0
2024-03-01	GCCcore/13.2.0

re2c

re2c is a free and open-source lexer generator for C and C++. Its main goal is generating fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using traditional table-driven approach, re2c encodes the generated finite state automata directly in the form of conditional jumps and comparisons.

homepage: https://re2c.org

version	toolchain
1.1.1	GCCcore/8.2.0
1.2.1	GCCcore/8.3.0
1.3	GCCcore/9.3.0
2.0.3	GCCcore/10.2.0
2.1.1	GCCcore/10.3.0
2.2	GCCcore/11.2.0, GCCcore/11.3.0
3.0	GCCcore/12.2.0
3.1	GCCcore/12.3.0, GCCcore/13.2.0

Reads2snp

reads2snp is a SNP and genotype caller: it predicts the genotype of distinct individuals at distinct positions of a set of sequences based on read mapping / read counts. Its typical input is a bam file. Its typical output is a vcf file. It is written in C++, based on the bio++ libraries, multi-threaded with openMP, available under Linux and MacOS

homepage: http://kimura.univ-montp2.fr/PopPhyl/index.php?section=tools

version	toolchain
2.0	system

Reapr

A tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison.

homepage: https://www.sanger.ac.uk/science/tools/reapr

version	toolchain
1.0.18	foss/2019a

ReaxFF

simulation code of the REAXFF Reactive force field program

homepage: https://www.engr.psu.edu/adri/ReaxffManual.aspx

version	versionsuffix	toolchain
2.0	-param	GCC/11.3.0
2.0	-sim	GCC/11.3.0

RECON

Patched version of RECON to be used with RepeatModeler.

homepage: https://www.repeatmasker.org/RepeatModeler/

version	toolchain
1.08	GCC/10.2.0, GCC/11.3.0

Red

Red (REpeat Detector)

homepage: http://toolsmith.ens.utulsa.edu/

version	toolchain
2015-05-22	iccifort/2019.1.144-GCC-8.2.0-2.31.1

Redis

Redis is an open source (BSD licensed), in-memory data structure store, used as a database, cache, and message broker. Redis provides data structures such as strings, hashes, lists, sets, sorted sets with range queries, bitmaps, hyperloglogs, geospatial indexes, and streams. Redis has built-in replication, Lua scripting, LRU eviction, transactions, and different levels of on-disk persistence, and provides high availability via Redis Sentinel and automatic partitioning with Redis Cluster.

homepage: https://redis.io

version	toolchain
6.2.6	GCC/10.3.0, GCC/11.2.0
7.0.8	GCC/11.3.0
7.2.3	GCCcore/12.3.0
7.2.4	GCCcore/13.2.0

redis-py

The Python interface to the Redis key-value store.

homepage: https://github.com/redis/redis-py

version	toolchain
4.3.1	foss/2021a
4.3.3	foss/2021b
4.5.1	foss/2022a
5.0.1	GCCcore/12.3.0

Redundans

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

homepage: https://github.com/lpryszcz/redundans

version	toolchain
0.13c	intel/2017b

ReFrame

ReFrame is a framework for writing regression tests for HPC systems.

homepage: https://github.com/reframe-hpc/reframe

version	toolchain
2.18	system
2.19	system
2.20	system
2.21	system
3.0	system
3.2	system
3.3	system
3.4.1	system
3.5.0	system
3.5.1	system
3.5.2	system
3.6.2	system
3.6.3	system
3.7.3	system
3.8.0	system
3.9.0	system
3.9.1	system
3.10.1	system
3.11.0	system
3.11.1	system
3.11.2	system
3.12.0	system
4.0.1	system
4.0.5	system
4.2.0	system
4.3.2	system
4.3.3	system

regionmask

regionmask creates masks of geographical regions. It determines to which geographic region each grid point belongs.

homepage: https://regionmask.readthedocs.io

version	versionsuffix	toolchain
0.9.0		foss/2021b, foss/2022a
0.9.0	-Python-3.8.2	foss/2020a
0.10.0		foss/2022b

RegTools

RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.

homepage: https://regtools.readthedocs.org

version	toolchain
0.4.2	foss/2020b
0.5.2	foss/2020b, foss/2021b
1.0.0	foss/2022b

Relate

Software for estimating genome-wide genealogies for thousands of samples

homepage: https://myersgroup.github.io/relate/

version	versionsuffix	toolchain
20211123	-R-4.0.3	foss/2020b

RELION

RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM).

homepage: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page

version	versionsuffix	toolchain
1.4		intel/2016b
1.4	-single	intel/2016b
2.0.1		intel/2016b
2.1		foss/2017b, foss/2018a, fosscuda/2017b, fosscuda/2018a, intel/2017b, intelcuda/2017b
2.1	-CUDA-9.1.85	foss/2018a
3.0.4		foss/2017b, intel/2017b
3.0_beta.2018.08.02		fosscuda/2018a, intel/2018a

remake

remake is an enhanced version of GNU Make that adds improved error reporting, better tracing, profiling and a debugger

homepage: https://bashdb.sourceforge.net/remake

version	toolchain
4.3+dbg-1.6	GCCcore/11.3.0

ReMatCh

Reads mapping against target sequences, checking mapping and consensus sequences production

homepage: https://github.com/B-UMMI/ReMatCh

version	versionsuffix	toolchain
3.2	-Python-2.7.12	foss/2016b

REMORA

REsource MOnitoring for Remote Applications

homepage: https://github.com/TACC/remora

version	toolchain
1.8.2	foss/2017a, foss/2018a, intel/2017a, intel/2018a
1.8.3	gompi/2019a

renderproto

Xrender protocol and ancillary headers

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
0.11	foss/2016a, gimkl/2.11.5, intel/2016a, intel/2017b

RepastHPC

The Repast Suite is a family of advanced, free, and open source agent-based modeling and simulation platforms that have collectively been under continuous development for over 15 years: Repast for High Performance Computing 2.2.0, released on 30 September 2016, is a lean and expert-focused C++-based modeling system that is designed for use on large computing clusters and supercomputers.

homepage: https://repast.github.io/

version	toolchain
2.2.0	foss/2016a

RepeatMasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

homepage: https://www.repeatmasker.org/

version	versionsuffix	toolchain
4.0.8	-Perl-5.26.0-HMMER	GCC/6.4.0-2.28, iccifort/2017.4.196-GCC-6.4.0-2.28
4.0.8	-Perl-5.28.0-HMMER	intel/2018b
4.0.9-p2	-HMMER	gompi/2019b
4.1.2-p1		foss/2020b
4.1.4		foss/2022a
4.1.5		foss/2021a, foss/2022a

RepeatModeler

RepeatModeler is a de novo transposable element (TE) family identification and modeling package.

homepage: https://www.repeatmasker.org/

version	toolchain
2.0.2a	foss/2020b
2.0.4	foss/2022a

RepeatScout

De Novo Repeat Finder, Price A.L., Jones N.C. and Pevzner P.A. Developed and tested with our multiple sequence version of RepeatScout ( 1.0.6 )

homepage: https://www.repeatmasker.org/

version	toolchain
1.0.6	GCC/10.2.0, GCC/11.3.0

request

Request is designed to be the simplest way possible to make http calls. It supports HTTPS and follows redirects by default.

homepage: https://github.com/request/request/

version	versionsuffix	toolchain
2.88.1	-nodejs-12.19.0	fosscuda/2020b

requests

Python http for humans

homepage: https://pypi.python.org/pypi/requests

version	versionsuffix	toolchain
2.10.0	-Python-2.7.11	foss/2016a
2.10.0	-Python-3.5.1	foss/2016a
2.11.1	-Python-2.7.12	intel/2016b
2.11.1	-Python-3.5.2	intel/2016b
2.13.0	-Python-2.7.12	foss/2016b, intel/2016b

RERconverge

RERconverge is a set of software written in R that estimates the correlation between relative evolutionary rates of genes and the evolution of a convergent binary or continuous trait across a phylogeny.

homepage: https://github.com/nclark-lab/RERconverge

version	versionsuffix	toolchain
0.1.0	-R-3.4.3	foss/2017b, intel/2017b

ResistanceGA

An R package to optimize resistance surfaces using Genetic Algorithms.

homepage: https://github.com/wpeterman/ResistanceGA

version	versionsuffix	toolchain
4.2-5	-R-4.2.1-Julia-1.9.2	foss/2022a

resolos

Resolos is a toolkit written in Python for maintaining reproducible environments for scientific computations. It's main goal is to enable researchers to easily replicate environments through space (running code on HPC environment) and time (environment preservation for long term archival). For installation and detailed usage, check out the documentation.

homepage: https://gitlab.unige.ch/resolos/resolos

version	toolchain
0.3.5	GCCcore/11.3.0

Restrander

A fast, accurate program for orienting and quality-checking cDNA sequencing reads.

homepage: https://github.com/mritchielab/restrander

version	toolchain
20230713	GCCcore/12.2.0

rethinking

R package that contains tools for conducting both quick quadratic approximation of the posterior distribution as well as Hamiltonian Monte Carlo.

homepage: https://github.com/rmcelreath/rethinking

version	versionsuffix	toolchain
2.40-20230914	-R-4.3.2	foss/2023a

retworkx

retworkx is a general purpose graph library for python3 written in Rust to take advantage of the performance and safety that Rust provides. It was built as a replacement for qiskit's previous (and current) networkx usage (hence the name) but is designed to provide a high performance general purpose graph library for any python application. The project was originally started to build a faster directed graph to use as the underlying data structure for the DAG at the center of qiskit-terra's transpiler, but it has since grown to cover all the graph usage in Qiskit and other applications.

homepage: https://github.com/Qiskit/retworkx

version	toolchain
0.9.0	foss/2021a

RevBayes

RevBayes provides an interactive environment for statistical computation in phylogenetics. It is primarily intended for modeling, simulation, and Bayesian inference in evolutionary biology, particularly phylogenetics.

homepage: https://revbayes.github.io

version	toolchain
1.1.1	GCC/10.2.0, GCC/11.2.0
1.2.1	gompi/2022a

RFdiffusion

RFdiffusion is an open source method for structure generation, with or without conditional information (a motif, target etc). It can perform a whole range of protein design challenges as we have outlined in the RFdiffusion paper.

homepage: https://github.com/RosettaCommons/RFdiffusion

version	versionsuffix	toolchain
1.1.0		foss/2022a
1.1.0	-CUDA-11.7.0	foss/2022a

rgdal

Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4 and <= 2.5.0) and access to projection/transformation operations from the 'PROJ.4' library.

homepage: https://rgdal.r-forge.r-project.org/

version	versionsuffix	toolchain
1.4-4	-R-3.6.0	foss/2019a
1.4-8	-R-3.6.2	foss/2019b
1.4-8	-R-4.0.0	foss/2020a
1.5-16	-R-4.0.0	foss/2020a
1.5-23	-R-4.0.4	foss/2020b
1.5-23	-R-4.1.0	foss/2021a
1.6-6		foss/2022a

rgeos

R interface to Geometry Engine - Open Source (GEOS) using the C API for topology operations on geometries

homepage: https://cran.r-project.org/web/packages/rgeos/

version	versionsuffix	toolchain
0.3-17	-R-3.2.3	intel/2016a
0.5-1	-R-3.6.0	foss/2019a
0.5-2	-R-3.6.2	foss/2019b
0.5-5	-R-4.0.0	foss/2020a
0.5-5	-R-4.1.0	foss/2021a

Rgurobi

Gurobi Optimizer 9.5 interface

homepage: https://www.gurobi.com

version	versionsuffix	toolchain
9.1.2	-R-4.1.0	foss/2021a
9.5.0	-R-4.1.0	foss/2021a

rhdf5

This R/Bioconductor package provides an interface between HDF5 and R.

homepage: https://bioconductor.org/packages/release/bioc/html/rhdf5.html

version	versionsuffix	toolchain
2.16.0	-R-3.2.3	intel/2016a
2.18.0	-R-3.3.1	intel/2016b

RHEIA

Robust design optimization of renewable Hydrogen and dErIved energy cArrier systems

homepage: https://github.com/rheia-framework/RHEIA

version	toolchain
1.1.6	foss/2022a

RheoTool

RheoTool is an open-source toolbox based on OpenFOAM to simulate Generalized Newtonian Fluids (GNF) and viscoelastic fluids under pressure-driven and/or electrically-driven flows.

homepage: https://github.com/fppimenta/rheoTool

version	toolchain
5.0	foss/2019b

Rhodium

Rhodium is an open source Python library for robust decision making (RDM) and multiobjective robust decision making (MORDM), and exploratory modelling (EM).

homepage: https://github.com/Project-Platypus/Rhodium

version	toolchain
1.2.0	foss/2022a

rickflow

Running and Analyzing OpenMM Jobs

homepage: https://gitlab.com/Olllom/rickflow

version	versionsuffix	toolchain
0.7.0	-Python-3.7.4	intel/2019b
0.7.0-20200529	-Python-3.7.4	intel/2019b

RInChI

The reaction IUPAC International Chemical Identifier (RInChI TM) is a non-proprietary identifier for chemical reactions that can be used in printed and electronic data sources thus enabling easier linking of diverse data compilations.

homepage: https://www.inchi-trust.org/

version	versionsuffix	toolchain
1.00	-x86_64	system

rioxarray

Geospatial xarray extension powered by rasterio

homepage: https://corteva.github.io/rioxarray

version	versionsuffix	toolchain
0.0.12	-Python-3.7.2	intel/2019a
0.0.24	-Python-3.7.4	foss/2019b
0.1.1	-Python-3.8.2	foss/2020a
0.11.1		foss/2021b
0.14.0		foss/2022a
0.15.0		foss/2023a

ripunzip

A tool to unzip files in parallel.

homepage: https://github.com/google/ripunzip

version	toolchain
0.4.0	system

rising

Provides everything needed for high performance data loading and augmentation in PyTorch.

homepage: https://rising.rtfd.io/

version	versionsuffix	toolchain
0.2.2		foss/2021a, foss/2022a
0.2.2	-CUDA-11.3.1	foss/2021a
0.2.2	-CUDA-11.7.0	foss/2022a

Rivet

Rivet toolkit (Robust Independent Validation of Experiment and Theory) To use your own analysis you must append the path to RIVET_ANALYSIS_PATH.

homepage: https://gitlab.com/hepcedar/rivet

version	versionsuffix	toolchain
3.1.7	-HepMC3-3.2.5	gompi/2022a
3.1.9	-HepMC3-3.2.6	gompi/2023a

rjags

The rjags package is an interface to the JAGS library.

homepage: https://cran.r-project.org/web/packages/rjags

version	versionsuffix	toolchain
4-6	-R-3.4.0	intel/2017a
4-6	-R-3.4.3	intel/2017b
4-8	-R-3.5.1	foss/2018b
4-9	-R-3.6.0	foss/2019a
4-10		foss/2019b
4-10	-R-4.0.0	foss/2020a
4-10	-R-4.0.3	foss/2020b, fosscuda/2020b
4-10	-R-4.0.4	foss/2020b, fosscuda/2020b
4-10	-R-4.0.5	foss/2020b, fosscuda/2020b
4-10	-R-4.1.0	foss/2021a
4-12	-R-4.1.2	foss/2021b
4-13	-R-4.2.1	foss/2022a
4-13	-R-4.2.2	foss/2022b

RLCard

RLCard is a toolkit for Reinforcement Learning (RL) in card games.

homepage: https://www.rlcard.org

version	toolchain
1.0.9	foss/2022a

rmarkdown

Convert R Markdown documents into a variety of formats.

homepage: https://cran.r-project.org/web/packages/rmarkdown

version	versionsuffix	toolchain
2.20	-R-4.1.0	foss/2021a

Rmath

Rmath is the standalone version of the R math library. Rmath can be used in your own C/C++ routines.

homepage: https://www.r-project.org/

version	toolchain
3.3.1	intel/2016b
4.0.4	foss/2020b

rMATS-turbo

rMATS turbo is the C/Cython version of rMATS (refer to https://rnaseq-mats.sourceforge.io).

homepage: https://github.com/Xinglab/rmats-turbo

version	toolchain
4.1.1	foss/2020b
4.2.0	gfbf/2023a

RMBlast

RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' for use with RepeatMasker and RepeatModeler.

homepage: http://www.repeatmasker.org/RMBlast.html

version	versionsuffix	toolchain
2.2.28	-Python-2.7.11	foss/2016a
2.9.0		gompi/2019b
2.10.0		gompi/2019b
2.11.0		gompi/2020b
2.13.0		gompi/2022a
2.14.0		gompi/2021a

RNA-Bloom

RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler.

homepage: https://github.com/bcgsc/RNA-Bloom

version	toolchain
1.2.3	GCC/8.3.0
1.4.3	GCC/11.2.0
2.0.1	GCC/12.3.0

RNA-SeQC

Fast, efficient RNA-Seq metrics for quality control and process optimization

homepage: https://github.com/getzlab/rnaseqc

version	versionsuffix	toolchain
1.1.8	-Java-1.8	foss/2018b
1.1.8	-Java-1.8.0_121	foss/2016b
1.1.8	-Java-11	GCCcore/11.2.0
2.4.2		foss/2021a, foss/2021b

RNAclust

RNAclust is a perl script summarizing all the single steps required for clustering of structured RNA motifs, i.e. identifying groups of RNA sequences sharing a secondary structure motif. It requires as input a multiple FASTA file.

homepage: http://www.bioinf.uni-leipzig.de/~kristin/Software/RNAclust/

version	versionsuffix	toolchain
1.3	-Perl-5.24.0	foss/2016b
1.3	-Python-3.6.6	foss/2018b

RNAcode

RNAcode - Analyze the protein coding potential in multiple sequence alignments

homepage: https://wash.github.io/rnacode/

version	toolchain
0.3	foss/2017a

RNAIndel

RNAIndel calls coding indels and classifies them into somatic, germline, and artifact from tumor RNA-Seq data.

homepage: https://github.com/stjude/RNAIndel

version	versionsuffix	toolchain
0.3.0	-Python-3.6.6	intel/2018b
1.0.0	-Python-3.6.6	intel/2018b

RNAmmer

This is an example description.

homepage: https://www.cbs.dtu.dk/services/RNAmmer

version	versionsuffix	toolchain
1.2	-Perl-5.28.0	intel/2018b

rnaQUAST

rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software.

homepage: https://cab.spbu.ru/software/rnaquast/

version	versionsuffix	toolchain
1.5.2	-Python-2.7.15	foss/2018b
2.2.0	-Python-3.8.2	foss/2020a
2.2.2		foss/2021b

RNAz

RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.

homepage: http://www.tbi.univie.ac.at/~wash/RNAz/

version	toolchain
2.1	foss/2016b, foss/2018b

RnBeads

RnBeads is an R package for comprehensive analysis of DNA methylation data obtained with any experimental protocol that provides single-CpG resolution.

homepage: https://rnbeads.org

version	versionsuffix	toolchain
2.6.0	-R-4.0.0	foss/2020a
2.14.0	-R-4.2.1	foss/2022a

Roary

Rapid large-scale prokaryote pan genome analysis

homepage: https://github.com/sanger-pathogens/Roary

version	versionsuffix	toolchain
3.12.0		system
3.12.0	-Perl-5.26.1	intel/2018a
3.13.0		foss/2020a, foss/2021a, foss/2022a

ROCm

AMD ROCm is the first open-source software development platform for HPC/Hyperscale-class GPU computing. AMD ROCm brings the UNIX philosophy of choice, minimalism and modular software development to GPU computing.

homepage: https://rocmdocs.amd.com/en/latest/

version	toolchain
4.5.0	GCCcore/11.2.0

rocm-cmake

ROCM cmake modules provides cmake modules for common build tasks needed for the ROCM software stack

homepage: https://github.com/RadeonOpenCompute/rocm-cmake

version	toolchain
4.5.0	GCCcore/11.2.0

ROCm-CompilerSupport

The compiler support repository provides various Lightning Compiler related services

homepage: https://github.com/RadeonOpenCompute/ROCm-CompilerSupport

version	toolchain
4.5.0	GCCcore/11.2.0

rocm-smi

The ROCm System Management Interface Library, or ROCm SMI library, is part of the Radeon Open Compute ROCm software stack. It is a C library for Linux that provides a user space interface for applications to monitor and control GPU applications.

homepage: https://github.com/RadeonOpenCompute/rocm_smi_lib

version	toolchain
4.5.0	GCCcore/11.2.0
5.4.4	GCCcore/11.3.0
5.6.0	GCCcore/11.3.0

rocminfo

ROCm Application for Reporting System Info

homepage: https://github.com/RadeonOpenCompute/rocminfo

version	toolchain
4.5.0	GCCcore/11.2.0

ROCR-Runtime

The user-mode API interfaces and libraries necessary for host applications to launch compute kernels to available HSA ROCm kernel agents

homepage: https://github.com/RadeonOpenCompute/ROCR-Runtime

version	toolchain
4.5.0	GCCcore/11.2.0

ROCT-Thunk-Interface

The user-mode API interfaces used to interact with the ROCk driver

homepage: https://github.com/RadeonOpenCompute/ROCT-Thunk-Interface

version	toolchain
4.5.0	GCCcore/11.2.0

ROI_PAC

Repeat Orbit Interferometry PACkage (ROI_PAC), software for processing synthetic aperture radar data to produce differential interferograms

homepage: http://roipac.org/

version	versionsuffix	toolchain
3.0.1	-Perl-5.24.1	intel/2017a

ROME

The ROME (Refinement and Optimization via Machine Learning for cryo-EM) Software package is one of the major research products at the Intel® PCCSB.

homepage: https://ipccsb.dfci.harvard.edu/rome

version	toolchain
1.1.2	intel/2019.02

ROOT

The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way.

homepage: http://root.cern.ch/drupal/

version	versionsuffix	toolchain
6.10.02	-Python-2.7.12	foss/2016b, intel/2016b
6.10.04	-Python-2.7.13	intel/2017a
6.10.08	-Python-2.7.14	foss/2017b, intel/2017b
6.14.06	-Python-2.7.15	foss/2018b
6.14.06	-Python-3.6.6	foss/2018b
6.20.04	-Python-3.7.4	foss/2019b
6.22.08		foss/2020b
6.24.06		foss/2021b
6.26.06		foss/2022a
6.26.10		foss/2022b
v5.34.34	-Python-2.7.11	intel/2016a
v5.34.36	-Python-2.7.11	intel/2016a
v6.06.02	-Python-2.7.12	intel/2016b
v6.08.02	-Python-2.7.11	foss/2016a

root_numpy

root_numpy is a Python extension module that provides an efficient interface between ROOT and NumPy. root_numpy’s internals are compiled C++ and can therefore handle large amounts of data much faster than equivalent pure Python implementations.

homepage: https://scikit-hep.org/root_numpy/

version	versionsuffix	toolchain
4.8.0	-Python-3.6.6	foss/2018b

rootpy

The rootpy project is a community-driven initiative aiming to provide a more pythonic interface with ROOT on top of the existing PyROOT bindings. Given Python’s reflective and dynamic nature, rootpy also aims to improve ROOT design flaws and supplement existing ROOT functionality. The scientific Python community also offers a multitude of powerful packages such as SciPy, NumPy, matplotlib, scikit-learn, and PyTables, but a suitable interface between them and ROOT has been lacking. rootpy provides the interfaces and conversion mechanisms required to liberate your data and to take advantage of these alternatives if needed.

homepage: http://www.rootpy.org/

version	versionsuffix	toolchain
0.8.0	-Python-2.7.11	foss/2016a
1.0.1	-Python-3.6.6	foss/2018b

Rosetta

Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and nucleic acids.

homepage: https://www.rosettacommons.org

version	toolchain
3.7	foss/2016b
2016.13.58602	foss/2016a
2016.46.59086	foss/2016b

rpmrebuild

rpmrebuild is a tool to build an RPM file from a package that has already been installed in a basic use

homepage: http://rpmrebuild.sourceforge.net/

version	toolchain
2.11	system

RPostgreSQL

Database interface and 'PostgreSQL' driver for 'R'. This package provides a Database Interface 'DBI' compliant driver for 'R' to access 'PostgreSQL' database systems.

homepage: https://cran.r-project.org/package=tesseract

version	toolchain
0.7-5	foss/2022a

rpy2

rpy2 is an interface to R running embedded in a Python process.

homepage: https://rpy2.github.io

version	versionsuffix	toolchain
2.7.9	-Python-2.7.12	foss/2016b
2.8.2	-Python-2.7.13	intel/2017a
3.2.6	-Python-3.7.4	foss/2019b
3.4.5		foss/2021a, foss/2021b
3.5.15		foss/2023a

RQGIS3

RQGIS3 establishes an interface between R and QGIS3, i.e., it allows the user to access QGIS3 functionalities from within R.

homepage: https://github.com/r-spatial/RQGIS3

version	versionsuffix	toolchain
20190903	-R-3.6.0	foss/2019a

RSEM

RNA-Seq by Expectation-Maximization

homepage: https://deweylab.github.io/RSEM/

version	toolchain
1.2.26	GNU/4.9.3-2.25
1.2.30	foss/2016a, intel/2016b
1.3.0	foss/2016b, intel/2017a
1.3.1	foss/2017b, intel/2017b, intel/2018a
1.3.2	foss/2018b
1.3.3	foss/2019b, foss/2021b, foss/2022a

RSeQC

RSeQC provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.

homepage: http://rseqc.sourceforge.net/

version	versionsuffix	toolchain
2.6.4	-Python-2.7.12-R-3.3.1	foss/2016b
2.6.4	-Python-2.7.14	intel/2018a
3.0.0	-Python-3.6.6	foss/2018b
4.0.0		foss/2021a, foss/2021b
4.0.0	-Python-3.8.2	foss/2020a

RStan

RStan is the R interface to Stan. Stan is a state-of-the-art platform for statistical modeling and high-performance statistical computation.

homepage: https://github.com/stan-dev/rstan

version	versionsuffix	toolchain
2.18.2	-R-3.4.3	foss/2017b, intel/2017b
2.18.2	-R-3.5.1	foss/2018b

rstanarm

Estimates previously compiled regression models using the 'rstan' package, which provides the R interface to the Stan C++ library for Bayesian estimation.

homepage: https://r-forge.r-project.org/projects/rstanarm

version	versionsuffix	toolchain
2.19.3	-R-3.6.2	foss/2019b

RStudio-Server

This is the RStudio Server version. RStudio is a set of integrated tools designed to help you be more productive with R. The server can be started with: rserver --server-daemonize=0 --www-port=8787 If you need a database config one can be created with: MYTMP=mktemp -d && echo -e "provider=sqlite\ndirectory=${MYTMP}/sqlite" > "${MYTMP}/db.conf" and then used with: rserver ... --database-config-file="${MYTMP}/db.conf"

homepage: https://www.rstudio.com/

version	versionsuffix	toolchain
1.2.5033	-Java-11	fosscuda/2019b
1.2.5042	-Java-11	foss/2019b
1.3.959	-Java-11-R-4.0.0	foss/2020a
1.3.1093	-Java-11-R-4.0.0	foss/2020a
1.4.1717	-Java-11-R-4.1.0	foss/2021a
2022.07.2+576	-Java-11-R-4.2.1	foss/2022a

RTG-Tools

RTG Tools contains utilities to easily manipulate and accurately compare multiple VCF files, as well as utilities for processing other common NGS data formats.

homepage: https://www.realtimegenomics.com/products/rtg-tools

version	versionsuffix	toolchain
3.9.1	-Java-1.8	system
3.12.1	-Java-11	system

Rtree

Rtree is a ctypes Python wrapper of libspatialindex that provides a number of advanced spatial indexing features for the spatially curious Python user.

homepage: https://toblerity.org/rtree/

version	versionsuffix	toolchain
0.8.3	-Python-2.7.14	intel/2018a
1.0.1		GCCcore/12.2.0

ruamel.yaml

ruamel.yaml is a YAML 1.2 loader/dumper package for Python.

homepage: https://sourceforge.net/projects/ruamel-yaml

version	toolchain
0.17.21	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0
0.17.32	GCCcore/12.3.0
0.18.6	GCCcore/13.2.0

Ruby

Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.

homepage: https://www.ruby-lang.org

version	toolchain
2.1.6	system
2.3.1	intel/2016b, system
2.3.3	system
2.3.4	system
2.4.2	foss/2017b
2.5.0	foss/2018a, intel/2017a, intel/2017b
2.5.1	foss/2018a, intel/2018a
2.6.1	GCCcore/7.3.0
2.6.3	GCCcore/8.2.0
2.7.1	GCCcore/8.3.0
2.7.2	GCCcore/10.2.0, GCCcore/9.3.0
3.0.1	GCCcore/10.3.0, GCCcore/11.2.0
3.0.3	GCCcore/11.3.0
3.0.5	GCCcore/11.3.0
3.2.2	GCCcore/12.2.0
3.3.0	GCCcore/12.3.0

Ruby-Tk

Ruby Tk interface module using tcltklib

homepage: https://github.com/ruby/tk

version	versionsuffix	toolchain
0.2.0	-Ruby-2.5.1	foss/2018a, intel/2018a

ruffus

Ruffus is a Computation Pipeline library for python. It is open-sourced, powerful and user-friendly, and widely used in science and bioinformatics.

homepage: http://www.ruffus.org.uk/

version	toolchain
2.8.4	GCCcore/11.3.0, foss/2021b

ruptures

ruptures is a Python library for off-line change point detection. This package provides methods for the analysis and segmentation of non-stationary signals. Implemented algorithms include exact and approximate detection for various parametric and non-parametric models. ruptures focuses on ease of use by providing a well-documented and consistent interface. In addition, thanks to its modular structure, different algorithms and models can be connected and extended within this package.

homepage: https://github.com/deepcharles/ruptures/

version	toolchain
1.1.8	foss/2022a

Rust

Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.

homepage: https://www.rust-lang.org

version	toolchain
1.8.0	foss/2016a
1.12.0	foss/2016b
1.12.1	foss/2016b
1.18.0	foss/2017a
1.21.0	foss/2017b
1.22.1	GCCcore/6.4.0
1.29.2	GCCcore/7.3.0
1.30.1	GCCcore/6.4.0
1.35.0	GCCcore/8.2.0
1.37.0	GCCcore/8.3.0
1.42.0	GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
1.52.1	GCCcore/10.2.0, GCCcore/10.3.0
1.54.0	GCCcore/11.2.0
1.56.0	GCCcore/11.2.0
1.60.0	GCCcore/10.3.0, GCCcore/11.3.0
1.65.0	GCCcore/11.3.0, GCCcore/12.2.0
1.70.0	GCCcore/12.3.0
1.73.0	GCCcore/13.2.0
1.75.0	GCCcore/12.2.0, GCCcore/12.3.0
1.76.0	GCCcore/13.2.0

rustworkx

rustworkx (previously retworkx) is a general purpose graph library for Python written in Rust to take advantage of the performance and safety that Rust provides. It is designed to provide a high performance general purpose graph library for any Python application.

homepage: https://github.com/Qiskit/rustworkx

version	toolchain
0.12.1	foss/2022a

S

S-Lang - s3fs - S4 - Sabre - safestringlib - Safetensors - SAGE - Sailfish - SALib - Salmon - SALMON-TDDFT - Sambamba - samblaster - Samcef - samclip - samplot - SAMtools - sansa - SAP - SAS - Satsuma2 - savvy - Saxon-HE - SBCL - sbt - ScaFaCoS - ScaLAPACK - Scalasca - SCALCE - Scalene - scanpy - scArches - scCODA - sceasy - SCENIC - scGeneFit - SCGid - scGSVA - scHiCExplorer - Schrodinger - scib - scib-metrics - sciClone - ScientificPython - scikit-allel - scikit-bio - scikit-build - scikit-build-core - scikit-cuda - scikit-extremes - scikit-image - scikit-learn - scikit-lego - scikit-misc - scikit-multilearn - scikit-optimize - scikit-plot - scikit-uplift - SCIP - SCIPhI - scipy - SciPy-bundle - SCnorm - Scoary - SCons - SCOOP - SCopeLoomR - Score-P - SCOTCH - scp - scPred - Scrappie - scrublet - scVelo - scvi-tools - Scythe - SDCC - SDL - SDL2 - SDL2_image - SDL2_mixer - SDL2_ttf - SDL_image - SDSL - Seaborn - SEACells - SearchGUI - SeaView - SECAPR - Seeder - segemehl - segment-anything - segmentation-models - segmentation-models-pytorch - SeisSol - SelEstim - SELFIES - SemiBin - semla - Sentence-Transformers - SentencePiece - sentinelsat - sep - SEPP - Seq-Gen - seq2HLA - SeqAn - SeqAn3 - SeqKit - SeqLib - Seqmagick - SeqPrep - seqtk - Serf - setuptools - setuptools-rust - Seurat - SeuratData - SeuratDisk - SeuratWrappers - sf - sfftk - Shannon - SHAP - shapAAR - SHAPEIT - SHAPEIT4 - Shapely - sharutils - Shasta - ShengBTE - shift - SHORE - Short-Pair - shovill - shrinkwrap - SHTns - Sibelia - SICER2 - sickle - Siesta - SignalP - silhouetteRank - silx - simanneal - simint - SimNIBS - SimPEG - SIMPLE - Simple-DFTD3 - SimpleElastix - SimpleITK - simpy - Simstrat - SimVascular - SingleM - Singular - sinto - SiNVICT - SIONlib - SIP - siscone - SISSO - SISSO++ - SKESA - sketchmap - skewer - sklearn-pandas - sklearn-som - skorch - sktime - SlamDunk - SLATEC - SLEPc - slepc4py - sleuth - slidingwindow - SLiM - slow5tools - slurm-drmaa - smafa - smallgenomeutilities - SMAP - SMARTdenovo - SMC++ - smfishHmrf - smithwaterman - Smoldyn - smooth-topk - SMRT-Link - SMV - snakemake - SNAP - SNAP-ESA - SNAP-ESA-python - SNAP-HMM - SNAPE-pooled - snaphu - snappy - Sniffles - snippy - snp-sites - snpEff - SNPhylo - SNPomatic - SOAPaligner - SOAPdenovo-Trans - SOAPdenovo2 - SOAPfuse - socat - SOCI - SolexaQA++ - solo - sonic - SoPlex - SoQt - SortMeRNA - SoupX - SoX - SoXt - SpaceRanger - Spack - spaCy - SPAdes - spaln - Spark - sparse-neighbors-search - sparsehash - SpatialDE - spatialreg - spdlog - SpectrA - spectral.methods - speech_tools - SPEI - spektral - spglib - spglib-python - Sphinx - Sphinx-RTD-Theme - SpiceyPy - SpiecEasi - SplAdder - SPLASH - SpliceMap - split-seq - splitRef - SPM - spoa - SPOOLES - SPOTPY - SPRNG - Spyder - SQLAlchemy - SQLite - SqueezeMeta - Squidpy - SRA-Toolkit - sradownloader - SRPRISM - SRST2 - SSAHA2 - SSN - SSPACE_Basic - SSW - STACEY - Stack - Stacks - STAMP - StaMPS - Stampy - STAR - STAR-CCM+ - STAR-Fusion - stardist - starparser - stars - Stata - Statistics-R - statsmodels - STEAK - STIR - stpipeline - strace - Strainberry - STREAM - strelka - StringTie - stripy - STRique - Structure - Structure_threader - STRUMPACK - suave - SuAVE-biomat - Subread - subset-bam - Subversion - suds - SuiteSparse - SUMACLUST - SUMATRA - SUMO - SUNDIALS - SunPy - SuperLU - SuperLU_DIST - supermagic - supernova - SUPPA - SURVIVOR - SVclone - SVDetect - SVDquest - SVG - SVIM - svist4get - swarm - SWASH - SWAT+ - swifter - SWIG - SWIPE - swissknife - SymEngine - SymEngine-python - SYMMETRICA - SYMPHONY - sympy - synapseclient - synthcity - SyRI - sysbench - Szip

S-Lang

S-Lang is a multi-platform programmer's library designed to allow a developer to create robust multi-platform software. It provides facilities required by interactive applications such as display/screen management, keyboard input, keymaps, and so on.

homepage: http://www.jedsoft.org/slang/

version	toolchain
2.3.0	GCC/4.9.2

s3fs

S3FS builds on aiobotocore to provide a convenient Python filesystem interface for S3..

homepage: https://github.com/fsspec/s3fs/

version	toolchain
2023.12.2	foss/2023a

S4

S4 stands for Stanford Stratified Structure Solver, a frequency domain code to solve the linear Maxwell’s equations in layered periodic structures. Internally, it uses Rigorous Coupled Wave Analysis (RCWA, also called the Fourier Modal Method (FMM)) and the S-matrix algorithm.

homepage: https://web.stanford.edu/group/fan/S4

version	toolchain
1.1.1-20180610	foss/2017b

Sabre

Sabre is a tool that will demultiplex barcoded reads into separate files. It will work on both single-end and paired-end data in fastq format. It simply compares the provided barcodes with each read and separates the read into its appropriate barcode file, after stripping the barcode from the read (and also stripping the quality values of the barcode bases).

homepage: https://github.com/najoshi/sabre

version	toolchain
2013-09-28	GCC/12.2.0

safestringlib

The Secure Development Lifecycle (SDL) recommends banning certain C Library functions because they directly contribute to security vulnerabilities such as buffer overflows. However routines for the manipulation of strings and memory buffers are common in software and firmware, and are essential to accomplish certain programming tasks. Safer replacements for these functions that avoid or prevent serious security vulnerabilities (e.g. buffer overflows, string format attacks, conversion overflows/underflows, etc.) are available in the SafeString Library.

homepage: https://github.com/intel/safestringlib

version	toolchain
20240228	intel-compilers/2023.1.0

Safetensors

Safetensors is a new simple format for storing tensors safely (as opposed to pickle) and that is still fast (zero-copy). Safetensors is really fast.

homepage: https://huggingface.co/docs/safetensors

version	versionsuffix	toolchain
0.3.1		foss/2022a
0.3.1	-CUDA-11.7.0	foss/2022a

SAGE

S.A.G.E. (Statistical Analysis for Genetic Epidemiology) is free software package containing programs for use in the genetic analysis of family, pedigree and individual data.

homepage: http://darwin.cwru.edu/sage/

version	toolchain
6.3	system
6.4	system

Sailfish

Sailfish is a software tool that implements a novel, alignment-free algorithm for the estimation of isoform abundances directly from a set of reference sequences and RNA-seq reads.

homepage: http://www.cs.cmu.edu/~ckingsf/software/sailfish/

version	versionsuffix	toolchain
0.10.1		gompi/2019b
0.10.1	-Python-2.7.12	foss/2016b

SALib

Sensitivity Analysis Library in Python (Numpy). Contains Sobol, Morris, Fractional Factorial and FAST methods.

homepage: https://SALib.github.io/SALib/

version	versionsuffix	toolchain
1.1.3	-Python-2.7.14	intel/2017b

Salmon

Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.

homepage: https://github.com/COMBINE-lab/salmon

version	versionsuffix	toolchain
0.8.2		system
0.8.2	-Python-2.7.12	foss/2016b
0.11.2		intel/2018a
0.12.0		foss/2018b
0.14.1		foss/2018b
0.14.2		gompi/2019a
1.0.0		gompi/2019a, gompi/2019b
1.1.0		gompi/2019b
1.2.0		gompi/2019b
1.3.0		gompi/2020a
1.4.0		GCC/11.2.0, gompi/2020b
1.9.0		GCC/11.3.0
1.10.1		GCC/12.2.0

SALMON-TDDFT

SALMON is an open-source computer program for ab-initio quantum-mechanical calculations of electron dynamics at the nanoscale that takes place in various situations of light-matter interactions. It is based on time-dependent density functional theory, solving time-dependent Kohn-Sham equation in real time and real space with norm-conserving pseudopotentials.

homepage: https://salmon-tddft.jp

version	toolchain
1.2.1	foss/2018b, intel/2018b

Sambamba

Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth.

homepage: https://lomereiter.github.io/sambamba/

version	toolchain
0.6.6	system
0.7.1	system
0.8.0	GCC/10.2.0
0.8.2	GCC/10.3.0
1.0.1	GCC/11.3.0

samblaster

samblaster is a fast and flexible program for marking duplicates in read-id grouped1 paired-end SAM files.

homepage: https://github.com/GregoryFaust/samblaster

version	toolchain
0.1.24	foss/2018b
0.1.26	GCC/10.2.0, GCC/10.3.0, GCC/11.3.0

Samcef

FEM solver solution suite for basic linear structures to advanced, flexible nonlinear mechanisms and thermal applications.

homepage: http://www.plm.automation.siemens.com/en_us/products/lms/samtech/samcef-solver-suite/

version	toolchain
17.0-03	system

samclip

Filter SAM file for soft and hard clipped alignments.

homepage: https://github.com/tseemann/samclip

version	versionsuffix	toolchain
0.2	-Perl-5.28.0	GCCcore/7.3.0
0.4.0		GCCcore/10.2.0, GCCcore/11.2.0, GCCcore/9.3.0

samplot

Plot structural variant signals from many BAMs and CRAMs.

homepage: https://github.com/ryanlayer/samplot

version	toolchain
1.3.0	foss/2021b

SAMtools

SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

homepage: http://www.htslib.org/

version	versionsuffix	toolchain
0.1.17		intel/2017a
0.1.19		GCC/10.3.0, foss/2016a, foss/2016b
0.1.20		GCC/12.3.0, GCC/8.3.0, foss/2018b, intel/2017a, intel/2017b, intel/2018a, intel/2018b, intel/2019b
1.2		foss/2016b
1.3		foss/2016a, intel/2016a
1.3.1		foss/2016a, foss/2016b, intel/2016a, intel/2016b
1.3.1	-HTSlib-1.3.2	intel/2016b
1.4		foss/2016b, intel/2016b, intel/2017a
1.4.1		intel/2017a
1.5		foss/2016b, intel/2017a
1.6		GCC/6.4.0-2.28, foss/2017a, iccifort/2017.4.196-GCC-6.4.0-2.28, intel/2017b
1.7		foss/2018a, intel/2018a
1.8		intel/2018a
1.9		GCC/6.4.0-2.28, GCC/7.3.0-2.30, GCC/8.2.0-2.31.1, foss/2018b, iccifort/2019.1.144-GCC-8.2.0-2.31.1, intel/2018b
1.10		GCC/8.2.0-2.31.1, GCC/8.3.0, GCC/9.3.0, iccifort/2019.5.281
1.11		GCC/10.2.0, GCC/9.3.0, iccifort/2020.4.304
1.12		GCC/10.2.0, GCC/10.3.0, GCC/9.3.0
1.13		GCC/10.3.0, GCC/11.3.0, GCC/12.3.0
1.14		GCC/11.2.0
1.15		GCC/11.2.0
1.15.1		GCC/11.2.0, GCC/11.3.0
1.16.1		GCC/11.2.0, GCC/11.3.0
1.17		GCC/12.2.0
1.18		GCC/12.3.0

sansa

Structural variant (SV) annotation, a companion to the 'dolly' tool.

homepage: https://github.com/dellytools/sansa/

version	toolchain
0.0.7	gompi/2020b

SAP

SAP is a pairwise structure alignment via double dynamic programming

homepage: https://github.com/mathbio-nimr-mrc-ac-uk/SAP

version	toolchain
1.1.3	GCC/11.3.0

SAS

SAS is a software suite for advanced analytics, multivariate analyses, business intelligence, data management, and predictive analytics.

homepage: https://www.sas.com

version	toolchain
9.4	system

Satsuma2

Satsuma2 is an optimised version of Satsuma, a tool to reliably align large and complex DNA sequences providing maximum sensitivity (to find all there is to find), specificity (to only find real homology) and speed (to accommodate the billions of base pairs in vertebrate genomes).

homepage: https://github.com/bioinfologics/satsuma2

version	toolchain
20220304	GCC/11.3.0

savvy

Interface to various variant calling formats.

homepage: https://github.com/statgen/savvy

version	toolchain
1.3.0	GCC/8.2.0-2.31.1

Saxon-HE

Open Source SAXON XSLT processor developed by Saxonica Limited.

homepage: http://saxon.sourceforge.net

version	versionsuffix	toolchain
9.7.0.4	-Java-1.7.0_79	system
9.7.0.21	-Java-1.8.0_162	system
9.9.1.7	-Java-13	system
12.4	-Java-21	system

SBCL

Steel Bank Common Lisp (SBCL) is a high performance Common Lisp compiler. It is open source / free software, with a permissive license. In addition to the compiler and runtime system for ANSI Common Lisp, it provides an interactive environment including a debugger, a statistical profiler, a code coverage tool, and many other extensions.

homepage: http://sbcl.sourceforge.net/

version	toolchain
2.0.9	GCCcore/9.3.0
2.2.1	GCCcore/10.3.0
2.3.11	GCCcore/11.3.0
2.4.1	GCCcore/12.3.0

sbt

sbt is a build tool for Scala, Java, and more.

homepage: http://www.scala-sbt.org/

version	versionsuffix	toolchain
1.0.2	-Java-1.8.0_152	system
1.3.13	-Java-1.8	system

ScaFaCoS

ScaFaCoS is a library of scalable fast coulomb solvers.

homepage: http://www.scafacos.de/

version	toolchain
1.0.1	foss/2020a, foss/2020b, foss/2021a, foss/2021b, intel/2020a
1.0.4	foss/2022a, foss/2022b, foss/2023a

ScaLAPACK

The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.

homepage: https://www.netlib.org/scalapack/

version	versionsuffix	toolchain
2.0.2		gompi/2019b, gompic/2019b
2.0.2	-BLIS-0.3.2	gompi/2018b
2.0.2	-OpenBLAS-0.2.13-LAPACK-3.5.0	gmvapich2/1.7.20
2.0.2	-OpenBLAS-0.2.15-LAPACK-3.6.0	gmpich/2016a, gmvapich2/2016a, gompi/2016a
2.0.2	-OpenBLAS-0.2.18-LAPACK-3.6.0	gompi/2016.04, gompi/2016.06
2.0.2	-OpenBLAS-0.2.18-LAPACK-3.6.1	gompi/2016.07, gompi/2016b
2.0.2	-OpenBLAS-0.2.19-LAPACK-3.6.1	gompi/2016.09
2.0.2	-OpenBLAS-0.2.19-LAPACK-3.7.0	gompi/2017a
2.0.2	-OpenBLAS-0.2.20	gimpi/2017b, gimpi/2018a, gimpic/2017b, gmpich/2017.08, gompi/2017b, gompi/2018a, gompic/2017b, gompic/2018a
2.0.2	-OpenBLAS-0.3.1	gompi/2018b, gompic/2018b
2.0.2	-OpenBLAS-0.3.3	gompi/2018.08
2.0.2	-OpenBLAS-0.3.5	gompi/2019a, gompic/2019a
2.1.0		gompi/2020a, gompi/2020b, gompic/2020a, gompic/2020b
2.1.0	-bf	gompi/2020a, gompi/2020b, gompi/2021a, iimpi/2020b
2.1.0	-bl	gompi/2020b
2.1.0	-fb	gompi/2021a, gompi/2021b
2.2	-amd	gompi/2020a
2.2.0	-fb	gompi/2022.05, gompi/2022.10, gompi/2022a, gompi/2022b, gompi/2023.09, gompi/2023a, gompi/2023b, nvompi/2022.07

Scalasca

Scalasca is a software tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior. The analysis identifies potential performance bottlenecks -- in particular those concerning communication and synchronization -- and offers guidance in exploring their causes.

homepage: https://www.scalasca.org/

version	toolchain
2.3	foss/2016a
2.5	gompi/2019a, gompi/2020a
2.6	gompi/2021a, gompic/2020b
2.6.1	gompi/2022a

SCALCE

SCALCE [skeɪlz] is a FASTQ compression tool that uses locally consistet parsing to obtain better compression rate. SCALCE has been specifically designed for Illumina reads but it can handle other technologies (that generate base pair reads) if the read length is the same throughout the file.

homepage: http://scalce.sourceforge.net/Home

version	toolchain
2.7	GCC/4.8.2

Scalene

Scalene is a high-performance CPU, GPU and memory profiler for Python that does a number of things that other Python profilers do not and cannot do. It runs orders of magnitude faster than other profilers while delivering far more detailed information.

homepage: https://github.com/plasma-umass/scalene

version	toolchain
1.5.13	GCCcore/11.2.0
1.5.20	GCCcore/11.3.0
1.5.26	GCCcore/12.2.0, GCCcore/12.3.0
1.5.35	GCCcore/13.2.0

scanpy

Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.

homepage: https://scanpy.readthedocs.io/en/stable/

version	toolchain
1.7.2	foss/2020b
1.8.1	foss/2020b, foss/2021a
1.8.2	foss/2021b
1.9.1	foss/2021b, foss/2022a
1.9.8	foss/2023a

scArches

Single-cell architecture surgery (scArches) is a package for reference-based analysis of single-cell data.

homepage: https://github.com/theislab/scarches

version	versionsuffix	toolchain
0.5.6		foss/2021a
0.5.6	-CUDA-11.3.1	foss/2021a

scCODA

scCODA allows for identification of compositional changes in high-throughput sequencing count data, especially cell compositions from scRNA-seq.

homepage: https://github.com/theislab/scCODA

version	toolchain
0.1.9	foss/2021a, foss/2023a

sceasy

sceasy is a package that helps easy conversion of different single-cell data formats to each other

homepage: https://github.com/cellgeni/sceasy

version	versionsuffix	toolchain
0.0.7	-R-4.2.1	foss/2022a

SCENIC

SCENIC Suite is a set of tools to study and decipher gene regulation.

homepage: https://scenic.aertslab.org

version	versionsuffix	toolchain
1.2.4	-R-4.1.0	foss/2021a
1.3.0	-R-4.2.1	foss/2022a
1.3.0	-R-4.3.2	foss/2023a

scGeneFit

Python code for genetic marker selection using linear programming.

homepage: https://github.com/solevillar/scGeneFit-python

version	toolchain
1.0.2	foss/2021a

SCGid

A consensus approach to contig filtering and genome prediction from single-cell sequencing libraries

homepage: https://github.com/amsesk/SCGid

version	toolchain
0.9b0	foss/2021b

scGSVA

scGSVA provides wrap functions to do GSVA analysis for single cell data. And scGSVA includes functions to build annotation for almost all species. scGSVA also provides function to generate figures based on the GSVA results.

homepage: https://github.com/guokai8/scGSVA

version	versionsuffix	toolchain
0.0.14	-R-4.2.1	foss/2022a

scHiCExplorer

The scHiCExplorer is a software to demultiplex, process, correct, normalize, manipulate, analyse and visualize single-cell Hi-C data.

homepage: https://schicexplorer.readthedocs.io

version	toolchain
7	foss/2022a

Schrodinger

Schrodinger aims to provide integrated software solutions and services that truly meet its customers needs. We want to empower researchers around the world to achieve their goals of improving human health and quality of life through advanced computational techniques that transform the way chemists design compounds and materials.

homepage: https://www.schrodinger.com/

version	toolchain
2020-4	system
2021-4	system
2022-1	system
2022-2	system
2022-3	system

scib

Benchmarking atlas-level data integration in single-cell genomics.

homepage: https://github.com/theislab/scib

version	toolchain
1.1.1	foss/2022a
1.1.3	foss/2021a
1.1.4	foss/2023a

scib-metrics

Accelerated and Python-only metrics for benchmarking single-cell integration outputs

homepage: https://scib-metrics.readthedocs.io

version	toolchain
0.3.3	foss/2021a

sciClone

An R package for inferring the subclonal architecture of tumors

homepage: https://github.com/genome/sciclone

version	versionsuffix	toolchain
1.1	-R-3.5.1	foss/2018b

ScientificPython

ScientificPython is a collection of Python modules for scientific computing. It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, and parallelization.

homepage: http://dirac.cnrs-orleans.fr/ScientificPython

version	versionsuffix	toolchain
2.9.4	-Python-2.7.11	foss/2016a, intel/2016a

scikit-allel

This package provides utilities for exploratory analysis of large scale genetic variation data. It is based on numpy, scipy and other general-purpose Python scientific libraries.

homepage: https://scikit-allel.readthedocs.io/en/latest/

version	versionsuffix	toolchain
1.1.8	-Python-2.7.13	foss/2017a
1.2.1	-Python-3.8.2	foss/2020a
1.3.2		foss/2020b
1.3.3		foss/2021a

scikit-bio

scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms and educational resources for bioinformatics.

homepage: http://scikit-bio.org

version	versionsuffix	toolchain
0.5.6	-Python-3.8.2	foss/2020a
0.5.7		foss/2020b, foss/2021a, foss/2021b, foss/2022a
0.5.9		foss/2023a

scikit-build

Scikit-Build, or skbuild, is an improved build system generator for CPython C/C++/Fortran/Cython extensions.

homepage: https://scikit-build.readthedocs.io/en/latest

version	versionsuffix	toolchain
0.10.0	-Python-3.6.6	foss/2018b, intel/2018b
0.10.0	-Python-3.8.2	foss/2020a, fosscuda/2020a
0.11.1		GCCcore/10.3.0, GCCcore/11.2.0, foss/2020b, fosscuda/2020b, intel/2020b, intelcuda/2020b
0.15.0		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0
0.17.2		GCCcore/12.2.0
0.17.6		GCCcore/12.3.0, GCCcore/13.2.0

scikit-build-core

Scikit-build-core is a complete ground-up rewrite of scikit-build on top of modern packaging APIs. It provides a bridge between CMake and the Python build system, allowing you to make Python modules with CMake.

homepage: https://scikit-build.readthedocs.io/en/latest/

version	toolchain
0.5.0	GCCcore/12.3.0

scikit-cuda

SciKit-cuda, a.k.a. skcuda, provides Python interfaces to many of the functions in the CUDA device/runtime, CUBLAS, CUFFT, and CUSOLVER libraries distributed as part of NVIDIA's CUDA Programming Toolkit.

homepage: https://github.com/lebedov/scikit-cuda

version	versionsuffix	toolchain
0.5.3	-Python-3.7.4	fosscuda/2019b

scikit-extremes

scikit-extremes is a basic statistical package to perform univariate extreme value calculations using Python

homepage: https://github.com/kikocorreoso/scikit-extremes

version	toolchain
2022.4.10	foss/2022a

scikit-image

scikit-image is a collection of algorithms for image processing.

homepage: https://scikit-image.org/

version	versionsuffix	toolchain
0.12.3	-Python-2.7.11	foss/2016a
0.12.3	-Python-2.7.12	intel/2016b
0.12.3	-Python-3.5.2	foss/2016b, intel/2016b
0.13.0	-Python-2.7.13	intel/2017a
0.13.0	-Python-3.6.1	intel/2017a
0.13.0	-Python-3.6.3	foss/2017b
0.13.1	-Python-2.7.14	intel/2017b
0.13.1	-Python-3.6.3	foss/2017b
0.13.1	-Python-3.6.4	foss/2018a
0.14.0	-Python-3.6.4	intel/2018a
0.14.1	-Python-3.6.6	foss/2018b, fosscuda/2018b, intel/2018b
0.15.0	-Python-3.7.2	foss/2019a
0.16.2	-Python-3.7.4	foss/2019b, fosscuda/2019b, intel/2019b
0.17.1	-Python-3.8.2	foss/2020a
0.18.1		foss/2020b, fosscuda/2020b, intel/2020b, intelcuda/2020b
0.18.3		foss/2021a
0.19.1		foss/2021b
0.19.3		foss/2022a
0.21.0		foss/2022b
0.22.0		foss/2023a

scikit-learn

Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.

homepage: https://scikit-learn.org/stable/index.html

version	versionsuffix	toolchain
0.16.1	-Python-2.7.13	foss/2017a
0.17.1	-Python-2.7.11	foss/2016a, intel/2016a
0.17.1	-Python-2.7.11-freetype-2.6.3	intel/2016a
0.17.1	-Python-2.7.12	intel/2016b
0.17.1	-Python-3.5.1	foss/2016a, intel/2016a
0.18	-Python-2.7.12	intel/2016b
0.18	-Python-3.5.2	intel/2016b
0.18.1	-Python-2.7.12	foss/2016b, intel/2016b
0.18.1	-Python-2.7.13	intel/2017a
0.18.1	-Python-3.5.2	foss/2016b, intel/2016b
0.18.1	-Python-3.6.1	intel/2017a
0.18.2	-Python-3.6.1	intel/2017a
0.19.0	-Python-3.6.1	intel/2017a
0.19.1	-Python-2.7.13	foss/2017a
0.19.1	-Python-2.7.14	foss/2017b, fosscuda/2017b, intel/2017b, intelcuda/2017b
0.19.1	-Python-3.6.3	foss/2017b, fosscuda/2017b, intel/2017b, intelcuda/2017b
0.19.1	-Python-3.6.4	foss/2018a, intel/2018a
0.20.0	-Python-2.7.15	foss/2018b, intel/2018b
0.20.0	-Python-3.6.6	foss/2018b, fosscuda/2018b, intel/2018b
0.20.2	-Python-2.7.15	foss/2018b
0.20.2	-Python-3.6.6	foss/2018b
0.20.3		foss/2019a, fosscuda/2019a, intel/2019a
0.20.4	-Python-2.7.16	intel/2019b
0.20.4	-Python-2.7.18	foss/2020b, foss/2021b
0.21.3	-Python-3.7.4	foss/2019b, fosscuda/2019b, intel/2019b
0.23.1	-Python-3.8.2	foss/2020a, fosscuda/2020a, intel/2020a, intelcuda/2020a
0.23.2		foss/2020b, fosscuda/2020b, intel/2020b, intelcuda/2020b
0.24.2		foss/2021a, intel/2021a
1.0.1		foss/2021b, intel/2021b
1.0.2		foss/2021b
1.1.2		foss/2022a, intel/2022a
1.2.1		gfbf/2022b
1.3.1		gfbf/2023a, iimkl/2023a
1.3.2		gfbf/2023b
1.4.0		gfbf/2023b

scikit-lego

We love scikit learn but very often we find ourselves writing custom transformers, metrics and models. The goal of this project is to attempt to consolidate these into a package that offers code quality/testing.

homepage: https://github.com/koaning/scikit-lego

version	toolchain
0.6.16	foss/2022a
0.7.4	foss/2023a

scikit-misc

Miscellaneous tools for data analysis and scientific computing

homepage: https://github.com/has2k1/scikit-misc

version	toolchain
0.1.4	foss/2021a, foss/2022a
0.3.1	foss/2023a

scikit-multilearn

Scikit-multilearn is a BSD-licensed library for multi-label classification that is built on top of the well-known scikit-learn ecosystem.

homepage: http://scikit.ml

version	versionsuffix	toolchain
0.2.0	-Python-3.6.6	foss/2018b

scikit-optimize

Scikit-Optimize, or skopt, is a simple and efficient library to minimize (very) expensive and noisy black-box functions.

homepage: https://scikit-optimize.github.io

version	versionsuffix	toolchain
0.5.2	-Python-3.6.6	intel/2018b
0.7.4	-Python-3.7.4	foss/2019b
0.8.1	-Python-3.8.2	foss/2020a
0.9.0		foss/2021a, foss/2022a

scikit-plot

Scikit-plot is the result of an unartistic data scientist's dreadful realization that visualization is one of the most crucial components in the data science process, not just a mere afterthought.

homepage: https://github.com/reiinakano/scikit-plot

version	toolchain
0.3.7	foss/2022b

scikit-uplift

scikit-uplift is a Python module for classic approaches for uplift modeling built on top of scikit-learn. Uplift prediction aims to estimate the causal impact of a treatment at the individual level.

homepage: https://github.com/maks-sh/scikit-uplift

version	versionsuffix	toolchain
0.2.0	-Python-3.8.2	foss/2020a

SCIP

SCIP is currently one of the fastest non-commercial solvers for mixed integer programming (MIP) and mixed integer nonlinear programming (MINLP). It is also a framework for constraint integer programming and branch-cut-and-price. It allows for total control of the solution process and the access of detailed information down to the guts of the solver.

homepage: https://www.scipopt.org/

version	toolchain
3.2.1	GCC/11.3.0

SCIPhI

Single-cell mutation identification via phylogenetic inference (SCIPhI) is a new approach to mutation detection in individual tumor cells by leveraging the evolutionary relationship among cells.

homepage: https://github.com/cbg-ethz/SCIPhI

version	toolchain
0.1.3	intel/2018b

scipy

SciPy is a collection of mathematical algorithms and convenience functions built on the Numpy extension for Python.

homepage: https://www.scipy.org

version	versionsuffix	toolchain
0.16.0	-Python-2.7.12	intel/2016b
0.17.0	-Python-2.7.11	intel/2016a
0.19.0	-Python-3.5.2	intel/2016b
1.4.1	-Python-3.7.4	foss/2019b, fosscuda/2019b

SciPy-bundle

Bundle of Python packages for scientific software

homepage: https://python.org/

version	versionsuffix	toolchain
2019.03		foss/2019a, fosscuda/2019a, intel/2019a, intelcuda/2019a
2019.10	-Python-2.7.16	foss/2019b, fosscuda/2019b, intel/2019b
2019.10	-Python-3.7.2	intel/2019a
2019.10	-Python-3.7.4	foss/2019b, fosscuda/2019b, intel/2019b, intelcuda/2019b
2020.03	-Python-2.7.18	foss/2020a, fosscuda/2020a, intel/2020a
2020.03	-Python-3.8.2	foss/2020a, fosscuda/2020a, intel/2020a, intelcuda/2020a
2020.11		foss/2020b, fosscuda/2020b, intel/2020b, intelcuda/2020b
2020.11	-Python-2.7.18	foss/2020b
2021.05		foss/2021a, gomkl/2021a, intel/2021a
2021.10		foss/2021b, intel/2021b
2021.10	-Python-2.7.18	foss/2021b
2022.05		foss/2022.05, foss/2022a, intel/2022.05, intel/2022a
2023.02		gfbf/2022b
2023.07		gfbf/2023a, iimkl/2023a
2023.11		gfbf/2023.09, gfbf/2023b

SCnorm

This package implements SCnorm — a method to normalize single-cell RNA-seq data.

homepage: https://bioconductor.org/packages/SCnorm

version	versionsuffix	toolchain
0.99.7	-R-3.4.0	intel/2017a

Scoary

Microbial pan-GWAS using the output from Roary

homepage: https://github.com/AdmiralenOla/Scoary

version	versionsuffix	toolchain
1.6.16		foss/2021a
1.6.16	-Python-2.7.14	intel/2018a

SCons

SCons is a software construction tool.

homepage: https://www.scons.org

version	versionsuffix	toolchain
2.4.1	-Python-2.7.11	foss/2016a
2.5.0	-Python-2.7.12	foss/2016b, intel/2016b
2.5.1		intel/2017a
2.5.1	-Python-2.7.12	foss/2016b, intel/2016b
2.5.1	-Python-2.7.13	intel/2017a
3.0.1	-Python-2.7.14	foss/2017b, foss/2018a, intel/2017b, intel/2018a, iomkl/2018a
3.0.1	-Python-2.7.15	foss/2018b, fosscuda/2018b
3.0.1	-Python-2.7.15-bare	GCCcore/7.3.0
3.0.1	-Python-3.6.3	foss/2017b, intel/2017b
3.0.1	-Python-3.6.4	foss/2018a, intel/2018a
3.0.4	-Python-2.7.15	foss/2018b
3.0.5		GCCcore/8.2.0
3.0.5	-Python-2.7.15	GCCcore/8.2.0
3.0.5	-Python-3.7.2	GCCcore/8.2.0
3.1.1		GCCcore/8.3.0
3.1.2		GCCcore/9.3.0
4.0.1		GCCcore/10.2.0
4.1.0.post1		GCCcore/10.2.0, GCCcore/10.3.0
4.2.0		GCCcore/11.2.0
4.4.0		GCCcore/11.3.0
4.5.2		GCCcore/12.3.0
4.6.0		GCCcore/13.2.0

SCOOP

SCOOP (Scalable COncurrent Operations in Python) is a distributed task module allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers.

homepage: http://code.google.com/p/scoop/

version	versionsuffix	toolchain
0.6.2	-Python-2.7.12	intel/2016b
0.7.1.1		GCCcore/8.2.0
0.7.1.1	-Python-2.7.11	intel/2016a
0.7.1.1	-Python-2.7.14	intel/2017b
0.7.1.1	-Python-3.5.1	intel/2016a

SCopeLoomR

An R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ...

homepage: https://github.com/aertslab/SCopeLoomR

version	versionsuffix	toolchain
0.13.0	-R-4.1.2	foss/2021b
0.13.0_20220408	-R-4.2.1	foss/2022a

Score-P

The Score-P measurement infrastructure is a highly scalable and easy-to-use tool suite for profiling, event tracing, and online analysis of HPC applications.

homepage: https://www.score-p.org

version	versionsuffix	toolchain
2.0.1		foss/2016a
6.0		gompi/2019a, gompi/2019b, gompi/2020a, gompic/2019a, gompic/2019b, gompic/2020a
7.0		gompi/2020b, gompi/2021a, gompic/2020b
7.1	-CUDA-11.3.1	gompi/2021a
8.0		gompi/2021b, gompi/2022a
8.0	-CUDA-11.4.1	gompi/2021b
8.0	-CUDA-11.7.0	gompi/2022a
8.1		gompi/2022b, gompi/2023a
8.1	-CUDA-12.0.0	gompi/2022b
8.1	-CUDA-12.1.1	gompi/2023a
8.3		gompi/2022b
8.4		gompi/2023b
8.4	-CUDA-12.4.0	gompi/2023b

SCOTCH

Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.

homepage: https://www.labri.fr/perso/pelegrin/scotch/

version	versionsuffix	toolchain
5.1.12b_esmumps		foss/2017b
6.0.4		foss/2016a, foss/2016b, foss/2017b, gimkl/2.11.5, intel/2016a, intel/2016b, intel/2017a, intel/2017b, intel/2018a
6.0.4	-64bitint	foss/2017b
6.0.6		foss/2018a, foss/2018b, gompi/2019a, iimpi/2019a, intel/2018a
6.0.9		gompi/2019b, gompi/2020a, iimpi/2019b, iimpi/2020a, iimpic/2019b
6.1.0		gompi/2020b, gompi/2021a, iimpi/2020b, iimpi/2021a
6.1.2		gompi/2021b, iimpi/2021b
7.0.1		gompi/2022a, iimpi/2022a
7.0.1	-int64	gompi/2022a
7.0.3		gompi/2022b, gompi/2023a

scp

The scp.py module uses a paramiko transport to send and recieve files via the scp1 protocol.

homepage: https://github.com/jbardin/scp.py

version	versionsuffix	toolchain
0.10.2	-Python-2.7.12	intel/2016b
0.13.1	-Python-2.7.15	intel/2018b
0.13.2	-Python-2.7.15	intel/2018b

scPred

scPred package for cell type prediction from scRNA-seq data

homepage: https://github.com/powellgenomicslab/scPred

version	versionsuffix	toolchain
1.9.2	-R-4.1.2	foss/2021b

Scrappie

Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group.

homepage: https://github.com/nanoporetech/scrappie

version	toolchain
1.3.2	intel/2018a

scrublet

Single-Cell Remover of Doublets - Python code for identifying doublets in single-cell RNA-seq data

homepage: https://github.com/swolock/scrublet

version	toolchain
0.2.3	foss/2022a

scVelo

scVelo is a scalable toolkit for estimating and analyzing RNA velocities in single cells using dynamical modeling.

homepage: https://scvelo.org

version	versionsuffix	toolchain
0.1.24	-Python-3.7.4	foss/2019b
0.2.3		foss/2021a
0.3.1		foss/2023a

scvi-tools

scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and analysis of single-cell omics data, built on top of PyTorch and AnnData.

homepage: https://github.com/scverse/scvi-tools

version	versionsuffix	toolchain
0.16.4		foss/2021a
0.16.4	-CUDA-11.3.1	foss/2021a

Scythe

Scythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. It considers quality information, which can make it robust in picking out 3'-end adapters, which often include poor quality bases.

homepage: https://github.com/ucdavis-bioinformatics/scythe

version	toolchain
0.994	GCCcore/9.3.0

SDCC

SDCC is a retargettable, optimizing ANSI - C compiler suite that targets the Intel MCS51 based microprocessors (8031, 8032, 8051, 8052, etc.), Maxim (formerly Dallas) DS80C390 variants, Freescale (formerly Motorola) HC08 based (hc08, s08) and Zilog Z80 based MCUs (z80, z180, gbz80, Rabbit 2000/3000, Rabbit 3000A). Work is in progress on supporting the Microchip PIC16 and PIC18 targets. It can be retargeted for other microprocessors.

homepage: http://sdcc.sourceforge.net/

version	toolchain
3.3.0	system

SDL

SDL: Simple DirectMedia Layer, a cross-platform multimedia library

homepage: https://www.libsdl.org/

version	toolchain
1.2.15	GCCcore/6.4.0

SDL2

SDL: Simple DirectMedia Layer, a cross-platform multimedia library

homepage: https://www.libsdl.org/

version	toolchain
2.0.4	intel/2016b
2.0.8	GCCcore/6.4.0, foss/2017b, intel/2017b, intel/2018a
2.0.9	GCCcore/8.2.0, foss/2018b, fosscuda/2018b, intel/2018b
2.0.10	GCCcore/8.3.0
2.0.14	GCCcore/10.2.0, GCCcore/10.3.0
2.0.20	GCCcore/11.2.0
2.0.22	GCCcore/11.3.0
2.26.3	GCCcore/12.2.0
2.28.2	GCCcore/12.3.0
2.28.5	GCCcore/13.2.0

SDL2_image

This is a simple library to load images of various formats as SDL surfaces. It can load BMP, GIF, JPEG, LBM, PCX, PNG, PNM (PPM/PGM/PBM), QOI, TGA, XCF, XPM, and simple SVG format images. It can also load AVIF, JPEG-XL, TIFF, and WebP images, depending on build options (see the note below for details.)

homepage: https://github.com/libsdl-org/SDL_image

version	toolchain
2.0.3	GCCcore/6.4.0
2.6.3	GCCcore/11.3.0

SDL2_mixer

Due to popular demand, here is a simple multi-channel audio mixer. It supports 8 channels of 16 bit stereo audio, plus a single channel of music. It can load FLAC, MP3, Ogg, VOC, and WAV format audio. It can also load MIDI, MOD, and Opus audio, depending on build options (see the note below for details.)

homepage: https://github.com/libsdl-org/SDL_mixer

version	toolchain
2.6.3	GCCcore/11.3.0

SDL2_ttf

This library is a wrapper around the FreeType and Harfbuzz libraries, allowing you to use TrueType fonts to render text in SDL applications.

homepage: https://github.com/libsdl-org/SDL_ttf

version	toolchain
2.20.2	GCCcore/11.3.0

SDL_image

SDL_image is an image file loading library.

homepage: https://www.libsdl.org/projects/SDL_image/release-1.2.html

version	toolchain
1.2.12	GCCcore/6.4.0

SDSL

The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing succinct data structures.

homepage: https://github.com/simongog/sdsl-lite

version	toolchain
2.1.1-20191211	GCCcore/8.3.0

Seaborn

Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics.

homepage: https://seaborn.pydata.org/

version	versionsuffix	toolchain
0.7.1	-Python-2.7.12	intel/2016b
0.8.1	-Python-2.7.13	foss/2017a
0.8.1	-Python-2.7.14	intel/2018a
0.9.0	-Python-2.7.14	foss/2017b, fosscuda/2017b, intel/2017b, intel/2018a, intelcuda/2017b
0.9.0	-Python-2.7.15	foss/2018b, foss/2019a, intel/2018b, intel/2019a
0.9.0	-Python-3.6.3	foss/2017b, fosscuda/2017b, intel/2017b, intelcuda/2017b
0.9.0	-Python-3.6.4	intel/2018a
0.9.0	-Python-3.6.6	foss/2018b, intel/2018b
0.9.0	-Python-3.7.2	foss/2019a, intel/2019a
0.9.1	-Python-2.7.16	foss/2019b
0.9.1	-Python-2.7.18	foss/2020b
0.10.0	-Python-3.7.4	foss/2019b, intel/2019b
0.10.1		intel/2020b
0.10.1	-Python-3.8.2	foss/2020a, intel/2020a
0.11.1		foss/2020b, fosscuda/2020b, intel/2020b
0.11.2		foss/2021a, foss/2021b
0.12.1		foss/2022a
0.12.2		foss/2022b
0.13.2		gfbf/2023a

SEACells

SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data

homepage: https://github.com/dpeerlab/SEACells

version	toolchain
20230731	foss/2021a

SearchGUI

SearchGUI is a user-friendly open-source graphical user interface for configuring and running proteomics identification search engines and de novo sequencing algorithms, currently supporting X! Tandem, MS-GF+, MS Amanda, MyriMatch, Comet, Tide, Andromeda, OMSSA, Novor and DirecTag.

homepage: https://github.com/compomics/searchgui

version	versionsuffix	toolchain
3.3.3	-Java-1.8.0_152	system

SeaView

SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny.

homepage: https://doua.prabi.fr/software/seaview

version	toolchain
5.0.5	GCCcore/11.2.0

SECAPR

SECAPR is a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments

homepage: https://github.com/AntonelliLab/seqcap_processor

version	versionsuffix	toolchain
1.1.15	-Python-2.7.16	foss/2019b

Seeder

Seeder is a framework for DNA motif discovery.

homepage: https://metacpan.org/pod/Seeder

version	versionsuffix	toolchain
0.01	-Perl-5.28.1	GCCcore/8.2.0

segemehl

segemehl is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is able to map primer- or polyadenylation contaminated reads correctly. segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads gziped queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping.

homepage: https://www.bioinf.uni-leipzig.de/Software/segemehl/

version	toolchain
0.2.0	foss/2016b, intel/2017b, intel/2018a
0.3.4	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/8.3.0, foss/2018b, iccifort/2020.4.304

segment-anything

The Segment Anything Model (SAM) produces high quality object masks from input prompts such as points or boxes, and it can be used to generate masks for all objects in an image. It has been trained on a dataset of 11 million images and 1.1 billion masks, and has strong zero-shot performance on a variety of segmentation tasks.

homepage: https://github.com/facebookresearch/segment-anything

version	toolchain
1.0	foss/2022a

segmentation-models

Python library with Neural Networks for Image Segmentation based on Keras and TensorFlow.

homepage: https://github.com/qubvel/segmentation_models

version	versionsuffix	toolchain
1.0.1	-Python-3.7.4	foss/2019b, fosscuda/2019b

segmentation-models-pytorch

Python library with Neural Networks for Image Segmentation based on PyTorch.

homepage: https://github.com/qubvel/segmentation_models.pytorch

version	versionsuffix	toolchain
0.3.3		foss/2022a
0.3.3	-CUDA-11.7.0	foss/2022a

SeisSol

SeisSol is a software package for simulating wave propagation and dynamic rupture based on the arbitrary high-order accurate derivative discontinuous Galerkin method (ADER-DG).

homepage: http://www.seissol.org

version	versionsuffix	toolchain
201703	-Python-2.7.15	foss/2018b

SelEstim

SelEstim is aimed at distinguishing neutral from selected polymorphisms and estimate the intensity of selection at the latter. The SelEstim model accounts explicitly for positive selection, and it is assumed that all marker loci in the dataset are responding to selection, to some extent

homepage: http://www1.montpellier.inra.fr/CBGP/software/selestim/index.html

version	versionsuffix	toolchain
1.1.4	-Linux-64bits	system

SELFIES

Robust representation of semantically constrained graphs, in particular for molecules in chemistry

homepage: https://github.com/aspuru-guzik-group/selfies

version	toolchain
2.1.1	GCC/11.2.0

SemiBin

SemiBin: Metagenomic Binning Using Siamese Neural Networks for short and long reads

homepage: https://semibin.readthedocs.io

version	versionsuffix	toolchain
2.0.2		foss/2022a
2.0.2	-CUDA-11.7.0	foss/2022a

semla

R interface to the Apache Arrow C++ library

homepage: https://cran.r-project.org/web/packages/arrow

version	versionsuffix	toolchain
1.1.6	-R-4.3.2	foss/2023a

Sentence-Transformers

Sentence Transformers provides an easy method to compute dense vector representations for sentences, paragraphs, and images

homepage: https://github.com/UKPLab/sentence-transformers

version	toolchain
2.2.2	foss/2022b

SentencePiece

Unsupervised text tokenizer for Neural Network-based text generation.

homepage: https://github.com/google/sentencepiece

version	versionsuffix	toolchain
0.1.85	-Python-3.7.4	GCC/8.3.0
0.1.94	-Python-3.8.2	GCC/9.3.0
0.1.96		GCC/10.2.0, GCC/10.3.0
0.1.97		GCC/11.3.0
0.1.99		GCC/12.2.0

sentinelsat

Sentinelsat makes searching, downloading and retrieving the metadata of Sentinel satellite images from the Copernicus Open Access Hub easy.

homepage: https://github.com/sentinelsat/sentinelsat

version	toolchain
1.2.1	GCCcore/11.3.0

sep

Python and C library for Source Extraction and Photometry. (this easyconfig provides python library only)

homepage: https://sep.readthedocs.io

version	versionsuffix	toolchain
1.0.3	-Python-2.7.15	foss/2018b, intel/2018b

SEPP

SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic placement of short reads into reference alignments and trees.

homepage: https://github.com/smirarab/sepp

version	versionsuffix	toolchain
4.3.10	-Python-3.7.4	foss/2019b
4.3.10	-Python-3.8.2	foss/2020a
4.4.0		foss/2020b
4.5.0		foss/2021a
4.5.1		foss/2021b, foss/2022a, foss/2022b

Seq-Gen

Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process.

homepage: http://tree.bio.ed.ac.uk/software/Seq-Gen

version	toolchain
1.3.4	intel/2017b

seq2HLA

In-silico method written in Python and R to determine HLA genotypes of a sample. seq2HLA takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes (in 4 digit resolution), a p-value for each call, and the expression of each class.

homepage: https://github.com/TRON-Bioinformatics/seq2HLA

version	versionsuffix	toolchain
2.3	-Python-2.7.14	intel/2018a
2.3	-Python-2.7.15	foss/2018b

SeqAn

SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data

homepage: https://www.seqan.de/

version	versionsuffix	toolchain
1.4.2	-library	system
2.3.2		foss/2016b
2.4.0		GCC/8.2.0-2.31.1, GCCcore/10.2.0, GCCcore/11.2.0, GCCcore/8.3.0, GCCcore/9.3.0, foss/2018b, intel/2018b

SeqAn3

SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. Our library applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. SeqAn is easy to use and simplifies the development of new software tools with a minimal loss of performance.

homepage: https://github.com/seqan/seqan3

version	toolchain
3.0.0	system

SeqKit

SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation

homepage: https://bioinf.shenwei.me/seqkit/

version	toolchain
0.8.1	system
0.13.2	system
2.1.0	system
2.2.0	system
2.3.1	system

SeqLib

C++ interface to HTSlib, BWA-MEM and Fermi.

homepage: https://github.com/walaj/SeqLib

version	toolchain
1.2.0	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/12.3.0, GCC/9.3.0

Seqmagick

We often have to convert between sequence formats and do little tasks on them, and it's not worth writing scripts for that. Seqmagick is a kickass little utility built in the spirit of imagemagick to expose the file format conversion in Biopython in a convenient way. Instead of having a big mess of scripts, there is one that takes arguments.

homepage: https://fhcrc.github.io/seqmagick/

version	versionsuffix	toolchain
0.6.1	-Python-2.7.11	foss/2016a
0.6.2	-Python-2.7.15	foss/2018b
0.8.6		foss/2023a

SeqPrep

Tool for stripping adaptors and/or merging paired reads with overlap into single reads.

homepage: https://github.com/jstjohn/SeqPrep

version	toolchain
1.3.2	GCCcore/7.3.0

seqtk

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.

homepage: https://github.com/lh3/seqtk/

version	toolchain
1.2	foss/2016b, intel/2017a
1.3	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/11.3.0, GCC/8.2.0-2.31.1, GCC/8.3.0, GCC/9.3.0, foss/2018a, foss/2018b
1.4	GCC/12.2.0, GCC/12.3.0

Serf

The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library

homepage: http://serf.apache.org/

version	toolchain
1.3.9	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/9.3.0, foss/2017b, intel/2017b, iomkl/2018a

setuptools

Easily download, build, install, upgrade, and uninstall Python packages

homepage: https://pypi.org/project/setuptools

version	versionsuffix	toolchain
1.4.2		system
41.0.1	-py3	system
64.0.3		GCCcore/12.2.0

setuptools-rust

setuptools-rust is a plugin for setuptools to build Rust Python extensions implemented with PyO3 or rust-cpython.

homepage: https://github.com/PyO3/setuptools-rust

version	toolchain
1.6.0	GCCcore/12.3.0
1.8.0	GCCcore/13.2.0

Seurat

Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data.

homepage: https://satijalab.org/seurat

version	versionsuffix	toolchain
1.4.0.16	-R-3.4.0	intel/2017a
2.3.4	-R-3.4.4	intel/2018a
2.3.4	-R-3.5.1	foss/2018b
3.1.2	-R-3.6.0	foss/2019a
3.1.5	-R-4.0.0	foss/2020a
4.0.1	-R-4.0.3	foss/2020b
4.0.3	-R-4.0.3	foss/2020b
4.1.0	-R-4.1.0	foss/2021a
4.2.0	-R-4.2.1	foss/2022a
4.3.0	-R-4.1.2	foss/2021b
4.3.0	-R-4.2.1	foss/2022a
4.4.0	-R-4.2.2	foss/2022b
5.0.1	-R-4.2.2	foss/2022b

SeuratData

SeuratData is a mechanism for distributing datasets in the form of Seurat objects using R's internal package and data management systems.

homepage: https://github.com/satijalab/seurat-data

version	versionsuffix	toolchain
20210514	-R-4.0.3	foss/2020b

SeuratDisk

Interfaces for HDF5-based Single Cell File Formats

homepage: https://github.com/mojaveazure/seurat-disk

version	versionsuffix	toolchain
0.0.0.9020	-R-4.2.1	foss/2022a

SeuratWrappers

SeuratWrappers is a collection of community-provided methods and extensions for Seurat

homepage: https://github.com/satijalab/seurat-wrappers

version	versionsuffix	toolchain
20210528	-R-4.0.3	foss/2020b
20221022	-R-4.2.1	foss/2022a

sf

Support for simple features, a standardized way to encode spatial vector data. Binds to GDAL for reading and writing data, to GEOS for geometrical operations, and to PROJ for projection conversions and datum transformations.

homepage: https://cran.r-project.org/package=sf

version	versionsuffix	toolchain
0.9-5	-R-4.0.0-Python-3.8.2	foss/2020a

sfftk

sfftk is a set of utilities that facilitate creation, conversion and modification of Electron Microscopy Data Bank - Segmentation File Format (EMDB-SFF) files. EMDB-SFF is an open, community-driven file format to handle annotated segmentations and subtomogram averages that facilitates segmentation file interchange. It is written in Python and provides both a command-line suite of commands and a Python API.

homepage: https://emdb-empiar.github.io/EMDB-SFF/

version	toolchain
0.7.4	foss/2021a

Shannon

Shannon is a program for assembling transcripts from RNA-Seq data

homepage: https://sreeramkannan.github.io/Shannon/

version	versionsuffix	toolchain
20170511	-Python-2.7.13	intel/2017a

SHAP

SHAP (SHapley Additive exPlanations) is a game theoretic approach to explain the output of any machine learning model. It connects optimal credit allocation with local explanations using the classic Shapley values from game theory and their related extensions.

homepage: https://github.com/slundberg/shap

version	versionsuffix	toolchain
0.35.0	-Python-3.7.4	foss/2019b
0.41.0		foss/2022a
0.42.1		foss/2022a
0.42.1	-Python-3.7.4	foss/2019b

shapAAR

An R package for the extraction, analysis and classification of (not only) archaeological objects from scanned images.

homepage: https://github.com/ISAAKiel/shapAAR

version	versionsuffix	toolchain
0.1.0-20180425	-R-3.6.0	foss/2019a

SHAPEIT

SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.

homepage: https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html

version	versionsuffix	toolchain
2.r837	.GLIBCv2.12	system
2.r904	.glibcv2.17	system

SHAPEIT4

SHAPEIT4 is a fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and high coverage sequencing data.

homepage: https://odelaneau.github.io/shapeit4/

version	toolchain
4.1.3	foss/2019b
4.2.0	foss/2019b, foss/2020a, foss/2020b
4.2.2	foss/2020b, foss/2021a

Shapely

Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries.

homepage: https://github.com/Toblerity/Shapely

version	versionsuffix	toolchain
1.7.0	-Python-3.7.2	foss/2019a
1.7.0	-Python-3.7.4	GCC/8.3.0, iccifort/2019.5.281
1.7.1	-Python-3.8.2	GCC/9.3.0
1.8.1.post1		GCC/11.2.0
1.8.2		foss/2021b, foss/2022a
1.8a1		GCC/10.2.0, GCC/10.3.0, iccifort/2020.4.304
2.0.1		foss/2022b, gfbf/2023a

sharutils

GNU shar makes so-called shell archives out of many files, preparing them for transmission by electronic mail services, while unshar helps unpacking shell archives after reception.

homepage: https://www.gnu.org/software/sharutils/

version	toolchain
4.15	GCCcore/6.3.0

Shasta

The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using DNA reads generated by Oxford Nanopore flow cells as input. Computational methods used by the Shasta assembler include: Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in homopolymer repeat counts, which are the most common type of errors in Oxford Nanopore reads. Using in some phases of the computation a representation of the read sequence based on markers, a fixed subset of short k-mers (k ≈ 10).

homepage: https://github.com/chanzuckerberg/shasta

version	toolchain
0.8.0	foss/2020b

ShengBTE

A solver for the Boltzmann transport equation for phonons.

homepage: https://bitbucket.org/sousaw/shengbte

version	toolchain
1.1.1	foss/2021a
1.5.0	foss/2022a

shift

Shift is a framework for Self-Healing Independent File Transfer that provides high performance and resilience for local and remote transfers through a variety of techniques.

homepage: http://people.nas.nasa.gov/~kolano/projects/shift.html

version	toolchain
4.0	intel/2016a

SHORE

SHORE, for Short Read, is a mapping and analysis pipeline for short read data produced on the Illumina platform.

homepage: http://1001genomes.org/software/shore.html

version	toolchain
0.9.3	foss/2016a

Short-Pair

Sensitive Short Read Homology Search for Paired-End Reads

homepage: https://sourceforge.net/projects/short-pair

version	versionsuffix	toolchain
20170125		foss/2021b
20170125	-Python-2.7.15	foss/2018b

shovill

Faster SPAdes assembly of Illumina reads

homepage: https://github.com/tseemann/shovill

version	versionsuffix	toolchain
0.9.0	-Python-2.7.14	foss/2018a
1.0.4	-Python-2.7.15	foss/2018b
1.1.0		gompi/2021b

shrinkwrap

A std::streambuf wrapper for compression formats.

homepage: https://github.com/jonathonl/shrinkwrap

version	toolchain
1.0.0-beta	GCCcore/8.2.0
1.1.0	GCCcore/10.2.0

SHTns

Spherical Harmonic Transform library aimed at high performance numerical simulations in spherical geometries.

homepage: https://bitbucket.org/nschaeff/shtns

version	toolchain
2.7	foss/2021b
3.5.1	foss/2021b

Sibelia

Sibelia: A comparative genomics tool: It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement studies for multiple strains of microorganisms.

homepage: http://bioinf.spbau.ru/en/sibelia

version	toolchain
3.0.6	foss/2016b
3.0.7	foss/2018b, foss/2020b

SICER2

Redesigned and improved ChIP-seq broad peak calling tool SICER

homepage: https://zanglab.github.io/SICER2/

version	versionsuffix	toolchain
1.0.3	-Python-3.8.2	foss/2020a

sickle

Windowed Adaptive Trimming for fastq files using quality

homepage: https://github.com/najoshi/sickle

version	toolchain
1.33	foss/2017a, intel/2018a

Siesta

SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.

homepage: http://departments.icmab.es/leem/siesta

version	versionsuffix	toolchain
4.0		foss/2017b, intel/2017a
4.0.1		intel/2017a
4.1-b2		intel/2017a
4.1-b3		intel/2017a
4.1-b4		foss/2018b, intel/2018b
4.1-MaX-1.0		intel/2019b
4.1-MaX-1.0	-PEXSI	intel/2019b
4.1.5		foss/2020a, foss/2021a, foss/2021b, foss/2022a, intel/2020a, intel/2022a

SignalP

SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms

homepage: https://services.healthtech.dtu.dk/software.php

version	versionsuffix	toolchain
5.0b	-Linux	system
6.0g	-fast	foss/2021b, foss/2022a
6.0g	-fast-CUDA-11.7.0	foss/2022a
6.0h	-fast	foss/2022b

silhouetteRank

silhouetteRank is a tool for finding spatially variable genes based on computing silhouette coefficient from binarized spatial gene expression data

homepage: https://pypi.org/project/silhouetteRank

version	toolchain
1.0.5.13	foss/2022a

silx

The silx project provides a collection of Python packages to support the development of data assessment, reduction and analysis applications at synchrotron radiation facilities.

homepage: http://www.silx.org/

version	versionsuffix	toolchain
0.13.2	-Python-3.7.4	foss/2019b, fosscuda/2019b
0.14.0		foss/2020b, fosscuda/2020b
1.0.0		foss/2021b

simanneal

This module performs simulated annealing optimization to find the optimal state of a system. It is inspired by the metallurgic process of annealing whereby metals must be cooled at a regular schedule in order to settle into their lowest energy state.

homepage: https://github.com/perrygeo/simanneal

version	toolchain
0.5.0	GCC/11.3.0

simint

Simint is a vectorized implementation of the Obara-Saika (OS) method of calculating electron repulsion integrals. Speedup is gained by vectorizing the primitive loop of the OS algorithm, with additional vectorization and optimizations left to the compiler.

homepage: https://www.bennyp.org/research/simint/

version	versionsuffix	toolchain
0.7	-lmax-5-vec-avx-psi4	GCC/11.2.0

SimNIBS

SimNIBS is a free and open source software package for the Simulation of Non-invasive Brain Stimulation.

homepage: https://simnibs.github.io/simnibs

version	toolchain
3.2.4	foss/2020b

SimPEG

Simulation and Parameter Estimation in Geophysics: a python package for simulation and gradient based parameter estimation in the context of geophysical applications.

homepage: https://simpeg.xyz

version	versionsuffix	toolchain
0.3.1	-Python-2.7.12	intel/2016b
0.14.1	-Python-3.8.2	intel/2020a
0.18.1		foss/2021b, intel/2021b

SIMPLE

Single-particle IMage Processing Linux Engine SIMPLE is an open-source software package for analysis of cryogenic transmission electron microscopy (cryo-EM) movies of single-particles (Single-Particle Analysis, SPA).

homepage: https://simplecryoem.com/

version	toolchain
2.5	foss/2018a
3.0.0	foss/2020b

Simple-DFTD3

Reimplementation of the D3 dispersion correction. The s-dftd3 project aims to provide a user-friendly and uniform interface to the D3 dispersion model and for the calculation of DFT-D3 dispersion corrections.

homepage: https://dftd3.readthedocs.io

version	toolchain
0.7.0	foss/2022a

SimpleElastix

Multi-lingual medical image registration library.

homepage: https://simpleelastix.github.io

version	versionsuffix	toolchain
0.10.0	-Python-3.6.3	foss/2017b
0.10.0	-Python-3.6.4	foss/2018a
1.1.0	-Python-3.7.4	foss/2019b

SimpleITK

SimpleITK is a simplified programming interface to the algorithms and data structures of the Insight Toolkit (ITK).

homepage: https://www.simpleitk.org

version	versionsuffix	toolchain
1.1.0	-Python-2.7.15	foss/2018b
1.1.0	-Python-3.6.4	foss/2018a
1.1.0	-Python-3.6.6	foss/2018b
1.2.4	-Python-3.7.4	foss/2019b
2.1.0		foss/2020b, fosscuda/2020b
2.1.1		foss/2021a
2.1.1.2		foss/2021b, foss/2022a
2.3.1		foss/2023a

simpy

SimPy is a process-based discrete-event simulation framework based on standard Python.

homepage: https://simpy.readthedocs.io

version	versionsuffix	toolchain
3.0.11		intel/2019a
3.0.11	-Python-3.6.6	intel/2018b

Simstrat

Simstrat is a one-dimensional physical lake model for the simulation of stratification and mixing in deep stratified lakes.

homepage: http://www.eawag.ch/en/department/surf/projects/simstrat/

version	toolchain
3.01	GCC/10.3.0

SimVascular

SimVascular is an open source software suite for cardiovascular simulation, providing a complete pipeline from medical image data to 3D model construction, meshing, and blood flow simulation.

homepage: http://simvascular.github.io/

version	toolchain
2.16.0406	intel/2016b

SingleM

SingleM is a tool to find the abundances of discrete operational taxonomic units (OTUs) directly from shotgun metagenome data, without heavy reliance on reference sequence databases.

homepage: https://github.com/wwood/singlem

version	versionsuffix	toolchain
0.12.1	-Python-2.7.15	intel/2019a

Singular

Singular is a computer algebra system for polynomial computations, with special emphasis on commutative and non-commutative algebra, algebraic geometry, and singularity theory.

homepage: https://www.singular.uni-kl.de/

version	toolchain
4.1.2	GCC/8.2.0-2.31.1, system
4.3.2p10	gfbf/2022a

sinto

Sinto is a toolkit for processing aligned single-cell data.

homepage: https://timoast.github.io/sinto/index.html

version	toolchain
0.7.4	foss/2021a

SiNVICT

SiNVICT is a tool for the detection of SNVs and indels from cfDNA/ctDNA samples obtained by ultra-deep sequencing.

homepage: https://github.com/sfu-compbio/sinvict

version	toolchain
1.0-20180817	GCC/9.3.0

SIONlib

SIONlib is a scalable I/O library for parallel access to task-local files. The library not only supports writing and reading binary data to or from several thousands of processors into a single or a small number of physical files, but also provides global open and close functions to access SIONlib files in parallel. This package provides a stripped-down installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols to avoid conflicts when an application using SIONlib itself is linked against a tool requiring a different SIONlib version.

homepage: https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html

version	versionsuffix	toolchain
1.6.1		foss/2016a
1.6.1	-tools	foss/2016a
1.7.1		foss/2017a
1.7.1	-tools	foss/2017a
1.7.4	-tools	GCCcore/8.2.0
1.7.6	-tools	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/8.3.0, GCCcore/9.3.0
1.7.7	-tools	GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

SIP

SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.

homepage: http://www.riverbankcomputing.com/software/sip/

version	versionsuffix	toolchain
4.18	-Python-2.7.11	foss/2016a, intel/2016a
4.18.1	-Python-2.7.11	foss/2016a
4.18.1	-Python-2.7.12	intel/2016b
4.19	-Python-2.7.12	foss/2016b, intel/2016b
4.19.2	-Python-2.7.13	intel/2017a
4.19.8	-Python-2.7.14	foss/2017b, foss/2018a, intel/2017b, intel/2018a
4.19.8	-Python-3.6.4	foss/2018a, intel/2018a
4.19.13	-Python-2.7.15	fosscuda/2018b
6.8.1		GCCcore/12.3.0

siscone

Hadron Seedless Infrared-Safe Cone jet algorithm

homepage: https://siscone.hepforge.org/

version	toolchain
3.0.5	GCCcore/11.3.0
3.0.6	GCCcore/12.3.0

SISSO

A data-driven method combining symbolic regression and compressed sensing toward accurate & interpretable models.

homepage: https://github.com/rouyang2017/SISSO

version	toolchain
3.0.2	iimpi/2021b
3.1-20220324	iimpi/2021b

SISSO++

C++ implementation of SISSO with built in Python bindings for an efficient python interface

homepage: https://gitlab.com/sissopp_developers/sissopp

version	toolchain
1.1	foss/2021b

SKESA

SKESA is a de-novo sequence read assembler for cultured single isolate genomes based on DeBruijn graphs.

homepage: https://github.com/ncbi/SKESA

version	versionsuffix	toolchain
2.2		foss/2018a
2.3.0		foss/2018b
2.4.0	_saute.1.3.0_1	gompi/2021b

sketchmap

Sketch-map is a dimensionality reduction algorithm that is particularly well suited to examining the high-dimensionality data that is routinely produced in atomistic simulations.

homepage: http://sketchmap.org/

version	toolchain
20170130	intel/2016b

skewer

skewer implements the bit-masked k-difference matching algorithm dedicated to the task of adapter trimming and it is specially designed for processing next-generation sequencing (NGS) paired-end sequences.

homepage: https://github.com/relipmoc/skewer

version	toolchain
0.2.2	intel/2016b

sklearn-pandas

This module provides a bridge between Scikit-Learn's machine learning methods and pandas-style Data Frames. In particular, it provides a way to map DataFrame columns to transformations, which are later recombined into features.

homepage: https://github.com/scikit-learn-contrib/sklearn-pandas

version	toolchain
2.2.0	foss/2021b

sklearn-som

A simple, planar self-organizing map with methods similar to clustering methods in Scikit Learn.

homepage: https://github.com/rileypsmith/sklearn-som

version	toolchain
1.1.0	foss/2020b

skorch

A scikit-learn compatible neural network library that wraps PyTorch.

homepage: https://skorch.readthedocs.io/

version	versionsuffix	toolchain
0.11.0	-PyTorch-1.10.0	foss/2021a
0.11.0	-PyTorch-1.10.0-CUDA-11.3.1	foss/2021a
0.15.0	-PyTorch-2.1.2	foss/2023a

sktime

sktime is a library for time series analysis in Python. It provides a unified interface for multiple time series learning tasks. Currently, this includes time series classification, regression, clustering, annotation, and forecasting. It comes with time series algorithms and scikit-learn compatible tools to build, tune and validate time series models.

homepage: https://www.sktime.net/en/stable/

version	toolchain
0.25.0	gfbf/2023a

SlamDunk

SlamDunk is a novel, fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis.

homepage: https://t-neumann.github.io/slamdunk

version	toolchain
0.4.3	foss/2021b

SLATEC

SLATEC Common Mathematical Library, a comprehensive software library containing over 1400 general purpose mathematical and statistical routines written in Fortran 77.

homepage: https://www.netlib.org/slatec/

version	toolchain
4.1	GCC/6.4.0-2.28, GCC/8.3.0, iccifort/2018.1.163-GCC-6.4.0-2.28

SLEPc

SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.

homepage: https://www.grycap.upv.es/slepc/

version	versionsuffix	toolchain
3.8.3		foss/2017b
3.9.2		foss/2018a
3.11.0		foss/2018b
3.12.2	-Python-2.7.16	intel/2019b
3.12.2	-Python-3.7.4	foss/2019b, intel/2019b
3.12.2	-Python-3.8.2	foss/2020a, intel/2020a
3.14.2		foss/2020b
3.15.1		foss/2021a
3.17.2		foss/2022a
3.18.2		intel/2021b
3.20.1		foss/2023a

slepc4py

Python bindings for SLEPc, the Scalable Library for Eigenvalue Problem Computations.

homepage: https://bitbucket.org/slepc/slepc4py

version	versionsuffix	toolchain
3.9.0	-Python-3.6.4	foss/2018a
3.12.0	-Python-3.7.4	foss/2019b
3.15.1		foss/2021a

sleuth

Investigate RNA-Seq transcript abundance from kallisto and perform differential expression analysis.

homepage: http://pachterlab.github.io/sleuth

version	versionsuffix	toolchain
0.29.0	-R-3.4.0	intel/2017a
0.30.0	-R-3.5.1	foss/2018b

slidingwindow

slidingwindow is a simple little Python library for computing a set of windows into a larger dataset, designed for use with image-processing algorithms that utilise a sliding window to break the processing up into a series of smaller chunks.

homepage: https://github.com/adamrehn/slidingwindow

version	versionsuffix	toolchain
0.0.13	-Python-2.7.15	intel/2018b
0.0.13	-Python-3.6.6	intel/2018b

SLiM

SLiM is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios.

homepage: https://messerlab.org/slim

version	toolchain
3.4	GCC/9.3.0
4.0	GCC/11.2.0
4.0.1	GCC/11.3.0

slow5tools

slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format.

homepage: https://hasindu2008.github.io/slow5tools

version	toolchain
0.4.0	gompi/2021b

slurm-drmaa

DRMAA for Slurm Workload Manager (Slurm) is an implementation of Open Grid Forum Distributed Resource Management Application API (DRMAA) version 1 for submission and control of jobs to Slurm. Using DRMAA, grid applications builders, portal developers and ISVs can use the same high-level API to link their software with different cluster/resource management systems.

homepage: https://github.com/natefoo/slurm-drmaa

version	toolchain
1.1.3	GCCcore/12.2.0

smafa

Smafa attempts to align or cluster pre-aligned biological sequences, handling sequences which are all the same length.

homepage: https://github.com/wwood/smafa

version	toolchain
0.4.0	GCCcore/8.2.0

smallgenomeutilities

The smallgenomeutilities are a collection of scripts that is useful for dealing and manipulating NGS data of small viral genomes. They are written in Python 3 with a small number of dependencies.

homepage: https://github.com/cbg-ethz/smallgenomeutilities

version	versionsuffix	toolchain
0.2.1	-Python-3.6.6	foss/2018b

SMAP

SMAP is an analysis tool for stack-based NGS read mapping

homepage: https://ngs-smap.readthedocs.io

version	toolchain
4.6.5	foss/2022a

SMARTdenovo

SMARTdenovo is a de novo assembler for PacBio and Oxford Nanopore (ONT) data. It produces an assembly from all-vs-all raw read alignments without an error correction stage. It also provides tools to generate accurate consensus sequences, though a platform dependent consensus polish tools (e.g. Quiver for PacBio or Nanopolish for ONT) are still required for higher accuracy.

homepage: https://github.com/ruanjue/smartdenovo

version	toolchain
20180219	foss/2018b

SMC++

SMC++ is a program for estimating the size history of populations from whole genome sequence data.

homepage: https://github.com/popgenmethods/smcpp

version	toolchain
1.15.4	foss/2022a

smfishHmrf

smFish spatial pattern mining and cell type prediction

homepage: https://pypi.org/project/smfishHmrf

version	toolchain
1.3.3	foss/2022a

smithwaterman

smith-waterman-gotoh alignment algorithm.

homepage: https://github.com/ekg/smithwaterman

version	toolchain
20160702	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.3.0, GCCcore/9.3.0

Smoldyn

Smoldyn is a computer program for cell-scale biochemical simulations. It simulates each molecule of interest individually to capture natural stochasticity and to yield nanometer-scale spatial resolution. It treats other molecules implicitly, enabling it to simulate hundreds of thousands of molecules over several minutes of real time. Simulated molecules diffuse, react, are confined by surfaces, and bind to membranes much as they would in a real biological system.

homepage: http://www.smoldyn.org/

version	toolchain
2.48	foss/2016a

smooth-topk

Smooth Loss Functions for Deep Top-k Classification

homepage: https://github.com/oval-group/smooth-topk

version	versionsuffix	toolchain
1.0-20210817		foss/2021a
1.0-20210817	-CUDA-11.3.1	foss/2021a

SMRT-Link

PacBio's open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data. You can analyze, visualize, and manage your data through an intuitive GUI or command-line interface. You can also integrate SMRT Analysis in your existing data workflow through the extensive set of APIs provided

homepage: https://www.pacb.com/support/software-downloads/

version	versionsuffix	toolchain
5.1.0.26412	-cli-tools-only	system
6.0.0.47841	-cli-tools-only	system
12.0.0.177059	-cli-tools-only	system

SMV

Smokeview is a visualization program that displays output of FDS and CFAST simulations.

homepage: https://github.com/firemodels/smv

version	toolchain
6.7.17	iccifort/2020.4.304

snakemake

The Snakemake workflow management system is a tool to create reproducible and scalable data analyses.

homepage: https://snakemake.readthedocs.io

version	versionsuffix	toolchain
5.2.2	-Python-3.6.4	intel/2018a
5.2.4	-Python-3.6.6	foss/2018b, intel/2018b
5.7.1	-Python-3.7.2	foss/2019a
5.26.1	-Python-3.8.2	intel/2020a
6.1.0		foss/2020b
6.6.1		foss/2021a
6.10.0		foss/2021b
7.18.2		foss/2021b
7.22.0		foss/2022a
7.32.3		foss/2022b
8.4.2		foss/2023a

SNAP

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data

homepage: https://www.microsoft.com/en-us/research/project/snap

version	toolchain
1.0beta.23	intel/2017b
2.0.1	GCC/11.2.0, GCC/11.3.0, GCC/12.2.0

SNAP-ESA

The Sentinel Application Platform (SNAP) is a common architecture for all Sentinel Toolboxes being jointly developed by Brockmann Consult, SkyWatch and C-S. The SNAP architecture is ideal for Earth Observation processing and analysis due to the following technological innovations: Extensibility, Portability, Modular Rich Client Platform, Generic EO Data Abstraction, Tiled Memory Management, and a Graph Processing Framework.

homepage: https://step.esa.int/main/toolboxes/snap/

version	versionsuffix	toolchain
8.0	-Java-1.8	system
9.0.0	-Java-11	system

SNAP-ESA-python

Python interface to the Sentinel Application Platform (SNAP) API

homepage: https://step.esa.int/main/toolboxes/snap/

version	versionsuffix	toolchain
8.0	-Java-1.8-Python-2.7.18	GCCcore/10.2.0
9.0.0	-Java-11-Python-2.7.18	GCCcore/11.2.0

SNAP-HMM

SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser.

homepage: https://korflab.github.io/

version	toolchain
2013-11-29	GCC/6.4.0-2.28, GCC/8.3.0, iccifort/2017.4.196-GCC-6.4.0-2.28
20190603	GCC/10.2.0
20221022	GCC/11.3.0

SNAPE-pooled

SNAPE-pooled computes the probability distribution for the frequency of the minor allele in a certain population, at a certain position in the genome.

homepage: https://code.google.com/archive/p/snape-pooled/

version	toolchain
20150707	GCC/11.3.0
r32	foss/2016a

snaphu

SNAPHU is an implementation of the Statistical-cost, Network-flow Algorithm for Phase Unwrapping proposed by Chen and Zebker

homepage: https://web.stanford.edu/group/radar/softwareandlinks/sw/snaphu/

version	toolchain
1.4.2	GCCcore/6.3.0, intel/2016b, intel/2017a

snappy

Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression.

homepage: https://github.com/google/snappy

version	toolchain
1.1.2	GCC/4.9.2
1.1.3	GCC/4.9.3, GCC/4.9.3-2.25
1.1.6	system
1.1.7	GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, intel/2017a, intel/2017b
1.1.8	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/9.3.0
1.1.9	GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0
1.1.10	GCCcore/12.3.0, GCCcore/13.2.0

Sniffles

A fast structural variant caller for long-read sequencing, Sniffles2 accurately detect SVs on germline, somatic and population-level for PacBio and Oxford Nanopore read data.

homepage: https://github.com/fritzsedlazeck/Sniffles

version	toolchain
2.0.7	GCC/11.3.0

snippy

Rapid haploid variant calling and core genome alignment

homepage: https://github.com/tseemann/snippy

version	versionsuffix	toolchain
4.4.1	-Perl-5.28.0	foss/2018b
4.6.0		GCC/10.2.0
4.6.0	-Java-13-Python-3.8.2	GCC/9.3.0
4.6.0	-R-4.1.2	foss/2021b

snp-sites

Finds SNP sites from a multi-FASTA alignment file.

homepage: https://sanger-pathogens.github.io/snp-sites/

version	toolchain
2.5.1	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/9.3.0

snpEff

SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes).

homepage: https://pcingola.github.io/SnpEff/

version	versionsuffix	toolchain
3.6	-Java-1.7.0_80	system
4.1d	-Java-1.7.0_80	system
4.3t	-Java-1.8	system
5.0	-Java-13	system
5.0	-Java-13-Python-3.8.2	GCCcore/9.3.0
5.0e	-Java-11	GCCcore/11.2.0
5.0e	-Java-13	GCCcore/10.2.0

SNPhylo

SNPhylo: a pipeline to generate a phylogenetic tree from huge SNP data

homepage: http://chibba.pgml.uga.edu/snphylo/

version	versionsuffix	toolchain
20140701		foss/2016a, intel/2016a
20160204	-Python-2.7.14-R-3.4.3	foss/2017b, intel/2017b

SNPomatic

High throughput sequencing technologies generate large amounts of short reads. Mapping these to a reference sequence consumes large amounts of processing time and memory, and read mapping errors can lead to noisy or incorrect alignments. SNP-o-matic is a fast, memory-efficient, and stringent read mapping tool offering a variety of analytical output functions, with an emphasis on genotyping.

homepage: https://github.com/magnusmanske/snpomatic

version	toolchain
1.0	GCCcore/9.3.0

SOAPaligner

SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment.

homepage: http://soap.genomics.org.cn/soapaligner.html

version	versionsuffix	toolchain
2.21	_Linux-x86_64	system

SOAPdenovo-Trans

SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.

homepage: http://soap.genomics.org.cn/SOAPdenovo-Trans.html

version	toolchain
1.0.4	intel/2017a
1.0.5	GCC/12.3.0

SOAPdenovo2

SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the successor of SOAPdenovo.

homepage: http://soap.genomics.org.cn/index.html

version	toolchain
r240	GCC/5.4.0-2.26
r241	GCC/6.4.0-2.28, foss/2018a, iccifort/2017.4.196-GCC-6.4.0-2.28, intel/2018a

SOAPfuse

SOAPfuse is an open source tool developed for genome-wide detection of fusion transcripts from paired-end RNA-Seq data.

homepage: https://sourceforge.net/p/soapfuse/wiki/Home/

version	versionsuffix	toolchain
1.27	-Perl-5.24.0	foss/2016b
1.27	-Perl-5.28.0	foss/2018b

socat

socat is a relay for bidirectional data transfer between two independent data channels.

homepage: http://www.dest-unreach.org/socat

version	toolchain
1.7.3.3	GCCcore/8.2.0

SOCI

SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the regular C++ code, staying entirely within the Standard C++.

homepage: http://soci.sourceforge.net/

version	toolchain
4.0.1	GCC/10.2.0, GCCcore/9.3.0
4.0.2	GCC/10.3.0
4.0.3	GCC/11.2.0, GCC/11.3.0, GCC/12.2.0

SolexaQA++

SolexaQA calculates sequence quality statistics and creates visual representations of data quality for second-generation sequencing data. Originally developed for the Illumina system (historically known as “Solexa”), SolexaQA now also supports Ion Torrent and 454 data.

homepage: http://solexaqa.sourceforge.net

version	toolchain
3.1.5	foss/2016b

solo

Doublet detection via semi-supervised deep learning

homepage: https://github.com/calico/solo

version	toolchain
1.3	foss/2022a

sonic

Sonic is a simple algorithm for speeding up or slowing down speech. However, it's optimized for speed ups of over 2X, unlike previous algorithms for changing speech rate. The Sonic library is a very simple ANSI C library that is designed to easily be integrated into streaming voice applications, like TTS back ends.

homepage: https://github.com/espeak-ng/sonic

version	toolchain
20180202	gfbf/2023a, gompi/2020a

SoPlex

SoPlex is an optimization package for solving linear programming problems (LPs) based on an advanced implementation of the primal and dual revised simplex algorithm. It provides special support for the exact solution of LPs with rational input data. It can be used as a standalone solver reading MPS or LP format files via a command line interface as well as embedded into other programs via a C++ class library.

homepage: https://soplex.zib.de/

version	toolchain
2.2.1	GCC/11.3.0

SoQt

SoQt is a library which provides the glue between Systems in Motion's Coin high-level 3D visualization library and the Qt 2D user interface library.

homepage: https://coin3d.github.io/SoQt/html/

version	toolchain
1.6.0	GCC/10.3.0, GCC/11.2.0

SortMeRNA

SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads.

homepage: http://bioinfo.lifl.fr/RNA/sortmerna/

version	toolchain
2.1	GCC/9.3.0, foss/2016a

SoupX

" Quantify, profile and remove ambient mRNA contamination (the "soup") from droplet based single cell RNA-seq experiments. Implements the method described in Young et al. (2018) .

homepage: https://github.com/constantAmateur/SoupX

version	versionsuffix	toolchain
1.6.2	-R-4.2.1	foss/2022a

SoX

Sound eXchange, the Swiss Army knife of audio manipulation

homepage: http://sox.sourceforge.net/

version	toolchain
14.4.2	GCC/8.3.0, GCCcore/11.3.0

SoXt

SoXt is an Xt/Motif glue library for Coin. It can also be used on top of the SGI or TGS implementation of Open Inventor, and is designed to be source code compatible with SGI's InventorXt library.

homepage: https://coin3d.github.io/SoXt/html/

version	toolchain
1.4.0	GCC/11.2.0

SpaceRanger

Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output and brightfield microscope images in order to detect tissue, align reads, generate feature-spot matrices, perform clustering and gene expression analysis, and place spots in spatial context on the slide image.

homepage: https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger

version	toolchain
1.1.0	GCC/9.3.0
1.2.2	GCC/9.3.0
1.3.0	GCC/10.3.0
1.3.1	GCC/11.2.0
2.0.0	GCC/11.2.0
2.0.1	GCC/11.3.0
2.1.0	GCC/11.3.0, GCC/12.2.0

Spack

Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, and all of these builds can coexist on the same machine.

homepage: https://spack.io/

version	toolchain
0.10.0	system
0.11.2	system
0.12.1	system
0.16.2	system
0.17.0	system
0.17.2	system

spaCy

Industrial-strength Natural Language Processing (NLP) in Python.

homepage: https://spacy.io/

version	toolchain
3.4.4	foss/2022a

SPAdes

Genome assembler for single-cell and isolates data sets

homepage: http://bioinf.spbau.ru/en/spades

version	versionsuffix	toolchain
3.9.0		foss/2016a, foss/2016b
3.10.1		foss/2016b, foss/2017a
3.11.1		foss/2017b, foss/2018a
3.12.0		foss/2016b, foss/2018a, foss/2018b
3.13.0		GCC/10.3.0, foss/2018b
3.13.1		GCC/8.2.0-2.31.1
3.14.0	-Python-3.7.2	GCC/8.2.0-2.31.1
3.14.0	-Python-3.7.4	GCC/8.3.0
3.14.1	-Python-3.8.2	GCC/9.3.0
3.15.2		GCC/10.2.0
3.15.2	-Python-2.7.18	GCC/10.2.0
3.15.3		GCC/10.3.0, GCC/11.2.0
3.15.4		GCC/12.2.0, GCC/12.3.0
3.15.5		GCC/11.3.0

spaln

Spaln (space-efficient spliced alignment) is a stand-alone program that maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job.

homepage: https://github.com/ogotoh/spaln

version	toolchain
2.3.3c	iccifort/2019.1.144-GCC-8.2.0-2.31.1
2.4.03	iccifort/2019.5.281
2.4.12	GCC/10.2.0, GCC/11.2.0
2.4.13f	GCC/11.3.0

Spark

Spark is Hadoop MapReduce done in memory

homepage: https://spark.apache.org

version	versionsuffix	toolchain
1.3.0		system
1.4.1		system
1.5.0		system
1.6.0		system
1.6.1		system
2.0.0		system
2.0.2		system
2.2.0	-Hadoop-2.6-Java-1.8.0_144	system
2.2.0	-Hadoop-2.6-Java-1.8.0_152	system
2.2.0	-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3	intel/2017b
2.3.0	-Hadoop-2.7-Java-1.8.0_162	system
2.4.0	-Hadoop-2.7-Java-1.8	system
2.4.0	-Hadoop-2.7-Java-1.8-Python-3.6.6	intel/2018b
2.4.0	-Python-2.7.15	foss/2018b, intel/2018b
2.4.0	-Python-3.6.6	intel/2018b
2.4.5	-Python-3.7.4-Java-1.8	intel/2019b
3.0.0	-Python-2.7.15	foss/2018b, intel/2018b
3.1.1		foss/2020b, fosscuda/2020b
3.1.1	-Python-3.8.2	foss/2020a
3.2.1		foss/2021b
3.3.1		foss/2022a
3.5.0		foss/2023a
3.5.1	-Java-17	foss/2023a

sparse-neighbors-search

A Python/C++ implementation of an approximate nearest neighbor search for sparse data structures based on the idea of local sensitive hash functions.

homepage: https://github.com/joachimwolff/sparse-neighbors-search

version	toolchain
0.7	foss/2022a

sparsehash

An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed.

homepage: https://github.com/sparsehash/sparsehash

version	toolchain
2.0.2	foss/2016a
2.0.3	GCCcore/5.4.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, foss/2016b, intel/2017a
2.0.4	GCCcore/10.2.0, GCCcore/11.3.0, GCCcore/12.3.0, GCCcore/9.3.0

SpatialDE

SpatialDE is a method to identify genes which significantly depend on spatial coordinates in non-linear and non-parametric ways. The intended applications are spatially resolved RNA-sequencing from e.g. Spatial Transcriptomics, or in situ gene expression measurements from e.g. SeqFISH or MERFISH.

homepage: https://pypi.org/project/SpatialDE

version	toolchain
1.1.3	foss/2022a

spatialreg

A collection of all the estimation functions for spatial cross-sectional models (on lattice/areal data using spatial weights matrices) contained up to now in 'spdep', 'sphet' and 'spse'.

homepage: https://cran.r-project.org/package=spatialreg

version	versionsuffix	toolchain
1.1-5	-R-3.6.2	foss/2019b
1.1-8	-R-4.1.0	foss/2021a

spdlog

Very fast, header-only/compiled, C++ logging library.

homepage: https://github.com/gabime/spdlog

version	toolchain
1.9.2	GCCcore/10.3.0
1.10.0	GCCcore/11.2.0
1.11.0	GCCcore/12.2.0, GCCcore/12.3.0
1.12.0	GCCcore/13.2.0

SpectrA

Spectra stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. It is a C++ library for large scale eigenvalue problems, built on top of Eigen, an open source linear algebra library.

homepage: https://spectralib.org/

version	toolchain
1.0.0	GCC/10.2.0
1.0.1	GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.3.0

spectral.methods

Contains some implementations of Singular Spectrum Analysis (SSA) for the gapfilling and spectral decomposition of time series.

homepage: https://cran.r-project.org/web/packages/spectral.methods

version	versionsuffix	toolchain
0.7.2.133	-R-3.4.3	intel/2017b
0.7.2.133	-R-3.4.4	intel/2018a

speech_tools

The Edinburgh Speech Tools Library is a collection of C++ class, functions and related programs for manipulating the sorts of objects used in speech processing. It includes support for reading and writing waveforms, parameter files (LPC, Ceptra, F0) in various formats and converting between them. It also includes support for linguistic type objects and support for various label files and ngrams (with smoothing).

homepage: <['http://festvox.org/festival/']>

version	toolchain
2.5.0	GCCcore/12.3.0, GCCcore/9.3.0

SPEI

A simple Python package to calculate drought indices for time series such as the SPI, SPEI and SGI.

homepage: https://github.com/martinvonk/spei

version	toolchain
0.3.5	foss/2022a

spektral

Spektral is a Python library for graph deep learning. The main goal of this project is to provide a simple but flexible framework for creating graph neural networks (GNNs).

homepage: https://github.com/danielegrattarola/spektral

version	versionsuffix	toolchain
1.1.0	-CUDA-11.4.1	foss/2021b

spglib

Spglib is a C library for finding and handling crystal symmetries.

homepage: https://spglib.github.io/spglib/

version	toolchain
1.9.2	intel/2016.02-GCC-4.9
1.9.9	intel/2017b
1.16.1	GCCcore/10.2.0
1.16.2	GCCcore/10.3.0
2.0.2	GCCcore/11.3.0, GCCcore/12.2.0

spglib-python

Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.

homepage: https://pypi.python.org/pypi/spglib

version	versionsuffix	toolchain
1.9.4.2	-Python-2.7.12	intel/2016b
1.9.5	-Python-2.7.12	intel/2016b
1.9.9.38	-Python-2.7.13	intel/2017a
1.10.0.2	-Python-2.7.14	intel/2017b
1.10.0.2	-Python-3.6.3	intel/2017b
1.14.1.post0	-Python-3.7.2	intel/2019a
1.16.0		foss/2020b, fosscuda/2020b, intel/2020b
1.16.0	-Python-3.7.4	fosscuda/2019b, intel/2019b, intelcuda/2019b
1.16.0	-Python-3.8.2	foss/2020a, intel/2020a
1.16.1		foss/2021a, gomkl/2021a, intel/2021a
1.16.3		foss/2021b, intel/2021b
2.0.0		foss/2022a, intel/2022a
2.0.2		gfbf/2022b
2.1.0		gfbf/2023a, iimkl/2023a

Sphinx

Sphinx is a tool that makes it easy to create intelligent and beautiful documentation. It was originally created for the new Python documentation, and it has excellent facilities for the documentation of Python projects, but C/C++ is already supported as well, and it is planned to add special support for other languages as well.

homepage: http://sphinx.pocoo.org/

version	versionsuffix	toolchain
1.4.8	-Python-2.7.11	foss/2016a
1.4.8	-Python-3.5.1	foss/2016a
1.8.1	-Python-2.7.14	foss/2017b, intel/2017b
1.8.1	-Python-2.7.15	foss/2018b
1.8.1	-Python-3.6.3	foss/2017b, intel/2017b
1.8.1	-Python-3.6.4	foss/2018a
1.8.1	-Python-3.6.6	foss/2018b, intel/2018b
1.8.3	-Python-3.6.4	intel/2018a

Sphinx-RTD-Theme

Sphinx theme designed to provide a great reader experience for documentation users on both desktop and mobile devices.

homepage: https://sphinx-rtd-theme.readthedocs.io

version	toolchain
1.1.1	GCCcore/10.2.0

SpiceyPy

SpiceyPy is a Python wrapper for the NAIF C SPICE Toolkit (N65)

homepage: https://github.com/AndrewAnnex/SpiceyPy

version	versionsuffix	toolchain
1.1.0	-Python-2.7.12	intel/2016b
1.1.1	-Python-3.6.1	intel/2017a
2.1.0	-Python-3.6.3	foss/2017b, intel/2017b
2.1.0	-Python-3.6.4	foss/2018a

SpiecEasi

Sparse InversE Covariance estimation for Ecological Association and Statistical Inference

homepage: https://github.com/zdk123/SpiecEasi

version	versionsuffix	toolchain
1.0.0	-R-3.4.4	intel/2018a
1.1.1	-R-4.2.1	foss/2022a
20160830	-R-3.3.1	intel/2016b

SplAdder

Splicing Adder is a toolbox for alternative splicing analysis based on RNA-Seq alignment data. Briefly, the software takes a given annotation and RNA-Seq read alignments in standardized formats, transforms the annotation into a splicing graph representation, augments the splicing graph with additional information extracted from the read data, extracts alternative splicing events from the graph and quantifies the events based on the alignment data.

homepage: https://github.com/ratschlab/spladder

version	versionsuffix	toolchain
2.4.2	-Python-3.8.2	foss/2020a

SPLASH

SPLASH is a free and open source visualisation tool for Smoothed Particle Hydrodynamics (SPH) simulations.

homepage: http://users.monash.edu.au/~dprice/splash/index.html

version	toolchain
2.8.0	foss/2018b

SpliceMap

SpliceMap is a de novo splice junction discovery and alignment tool. It offers high sensitivity and support for arbitrary RNA-seq read lengths.

homepage: https://web.stanford.edu/group/wonglab/SpliceMap/

version	toolchain
3.3.5.2	GCC/7.3.0-2.30

split-seq

Analysis tools for split-seq.

homepage: https://github.com/yjzhang/split-seq-pipeline

version	versionsuffix	toolchain
20190717	-Python-3.6.6	foss/2018b

splitRef

splitRef splits a reference haplotype file into smaller files with subsets of markers. The current version is a pre-release.

homepage: http://www.sph.umich.edu/csg/yli/splitRef/index.html

version	toolchain
0.0.2	system

SPM

SPM (Statistical Parametric Mapping) refers to the construction and assessment of spatially extended statistical processes used to test hypo- theses about functional imaging data. These ideas have been instantiated in software that is called SPM. The SPM software package has been designed for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject. The current release is designed for the analysis of fMRI, PET, SPECT, EEG and MEG.

homepage: https://www.fil.ion.ucl.ac.uk/spm

version	versionsuffix	toolchain
12.5_r7771	-MATLAB-2021a	system
12.5_r7771	-MATLAB-2021b	system

spoa

Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm which is used to generate consensus sequences

homepage: https://github.com/rvaser/spoa

version	toolchain
3.0.1	GCC/7.3.0-2.30
3.4.0	GCC/10.2.0
4.0.0	GCC/8.3.0
4.0.7	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/11.3.0, GCC/12.2.0
4.1.0	GCC/12.3.0

SPOOLES

SPOOLES is a library for solving sparse real and complex linear systems of equations, written in the C language using object oriented design.

homepage: https://netlib.org/linalg/spooles/spooles.2.2.html

version	toolchain
2.2	gompi/2021a, gompi/2022b, gompi/2023a

SPOTPY

SPOTPY is a Python framework that enables the use of Computational optimization techniques for calibration, uncertainty and sensitivity analysis techniques of almost every (environmental-) model.

homepage: https://spotpy.readthedocs.io

version	toolchain
1.5.14	intel/2021b

SPRNG

Scalable Parallel Pseudo Random Number Generators Library

homepage: http://www.sprng.org/

version	toolchain
2.0b	foss/2016a

Spyder

Spyder is an interactive Python development environment providing MATLAB-like features in a simple and light-weighted software.

homepage: https://github.com/spyder-ide/spyder

version	versionsuffix	toolchain
3.1.4	-Python-2.7.13	intel/2017a
3.3.1	-Python-3.6.4	foss/2018a
3.3.2	-Python-3.6.6	foss/2018b
4.1.5	-Python-3.7.2	foss/2019a
4.1.5	-Python-3.8.2	foss/2020a

SQLAlchemy

SQLAlchemy is the Python SQL toolkit and Object Relational Mapper that gives application developers the full power and flexibility of SQL. SQLAlchemy provides a full suite of well known enterprise-level persistence patterns, designed for efficient and high-performing database access, adapted into a simple and Pythonic domain language.

homepage: https://www.sqlalchemy.org/

version	toolchain
2.0.25	GCCcore/12.3.0
2.0.29	GCCcore/12.2.0, GCCcore/13.2.0

SQLite

SQLite: SQL Database Engine in a C Library

homepage: http://www.sqlite.org/

version	toolchain
3.8.8.1	GCC/4.8.4, GCC/4.9.2
3.8.10.2	GCC/4.9.3-2.25, GNU/4.9.3-2.25, gimkl/2.11.5
3.9.2	GCC/4.9.3-2.25, foss/2016a, gimkl/2.11.5, intel/2016.02-GCC-4.9, intel/2016a, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25
3.13.0	GCC/4.9.3-2.25, GCC/5.4.0-2.26, GCCcore/6.3.0, foss/2016.04, foss/2016a, foss/2016b, iccifort/2016.3.210-GCC-5.4.0-2.26, intel/2016b
3.14.1	GCCcore/4.9.3
3.17.0	GCCcore/6.3.0
3.20.1	GCCcore/6.4.0
3.21.0	GCCcore/6.4.0
3.23.0	GCCcore/6.4.0
3.24.0	GCCcore/7.2.0, GCCcore/7.3.0
3.26.0	GCCcore/8.2.0
3.27.2	GCCcore/8.2.0
3.29.0	GCCcore/8.3.0
3.31.1	GCCcore/9.3.0
3.33.0	GCCcore/10.2.0
3.35.4	GCCcore/10.3.0
3.36	GCCcore/11.2.0
3.38.3	GCCcore/11.3.0
3.39.4	GCCcore/12.2.0
3.41.2	GCCcore/13.1.0
3.42.0	GCCcore/12.3.0
3.43.1	GCCcore/13.2.0

SqueezeMeta

SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis.

homepage: https://github.com/jtamames/SqueezeMeta

version	versionsuffix	toolchain
0.4.3	-Python-2.7.15	foss/2018b
1.0.0	-Python-2.7.15	foss/2018b
1.5.0		foss/2021b

Squidpy

Squidpy is a tool for the analysis and visualization of spatial molecular data.

homepage: https://squidpy.readthedocs.io

version	toolchain
1.2.2	foss/2021b

SRA-Toolkit

The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format

homepage: https://github.com/ncbi/sra-tools

version	versionsuffix	toolchain
2.3.5	-centos_linux64	system
2.5.4-1	-centos_linux64	system
2.5.7	-centos_linux64	system
2.8.2-1	-centos_linux64	system
2.9.0	-centos_linux64	system
2.9.2	-ubuntu64	system
2.9.4	-centos_linux64	system
2.9.6-1	-centos_linux64	system
2.10.4		gompi/2019b
2.10.5	-centos_linux64	system
2.10.8		gompi/2020a
2.10.9		gompi/2020b
3.0.0		gompi/2021b
3.0.0	-centos_linux64	system
3.0.3		gompi/2022a
3.0.5		gompi/2021a
3.0.10		gompi/2023a

sradownloader

SRAdownloader takes the annotation table from the SRA run selector tool and retrieves the raw fastq files for the selected samples

homepage: https://github.com/s-andrews/sradownloader

version	toolchain
3.9	GCCcore/11.3.0

SRPRISM

Single Read Paired Read Indel Substitution Minimizer

homepage: https://github.com/ncbi/SRPRISM

version	versionsuffix	toolchain
3.0.0		foss/2018b
3.1.1	-Java-11	GCCcore/8.2.0
3.1.2		GCCcore/10.2.0

SRST2

Short Read Sequence Typing for Bacterial Pathogens

homepage: https://katholt.github.io/srst2

version	versionsuffix	toolchain
0.2.0-20210620	-Python-2.7.18	foss/2020b

SSAHA2

SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences. SSAHA2 reads of most sequencing platforms (ABI-Sanger, Roche 454, Illumina-Solexa) and a range of output formats (SAM, CIGAR, PSL etc.) are supported. A pile-up pipeline for analysis and genotype calling is available as a separate package.

homepage: http://www.sanger.ac.uk/resources/software/ssaha2/

version	versionsuffix	toolchain
2.5.5	-i686	system
2.5.5	-x86_64	system

SSN

Spatial statistical modeling and prediction for data on stream networks, including models based on in-stream distance. Models are created using moving average constructions. Spatial linear models, including explanatory variables, can be fit with (restricted) maximum likelihood. Mapping and other graphical functions are included.

homepage: https://cran.r-project.org/web/packages/SSN

version	versionsuffix	toolchain
1.1.14	-R-3.6.0	foss/2019a

SSPACE_Basic

SSPACE Basic, SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension

homepage: https://github.com/nsoranzo/sspace_basic

version	versionsuffix	toolchain
2.1.1	-Perl-5.24.1	intel/2017a
2.1.1	-Perl-5.26.0	intel/2017b
2.1.1	-Python-2.7.18	GCC/10.2.0

SSW

SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages. We also provide a software that can do protein and genome alignment directly. Current version of our implementation is ~50 times faster than an ordinary Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and location heuristically.

homepage: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library

version	toolchain
1.1	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/12.3.0, GCCcore/9.3.0
1.2.4	GCCcore/10.3.0

STACEY

The BEAST2 package STACEY can be used for species delimitation and species tree estimation, based on the multispecies coalescent model.

homepage: http://www.indriid.com/software.html

version	toolchain
1.2.5	GCC/10.2.0

Stack

Stack is a cross-platform program for developing Haskell projects. It is intended for Haskellers both new and experienced.

homepage: https://docs.haskellstack.org

version	versionsuffix	toolchain
2.3.3	-x86_64	system
2.11.1	-x86_64	system
2.13.1	-x86_64	system

Stacks

Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.

homepage: https://catchenlab.life.illinois.edu/stacks/

version	toolchain
1.40	foss/2016a
1.42	foss/2016a
1.44	foss/2016a
1.45	foss/2016a
1.46	intel/2017a
1.47	foss/2016a
1.48	intel/2017b, intel/2018b
2.0	foss/2018a, intel/2018a
2.0Beta7c	intel/2017b
2.0Beta8c	intel/2017b
2.0Beta9	intel/2018a
2.0Beta10a	foss/2018a
2.2	foss/2018a
2.3b	foss/2018a
2.3e	foss/2018b
2.5	iccifort/2019.5.281
2.41	GCC/8.2.0-2.31.1, foss/2018b, iccifort/2019.1.144-GCC-8.2.0-2.31.1
2.53	foss/2019b, iccifort/2019.5.281
2.54	foss/2020a
2.62	foss/2022a

STAMP

STAMP is a tool for characterizing similarities between transcription factor binding motifs

homepage: http://www.benoslab.pitt.edu/stamp/

version	toolchain
1.2	intel/2016a
1.3	intel/2016a, intel/2016b

StaMPS

A software package to extract ground displacements from time series of synthetic aperture radar (SAR) acquisitions.

homepage: http://homepages.see.leeds.ac.uk/~earahoo/stamps/

version	versionsuffix	toolchain
3.3b1	-Perl-5.24.1	intel/2017a

Stampy

Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome.

homepage: http://www.well.ox.ac.uk/stampy

version	versionsuffix	toolchain
1.0.31	-Python-2.7.12	intel/2016b
1.0.32	-Python-2.7.14	intel/2018a

STAR

STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.

homepage: https://github.com/alexdobin/STAR

version	toolchain
2.4.2a	foss/2018b
2.5.0a	GNU/4.9.3-2.25
2.5.2a	foss/2016a
2.5.2b	intel/2016b
2.5.3a	GCC/8.3.0, GCC/9.3.0, intel/2017a, intel/2017b
2.5.4b	foss/2016b, foss/2017b, intel/2017b
2.6.0c	foss/2018a, intel/2018a
2.6.1c	foss/2018b
2.7.0d	foss/2018b
2.7.0f	GCC/8.2.0-2.31.1, foss/2018b
2.7.1a	GCC/8.2.0-2.31.1, foss/2018b
2.7.2b	GCC/8.3.0
2.7.3a	GCC/8.3.0, GCC/9.3.0
2.7.4a	GCC/9.3.0
2.7.5b	GCC/9.3.0
2.7.6a	GCC/10.2.0, GCC/9.3.0
2.7.7a	GCC/10.2.0, GCC/9.3.0
2.7.8a	GCC/10.2.0
2.7.9a	GCC/10.3.0, GCC/11.2.0
2.7.10a_alpha_220601	GCC/10.3.0
2.7.10b	GCC/11.3.0, GCC/12.2.0
2.7.11a	GCC/12.2.0, GCC/12.3.0
2.7.11b	GCC/12.3.0

STAR-CCM+

STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products operating under real-world conditions.

homepage: https://mdx.plm.automation.siemens.com/star-ccm-plus

version	versionsuffix	toolchain
13.04.011		system
17.02.008		system
17.02.008	-r8	system
17.04.008		system
17.04.008	-r8	system
17.06.007		system
17.06.007	-r8	system
18.02.008		system
18.02.008	-r8	system
18.06.006		system
18.06.006	-r8	system
2302		system
2302	-r8	system
2310		system
2310	-r8	system

STAR-Fusion

STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set.

homepage: https://github.com/STAR-Fusion/STAR-Fusion

version	versionsuffix	toolchain
1.5.0	-Perl-5.28.0	foss/2018b
1.6.0	-Perl-5.28.1-Python-3.7.2	GCC/8.2.0-2.31.1
1.8.1	-Python-3.7.4	foss/2019b

stardist

Object Detection with Star-convex Shapes.

homepage: https://github.com/stardist/stardist

version	versionsuffix	toolchain
0.8.3		foss/2021b
0.8.3	-CUDA-11.4.1	foss/2021b

starparser

Use this package to manipulate Relion star files, including counting, modifying, plotting, and sifting the data. At the very least, this is a useful alternative to awk commands, which can get awkward. Below is a description of the command- line options with some examples. Alternatively, use starparser within Relion or load the modules in your own Python scripts.

homepage: https://github.com/sami-chaaban/starparser

version	toolchain
1.49	foss/2022a

stars

Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in R, using GDAL bindings provided by sf, and NetCDF bindings by ncmeta and RNetCDF.

homepage: https://cran.r-project.org/package=stars

version	versionsuffix	toolchain
0.4-3	-R-4.0.0-Python-3.8.2	foss/2020a

Stata

Stata is a complete, integrated statistical software package that provides everything you need for data analysis, data management, and graphics.

homepage: https://www.stata.com/

version	versionsuffix	toolchain
15		system
16	-legacy	system
17		system

Statistics-R

Perl interface with the R statistical program

homepage: https://metacpan.org/pod/Statistics::R

version	toolchain
0.34	foss/2020a

statsmodels

Statsmodels is a Python module that provides classes and functions for the estimation of many different statistical models, as well as for conducting statistical tests, and statistical data exploration.

homepage: https://www.statsmodels.org

version	versionsuffix	toolchain
0.6.1	-Python-2.7.13	foss/2017a
0.6.1	-Python-3.5.1	intel/2016a
0.6.1	-Python-3.5.2	intel/2016b
0.8.0	-Python-2.7.13	intel/2017a
0.9.0	-Python-2.7.15	foss/2018b, intel/2018b
0.9.0	-Python-2.7.16	intel/2019b
0.9.0	-Python-3.6.6	foss/2018b, intel/2018b
0.10.1		foss/2019a
0.11.0	-Python-3.7.4	foss/2019b, intel/2019b
0.11.1	-Python-3.8.2	foss/2020a, intel/2020a
0.12.1		foss/2020b, fosscuda/2020b, intel/2020b
0.12.2		foss/2021a
0.13.1		foss/2021b, foss/2022a, intel/2021b
0.14.0		gfbf/2022b
0.14.1		gfbf/2023a, gfbf/2023b

STEAK

Detects integrations of any sort in high-throughput sequencing (HTS) data. STEAK was built for validating and discovering transposable element (TE) and retroviral integrations in a variety of HTS data. The software performs on both single-end (SE) and paired-end ( PE) libraries and on a variety of HTS sequencing strategies. It can be applied to a broad range of research interests and clinical uses such as population genetic studies and detecting polymorphic integrations.

homepage: https://omictools.com/steak-tool

version	versionsuffix	toolchain
2019.09.12		foss/2021b
2019.09.12	-Python-2.7.16	foss/2019b

STIR

Software for Tomographic Image Reconstruction

homepage: http://stir.sourceforge.net/

version	toolchain
3.0	intel/2018a

stpipeline

The ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format to generated datasets for down-stream analysis. The ST pipeline can also be used to process single cell data as long as a file with barcodes identifying each cell is provided. The ST Pipeline can also process RNA-Seq datasets generated with or without UMIs.

homepage: https://github.com/SpatialTranscriptomicsResearch/st_pipeline

version	versionsuffix	toolchain
1.7.3	-Python-2.7.15	foss/2018b
1.7.6	-Python-3.7.2	foss/2019a
1.7.6	-Python-3.7.4	foss/2019b

strace

strace is a diagnostic, debugging and instructional userspace utility for Linux. It is used to monitor and tamper with interactions between processes and the Linux kernel, which include system calls, signal deliveries, and changes of process state.

homepage: https://strace.io/

version	toolchain
5.14	GCCcore/11.2.0
6.6	GCCcore/12.2.0

Strainberry

Strainberry is a method that performs strain separation in low-complexity metagenomes using error-prone long-read technologies. It exploits state-of-the-art tools for variant calling, haplotype phasing, and genome assembly, in order to achieve single-sample assembly of strains with higher quality than other state-of-the-art long-read assemblers.

homepage: https://github.com/rvicedomini/strainberry

version	toolchain
1.1	foss/2022a

STREAM

The STREAM benchmark is a simple synthetic benchmark program that measures sustainable memory bandwidth (in MB/s) and the corresponding computation rate for simple vector kernels.

homepage: https://www.cs.virginia.edu/stream/

version	toolchain
5.10	GCC/11.3.0, GCC/7.3.0-2.30, GCC/8.2.0-2.31.1, GCC/9.3.0, iccifort/2020.1.217, intel-compilers/2022.2.1, intel/2016b, intel/2018b

strelka

Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs.

homepage: https://github.com/Illumina/strelka

version	versionsuffix	toolchain
2.9.7		intel/2018a
2.9.9		foss/2018b
2.9.10	-Python-2.7.15	foss/2018b, intel/2018b

StringTie

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts

homepage: https://ccb.jhu.edu/software/stringtie/

version	versionsuffix	toolchain
1.3.0		intel/2016b
1.3.3		GCCcore/6.4.0, intel/2017a
1.3.3b		foss/2016b
1.3.5		GCCcore/8.2.0, foss/2018b
2.0.3		GCCcore/7.3.0
2.1.0		foss/2018b
2.1.1		GCC/8.3.0
2.1.3		GCC/8.3.0, GCC/9.3.0
2.1.4		GCC/8.3.0, GCC/9.3.0
2.1.7		GCC/10.3.0
2.2.1		GCC/11.2.0
2.2.1	-Python-2.7.18	GCC/11.2.0

stripy

A Python interface to TRIPACK and STRIPACK Fortran code for (constrained) triangulation in Cartesian coordinates and on a sphere. Stripy is an object-oriented package and includes routines from SRFPACK and SSRFPACK for interpolation (nearest neighbor, linear and hermite cubic) and to evaluate derivatives (Renka 1996a,b and 1997a,b).

homepage: https://github.com/underworldcode/stripy

version	toolchain
2.1.0	foss/2021a

STRique

STRique is a python package to analyze repeat expansion and methylation states of short tandem repeats (STR) in Oxford Nanopore Technology (ONT) long read sequencing data.

homepage: https://github.com/giesselmann/STRique

version	toolchain
0.4.2	foss/2021b

Structure

The program structure is a free software package for using multi-locus genotype data to investigate population structure.

homepage: https://web.stanford.edu/group/pritchardlab/structure.html

version	toolchain
2.3.4	GCC/11.3.0, GCC/12.2.0, GCC/8.2.0-2.31.1, iccifort/2019.3.199-GCC-8.3.0-2.32, iccifort/2019.5.281

Structure_threader

A program to parallelize the runs of Structure, fastStructure, MavericK and ALStructure software.

homepage: https://github.com/StuntsPT/Structure_threader

version	toolchain
1.3.10	foss/2022b

STRUMPACK

STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and preconditioner for both dense and sparse systems using low-rank structured factorization with randomized sampling.

homepage: https://fastmath-scidac.llnl.gov/software/strumpack.html

version	toolchain
6.1.0	foss/2020b, intel/2020b

suave

suave is an interactive web application to visualize read depth ratios between two samples and the structural variants of one of the samples (typically the "case" sample in a case/control setup such as tumor/normal comparison).

homepage: https://github.com/dellytools/suave

version	toolchain
20160529	foss/2020b

SuAVE-biomat

Surface Assessment via Grid Evaluation (SuAVE) for Every Surface Curvature and Cavity Shape

homepage: https://github.com/SuAVE-Software/source_v2.0

version	toolchain
2.0.0-20230815	intel/2023a

Subread

High performance read alignment, quantification and mutation discovery

homepage: https://subread.sourceforge.net/

version	toolchain
1.5.0-p1	foss/2016a, foss/2016b
1.6.3	foss/2018b
1.6.4	foss/2018b
2.0.0	GCC/7.3.0-2.30, GCC/8.3.0
2.0.2	GCC/10.2.0
2.0.3	GCC/10.3.0, GCC/11.2.0, GCC/9.3.0
2.0.4	GCC/11.3.0

subset-bam

subset-bam is a tool to subset a 10x Genomics BAM file based on a tag, most commonly the cell barcode tag.

homepage: https://github.com/10XGenomics/subset-bam

version	toolchain
1.1.0	GCCcore/10.3.0

Subversion

Subversion is an open source version control system.

homepage: http://subversion.apache.org/

version	toolchain
1.9.7	iomkl/2018a
1.9.9	GCCcore/7.3.0
1.10.0	foss/2017b, intel/2017b
1.12.0	GCCcore/8.2.0
1.14.0	GCCcore/10.2.0, GCCcore/9.3.0
1.14.1	GCCcore/10.3.0, GCCcore/11.2.0
1.14.2	GCCcore/11.3.0

suds

Lightweight SOAP client

homepage: https://pypi.python.org/pypi/suds-py3

version	versionsuffix	toolchain
1.3.3.0	-Python-3.6.4	intel/2018a

SuiteSparse

SuiteSparse is a collection of libraries to manipulate sparse matrices.

homepage: https://faculty.cse.tamu.edu/davis/suitesparse.html

version	versionsuffix	toolchain
4.5.1	-METIS-5.1.0	foss/2016a, intel/2016a
4.5.2	-METIS-5.1.0	foss/2016a, intel/2016a
4.5.3	-METIS-5.1.0	foss/2016a, foss/2016b, intel/2016b
4.5.3	-ParMETIS-4.0.3	foss/2016a, foss/2016b, intel/2016a, intel/2016b
4.5.5	-METIS-5.1.0	foss/2017a, intel/2017a
4.5.5	-ParMETIS-4.0.3	foss/2017a, foss/2017b, intel/2017a, intel/2017b
4.5.6	-METIS-5.1.0	foss/2017b
5.1.2	-METIS-5.1.0	foss/2017b, foss/2018a, foss/2018b, intel/2017b, intel/2018a, intel/2018b
5.1.2	-ParMETIS-4.0.3	foss/2017b, intel/2017b
5.4.0	-METIS-5.1.0	foss/2019a, intel/2018b, intel/2019a
5.6.0	-METIS-5.1.0	foss/2019b, intel/2019b
5.7.1	-METIS-5.1.0	foss/2020a, intel/2020a
5.8.1	-METIS-5.1.0	foss/2020b, intel/2020b
5.10.1	-METIS-5.1.0	foss/2021a, foss/2021b, intel/2021a, intel/2021b
5.10.1	-METIS-5.1.0-CUDA-11.3.1	foss/2021a
5.13.0	-METIS-5.1.0	foss/2022a, foss/2022b
7.1.0		foss/2023a

SUMACLUST

SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences.

homepage: http://metabarcoding.org/sumatra

version	toolchain
1.0.20	foss/2016a

SUMATRA

SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences.

homepage: http://metabarcoding.org/sumatra

version	toolchain
1.0.20	foss/2016a

SUMO

Simulation of Urban MObility" (SUMO) is an open source, highly portable, microscopic and continuous traffic simulation package designed to handle large networks. It allows for intermodal simulation including pedestrians and comes with a large set of tools for scenario creation.

homepage: https://www.eclipse.org/sumo/

version	versionsuffix	toolchain
1.3.1	-Python-3.7.4	GCCcore/8.3.0
1.7.0	-Python-3.8.2	foss/2020a
1.12.0		foss/2021b
1.14.1		foss/2021b

SUNDIALS

SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers

homepage: https://computing.llnl.gov/projects/sundials

version	versionsuffix	toolchain
2.6.2		intel/2016b, intel/2018b
2.7.0		foss/2016b, foss/2017b, foss/2018a, foss/2018b, intel/2016b, intel/2017a, intel/2017b, intel/2018a
5.1.0		foss/2019b, intel/2019b
5.7.0		foss/2020b, fosscuda/2020b, intel/2020b
6.2.0		foss/2020b, intel/2020b
6.3.0		foss/2021b, foss/2022a
6.5.1		foss/2022a
6.6.0		foss/2022b, foss/2023a
6.6.0	-CUDA-12.1.1	foss/2023a

SunPy

The community-developed, free and open-source solar data analysis environment for Python.

homepage: https://sunpy.org/

version	versionsuffix	toolchain
1.1.3	-Python-3.7.4	foss/2019b

SuperLU

SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.

homepage: https://crd-legacy.lbl.gov/~xiaoye/SuperLU/

version	toolchain
5.1.1	foss/2016a, intel/2016a
5.2.1	foss/2017b, intel/2017b
5.2.2	foss/2020a, intel/2020a
5.3.0	foss/2020b, foss/2021a, foss/2022a, intel/2020b, intel/2022a

SuperLU_DIST

SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.

homepage: https://crd-legacy.lbl.gov/~xiaoye/SuperLU/

version	versionsuffix	toolchain
5.4.0	-trisolve-merge	intel/2020a
6.4.0		foss/2020a, intel/2020a
8.1.0		foss/2022a
8.1.2		foss/2022b, foss/2023a

supermagic

Very simple MPI sanity code. Nothing more, nothing less.

homepage: https://github.com/hpc/supermagic

version	toolchain
20170824	foss/2017a, gompi/2019b

supernova

Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source

homepage: https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome

version	toolchain
2.0.1	system
2.1.1	system

SUPPA

Fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions.

homepage: https://github.com/comprna/SUPPA

version	toolchain
2.3-20231005	foss/2022b

SURVIVOR

Toolset for SV simulation, comparison and filtering

homepage: https://github.com/fritzsedlazeck/SURVIVOR

version	toolchain
1.0.7-19-ged1ca51	GCC/11.2.0, GCC/12.2.0

SVclone

Cluster structural variants of similar cancer cell fraction (CCF).

homepage: https://github.com/mcmero/SVclone

version	toolchain
1.1.2	foss/2022b

SVDetect

SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies. This tool aims to identifying structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale.

homepage: http://svdetect.sourceforge.net/Site/Home.html

version	versionsuffix	toolchain
0.8b	-Perl-5.26.0	GCC/6.4.0-2.28, iccifort/2017.4.196-GCC-6.4.0-2.28

SVDquest

SVDquartets-based species trees

homepage: https://github.com/pranjalv123/SVDquest

version	toolchain
20190627	gompi/2019a

SVG

Perl binding for SVG

homepage: https://metacpan.org/pod/SVG

version	versionsuffix	toolchain
2.84	-Perl-5.30.0	foss/2019b
2.87		GCC/11.2.0, GCC/11.3.0, GCC/12.2.0

SVIM

SVIM (pronounced swim) is a structural variant caller for third-generation sequencing reads. It is able to detect and classify the following six classes of structural variation: deletions, insertions, inversions, tandem duplications, interspersed duplications and translocations.

homepage: https://github.com/eldariont/svim

version	toolchain
2.0.0	foss/2022a

svist4get

Svist4get is a simple bioinformatics tool for visualization of genomic signal tracks in user-defined genomic windows, either arbitrary selected by genomic coordinates or anchored to particular transcripts or genes.

homepage: https://github.com/art-egorov/svist4get

version	toolchain
1.3.1	foss/2020b

swarm

A robust and fast clustering method for amplicon-based studies

homepage: https://github.com/torognes/swarm

version	toolchain
2.2.2	foss/2018b

SWASH

SWASH is a general-purpose numerical tool for simulating unsteady, non-hydrostatic, free-surface, rotational flow and transport phenomena in coastal waters as driven by waves, tides, buoyancy and wind forces.

homepage: http://swash.sourceforge.net/

version	versionsuffix	toolchain
3.14	-mpi	intel/2016b, intel/2017a
4.01	-mpi	intel/2017a

SWAT+

The Soil & Water Assessment Tool (SWAT) is a small watershed to river basin-scale model used to simulate the quality and quantity of surface and ground water and predict the environmental impact of land use, land management practices, and climate change. In order to face present and future challenges in water resources modeling SWAT code has undergone major modifications over the past few years, resulting in SWAT+, a completely revised version of the model. SWAT+ provides a more flexible spatial representation of interactions and processes within a watershed.

homepage: https://swatplus.gitbook.io

version	toolchain
60.4.1	GCC/9.3.0
60.5.1	iccifort/2020.4.304

swifter

A package which efficiently applies any function to a pandas dataframe or series in the fastest available manner.

homepage: https://github.com/jmcarpenter2/swifter

version	toolchain
1.0.9	foss/2020b, fosscuda/2020b

SWIG

SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.

homepage: http://www.swig.org/

version	versionsuffix	toolchain
3.0.8	-Python-2.7.11	foss/2016a, intel/2016a
3.0.8	-Python-3.5.1	foss/2016a
3.0.10	-Python-2.7.12	foss/2016b, intel/2016b
3.0.10	-Python-2.7.12-PCRE-8.39	intel/2016b
3.0.11	-Python-2.7.12	foss/2016b, intel/2016b
3.0.12		GCCcore/8.2.0, GCCcore/8.3.0
3.0.12	-Python-2.7.13	intel/2017a
3.0.12	-Python-2.7.14	foss/2017b, foss/2018a, intel/2017b, intel/2018a
3.0.12	-Python-2.7.14-bare	GCCcore/6.4.0
3.0.12	-Python-2.7.15	GCCcore/8.2.0, foss/2018b, intel/2018b
3.0.12	-Python-3.6.1	intel/2017a
3.0.12	-Python-3.6.2	foss/2017b, intel/2018.00
3.0.12	-Python-3.6.3	foss/2017b, intel/2017b, intel/2018.01
3.0.12	-Python-3.6.4	foss/2018a, intel/2018a, iomkl/2018a
3.0.12	-Python-3.6.6	foss/2018b, intel/2018b
3.0.12	-Python-3.7.2	GCCcore/8.2.0
4.0.1		GCCcore/8.3.0, GCCcore/9.3.0
4.0.2		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0
4.1.1		GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

SWIPE

Smith-Waterman database searches with inter-sequence SIMD parallelisation

homepage: https://github.com/torognes/swipe

version	toolchain
2.1.1	GCC/10.3.0

swissknife

Perl module for reading and writing UniProtKB data in plain text format.

homepage: https://sourceforge.net/projects/swissknife/

version	toolchain
1.80	GCCcore/8.3.0

SymEngine

SymEngine is a standalone fast C++ symbolic manipulation library

homepage: https://github.com/symengine/symengine

version	versionsuffix	toolchain
0.3.0	-20181006	intel/2018a
0.4.0		GCC/8.2.0-2.31.1
0.7.0		GCC/10.3.0

SymEngine-python

Python wrappers to the C++ library SymEngine, a fast C++ symbolic manipulation library.

homepage: https://github.com/symengine/symengine.py

version	toolchain
0.7.2	GCC/10.3.0

SYMMETRICA

Symmetrica is a Collection of C routines for representation theory.

homepage: https://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA

version	toolchain
2.0	GCCcore/11.3.0

SYMPHONY

SYMPHONY is an open-source solver for mixed-integer linear programs (MILPs) written in C.

homepage: https://projects.coin-or.org/SYMPHONY

version	toolchain
5.6.16	foss/2018b

sympy

SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries.

homepage: https://sympy.org/

version	versionsuffix	toolchain
1.0	-Python-2.7.11	foss/2016a, intel/2016a
1.3	-Python-2.7.14	intel/2018a
1.3	-Python-2.7.15	foss/2018b
1.3	-Python-3.6.4	intel/2018a
1.3	-Python-3.6.6	foss/2018b
1.4		foss/2019a, intel/2019a
1.5.1	-Python-3.7.4	foss/2019b
1.6.2	-Python-3.8.2	foss/2020a
1.7.1		foss/2020b, intel/2020b
1.8		foss/2021a
1.9		foss/2021b, intel/2021b
1.10.1		foss/2022a, intel/2022a
1.11.1		foss/2022a, intel/2022a
1.12		gfbf/2022b, gfbf/2023a, gfbf/2023b

synapseclient

The synapseclient package provides an interface to Synapse, a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate, providing support for: integrated presentation of data, code and text fine grained access control provenance tracking The synapseclient package lets you communicate with the cloud-hosted Synapse service to access data and create shared data analysis projects from within Python scripts or at the interactive Python console. Other Synapse clients exist for R, Java, and the web. The Python client can also be used from the command line.

homepage: https://help.synapse.org/docs/

version	toolchain
3.0.0	GCCcore/12.2.0

synthcity

A library for generating and evaluating synthetic tabular data.

homepage: https://github.com/vanderschaarlab/synthcity

version	toolchain
0.2.4	foss/2022a

SyRI

Synteny and Rearrangement Identifier (SyRI).

homepage: https://schneebergerlab.github.io/syri/

version	toolchain
1.4	foss/2021a

sysbench

sysbench is a scriptable multi-threaded benchmark tool based on LuaJIT. It is most frequently used for database benchmarks, but can also be used to create arbitrarily complex workloads that do not involve a database server.

homepage: https://github.com/akopytov/sysbench

version	toolchain
1.0.20	GCC/12.2.0

Szip

Szip compression software, providing lossless compression of scientific data

homepage: https://www.hdfgroup.org/doc_resource/SZIP/

version	toolchain
2.1	GCC/4.8.1, GCCcore/5.4.0, foss/2016a, foss/2016b, foss/2017a, gimkl/2.11.5, gimkl/2017a, gmpolf/2017.10, intel/2016.02-GCC-4.9, intel/2016a, intel/2016b, intel/2017.01, intel/2017a, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25
2.1.1	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0

T

T-Coffee - tabix - tabixpp - taco - TagDust - TagLib - Taiyaki - TALON - TALYS - TAMkin - tantan - Tapenade - task-spooler - taxator-tk - TBA - tbb - tbl2asn - TCC - Tcl - TCLAP - tcsh - tecplot360ex - TELEMAC-MASCARET - Telescope - Teneto - tensorboard - tensorboardX - TensorFlow - tensorflow-compression - TensorFlow-Datasets - TensorFlow-Graphics - tensorflow-probability - TensorRT - terastructure - termcolor - Tesla-Deployment-Kit - tesseract - testpath - TetGen - TEToolkit - TEtranscripts - texinfo - texlive - Text-CSV - TFEA - Theano - ThemisPy - THetA - thirdorder - thurstonianIRT - TiCCutils - tidybayes - tidymodels - Tika - TiMBL - time - timm - TINKER - tiny-cuda-nn - TinyDB - TinyXML - Tk - Tkinter - TM-align - tMAE - tmap - tmux - TN93 - TOBIAS - ToFu - Togl - toil - tokenizers - Tombo - TOML-Fortran - TOPAS - topaz - TopHat - torchaudio - torchdata - torchinfo - torchsampler - torchtext - torchvf - torchvision - tornado - TotalView - tox - tqdm - Tracer - TranscriptClean - TransDecoder - Transformers - Transrate - travis - TRAVIS-Analyzer - treatSens - TreeMix - TreeShrink - TRF - Triangle - Trilinos - Trim_Galore - trimAl - trimesh - Trimmomatic - Trinity - Trinotate - Triplexator - TRIQS - TRIQS-cthyb - TRIQS-dft_tools - TRIQS-tprf - Triton - tRNAscan-SE - TRUST - TRUST4 - Trycycler - tseriesEntropy - tsne - turbinesFoam - TurboVNC - TVB - tvb-data - TVB-deps - tvb-framework - tvb-library - TWL-NINJA - TXR - typing-extensions

T-Coffee

A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures

homepage: https://www.tcoffee.org/

version	toolchain
13.45.61.3c310a9	system
13.46.0.919e8c6b	system

tabix

Generic indexer for TAB-delimited genome position files

homepage: http://samtools.sourceforge.net

version	toolchain
0.2.6	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/5.4.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.3.0, foss/2016a, intel/2016a, intel/2016b

tabixpp

C++ wrapper to tabix indexer

homepage: https://github.com/ekg/tabixpp

version	toolchain
1.1.0	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/9.3.0
1.1.2	GCC/11.3.0, GCC/12.3.0

taco

Multi-sample transcriptome assembly from RNA-Seq

homepage: http://tacorna.github.io

version	versionsuffix	toolchain
0.5.1	-Python-2.7.12	intel/2016b

TagDust

Raw sequences produced by next generation sequencing (NGS) machines may contain adapter, linker, barcode and fingerprint sequences. TagDust2 is a program to extract and correctly label the sequences to be mapped in downstream pipelines.

homepage: http://tagdust.sourceforge.net/

version	toolchain
2.33	GCCcore/10.2.0, GCCcore/8.3.0

TagLib

TagLib is a library for reading and editing the meta-data of several popular audio formats.

homepage: https://taglib.org/

version	toolchain
1.11.1	GCCcore/8.2.0

Taiyaki

Taiyaki is research software for training models for basecalling Oxford Nanopore reads.

homepage: https://github.com/nanoporetech/taiyaki

version	versionsuffix	toolchain
5.1.0-20200617	-Python-3.7.2-PyTorch-1.2.0	foss/2019a, fosscuda/2019a

TALON

TALON is a Python package for identifying and quantifying known and novel genes/isoforms in long-read transcriptome data sets. TALON is technology-agnostic in that it works from mapped SAM files, allowing data from different sequencing platforms (i.e. PacBio and Oxford Nanopore) to be analyzed side by side.

homepage: https://github.com/mortazavilab/TALON

version	toolchain
5.0	foss/2020b

TALYS

TALYS is a nuclear reaction program.

homepage: https://tendl.web.psi.ch/tendl_2019/talys.html

version	toolchain
1.95	GCCcore/10.3.0, GCCcore/9.3.0

TAMkin

TAMkin is a post-processing toolkit for normal mode analysis, thermochemistry and reaction kinetics. It uses a Hessian computation from a standard computational chemistry program as its input.

homepage: https://molmod.github.io/tamkin/

version	versionsuffix	toolchain
1.0.9	-Python-2.7.11	intel/2016a
1.2.4	-Python-2.7.14	intel/2017b
1.2.6		foss/2020b, foss/2021a, foss/2021b
1.2.6	-Python-3.7.2	intel/2019a
1.2.6	-Python-3.8.2	foss/2020a, intel/2020a

tantan

tantan identifies simple regions / low complexity / tandem repeats in DNA or protein sequences

homepage: https://gitlab.com/mcfrith/tantan

version	toolchain
40	GCC/11.2.0

Tapenade

Tool for Algorithmic Differentiation of programs.

homepage: https://tapenade.gitlabpages.inria.fr/tapenade/docs/html/index.html

version	versionsuffix	toolchain
3.16	-Java-17	system

task-spooler

task spooler is a Unix batch system where the tasks spooled run one after the other.

homepage: http://viric.name/soft/ts/

version	toolchain
1.0.2	GCCcore/11.3.0

taxator-tk

A set of programs for the taxonomic analysis of nucleotide sequence data

homepage: https://github.com/fungs/taxator-tk

version	toolchain
1.3.3	GCC/10.2.0, foss/2018b, gompi/2019a

TBA

TBA (a Transcription factor Binding Analysis): TBA is a multi-functional machine learning tool for identifying transcription factors associated with genomic features

homepage: https://github.com/jenhantao/tba

version	toolchain
1.0	foss/2020b

tbb

Intel Threading Building Blocks (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based parallel applications that scale to available processor cores, are compatible with multiple environments, and are easier to maintain. Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms.

homepage: https://software.intel.com/en-us/articles/intel-tbb/

version	toolchain
4.0.0.233	system
4.0.5.339	system
4.3.6.211	system
4.4.2.152	system
2017.2.132	system
2017.4.174	system
2017.6.196	system
2017_U5	GCCcore/5.4.0, foss/2016b, intel/2017a
2017_U6	GCCcore/6.3.0, intel/2017a
2018_U1	GCCcore/6.4.0
2018_U2	GCCcore/6.4.0
2018_U3	GCCcore/6.4.0
2018_U5	GCCcore/6.4.0, GCCcore/7.3.0
2019_U4	GCCcore/8.2.0
2019_U9	GCCcore/8.3.0
2020.1	GCCcore/9.3.0
2020.2	GCCcore/8.3.0
2020.3	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0
2021.4.0	GCCcore/11.2.0
2021.5.0	GCCcore/11.3.0
2021.10.0	GCCcore/12.2.0
2021.11.0	GCCcore/12.3.0

tbl2asn

Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank

homepage: https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/

version	versionsuffix	toolchain
25.8	-linux64	system
20180227	-linux64	system
20200302	-linux64	system
20220427	-linux64	system
20230713	-linux64	system

TCC

The Tiny C Compiler (aka TCC, tCc, or TinyCC) is an x86 and x86-64 C compiler created by Fabrice Bellard. It is designed to work for slow computers with little disk space and can run shebang style !/usr/bin/tcc . TCC is distributed under the LGPL. TCC claims to implement all of ANSI C (C89/C90),[1] much of the new ISO C99 standard, and many GNU C extensions including inline assembly.

homepage: http://bellard.org/tcc/

version	toolchain
0.9.26	system

Tcl

Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.

homepage: https://www.tcl.tk/

version	toolchain
8.5.19	foss/2017a
8.6.3	GCC/4.8.4, GCC/4.9.2
8.6.4	GCC/4.9.3-2.25, GNU/4.9.3-2.25, foss/2016a, gimkl/2.11.5, intel/2016.02-GCC-4.9, intel/2016a, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25
8.6.5	GCC/4.9.3-2.25, GCC/5.4.0-2.26, GCCcore/6.3.0, foss/2016.04, foss/2016a, foss/2016b, iccifort/2016.3.210-GCC-5.4.0-2.26, intel/2016b
8.6.6	GCCcore/4.9.3, GCCcore/6.3.0
8.6.7	GCCcore/6.4.0
8.6.8	GCCcore/6.4.0, GCCcore/7.2.0, GCCcore/7.3.0
8.6.9	GCCcore/8.2.0, GCCcore/8.3.0
8.6.10	GCCcore/10.2.0, GCCcore/9.3.0
8.6.11	GCCcore/10.3.0, GCCcore/11.2.0
8.6.12	GCCcore/11.3.0, GCCcore/12.2.0
8.6.13	GCCcore/12.3.0, GCCcore/13.1.0, GCCcore/13.2.0

TCLAP

TCLAP is a small, flexible library that provides a simple interface for defining and accessing command line arguments. It was intially inspired by the user friendly CLAP libary.

homepage: http://tclap.sourceforge.net/

version	toolchain
1.2.2	GCCcore/8.3.0
1.2.4	GCCcore/10.2.0, GCCcore/9.3.0
1.2.5	GCCcore/10.3.0, GCCcore/11.2.0

tcsh

Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax.

homepage: https://www.tcsh.org

version	toolchain
6.19.00	intel/2016a
6.20.00	GCCcore/5.4.0, GCCcore/6.4.0, GCCcore/7.3.0
6.22.02	GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
6.22.03	GCCcore/10.2.0
6.22.04	GCCcore/10.3.0
6.24.01	GCCcore/11.2.0, GCCcore/11.3.0
6.24.07	GCCcore/12.2.0
6.24.10	GCCcore/12.3.0

tecplot360ex

Quickly plot and animate your CFD results exactly the way you want. Analyze complex solutions, arrange multiple layouts, and communicate your results with professional images and animations.

homepage: http://www.tecplot.com/products/tecplot-360/

version	toolchain
linux64	system

TELEMAC-MASCARET

TELEMAC-MASCARET is an integrated suite of solvers for use in the field of free-surface flow. Having been used in the context of many studies throughout the world, it has become one of the major standards in its field.

homepage: http://www.opentelemac.org

version	toolchain
8p3r1	foss/2021b

Telescope

Single locus resolution of Transposable ELEment expression using next-generation sequencing.

homepage: https://github.com/mlbendall/telescope

version	versionsuffix	toolchain
1.0.3	-Python-3.7.4	foss/2019b

Teneto

Teneto is package for deriving, analysing and plotting temporal network representations. Additional tools for temporal network analysis with neuroimaging contexts.

homepage: https://teneto.readthedocs.io

version	versionsuffix	toolchain
0.5.1	-Python-3.8.2	foss/2020a

tensorboard

TensorBoard is a suite of web applications for inspecting and understanding your TensorFlow runs and graphs.

homepage: https://github.com/tensorflow/tensorboard

version	toolchain
2.8.0	foss/2021a
2.10.0	foss/2022a
2.15.1	gfbf/2023a

tensorboardX

Tensorboard for PyTorch.

homepage: https://github.com/lanpa/tensorboardX

version	versionsuffix	toolchain
2.0	-Python-3.7.4	foss/2019b
2.1	-PyTorch-1.7.1	fosscuda/2020b
2.2	-PyTorch-1.7.1	foss/2020b, fosscuda/2020b
2.5.1		foss/2022a
2.6.2.2		foss/2022b, foss/2023a

TensorFlow

An open-source software library for Machine Intelligence

homepage: https://www.tensorflow.org/

version	versionsuffix	toolchain
0.12.1	-Python-2.7.12	foss/2016b, intel/2016b
0.12.1	-Python-3.5.2	foss/2016b, intel/2016b
1.0.1	-Python-2.7.12	intel/2016b
1.0.1	-Python-3.5.2	intel/2016b
1.1.0	-Python-2.7.13	intel/2017a
1.1.0	-Python-3.6.1	intel/2017a
1.2.0	-Python-3.6.1	intel/2017a
1.2.1	-GPU-Python-3.5.2	foss/2016b
1.2.1	-Python-3.5.2	foss/2016b
1.3.0	-Python-2.7.13	intel/2017a
1.3.0	-Python-3.6.1	intel/2017a
1.3.0	-Python-3.6.3	intel/2017b
1.4.0	-Python-3.6.3	foss/2017b, intel/2017b
1.4.1	-Python-3.6.3	foss/2017b
1.5.0	-Python-3.6.3	foss/2017b, intel/2017b
1.6.0	-Python-3.6.4	foss/2018a, intel/2018a
1.6.0	-Python-3.6.4-CUDA-9.1.85	foss/2018a
1.7.0	-Python-3.6.4	foss/2018a
1.7.0	-Python-3.6.4-CUDA-9.1.85	foss/2018a
1.8.0	-Python-2.7.14	foss/2017b, fosscuda/2017b
1.8.0	-Python-3.6.3	foss/2017b, fosscuda/2017b
1.8.0	-Python-3.6.4	foss/2018a, fosscuda/2018a, intel/2018a
1.10.0	-Python-2.7.15	fosscuda/2018b
1.10.1	-Python-2.7.15	fosscuda/2018b
1.10.1	-Python-3.6.6	foss/2018b
1.11.0	-Python-3.6.6	foss/2018b
1.12.0	-Python-2.7.15	fosscuda/2018b
1.12.0	-Python-3.6.6	foss/2018b, fosscuda/2018b
1.13.1	-Python-3.6.6	foss/2018b
1.13.1	-Python-3.7.2	foss/2019a, fosscuda/2019a
1.14.0	-Python-3.7.2	foss/2019a, fosscuda/2019a
1.15.0	-Python-3.7.4	foss/2019b, fosscuda/2019b
1.15.2	-Python-3.7.4	foss/2019b, fosscuda/2019b
1.15.5	-Python-3.7.4	fosscuda/2019b
1.15.5	-Python-3.7.4-nompi	fosscuda/2019b
2.0.0	-Python-3.7.2	foss/2019a
2.0.0	-Python-3.7.4	fosscuda/2019b
2.0.1	-Python-3.7.2	foss/2019a
2.0.1	-Python-3.7.4	fosscuda/2019b
2.1.0	-Python-3.7.4	foss/2019b, fosscuda/2019b
2.2.0	-Python-3.7.4	foss/2019b, fosscuda/2019b
2.2.2	-Python-3.7.4	foss/2019b
2.2.3		foss/2020b
2.3.1	-Python-3.7.4	foss/2019b, fosscuda/2019b
2.3.1	-Python-3.8.2	foss/2020a, fosscuda/2020a
2.4.1		foss/2020b, fosscuda/2020b
2.4.1	-Python-3.7.4	fosscuda/2019b
2.4.4		foss/2021a
2.5.0		foss/2020b, fosscuda/2020b
2.5.0	-Python-3.7.4	fosscuda/2019b
2.5.3		foss/2021a
2.5.3	-CUDA-11.3.1	foss/2021a
2.6.0		foss/2021a
2.6.0	-CUDA-11.3.1	foss/2021a
2.7.1		foss/2021b
2.7.1	-CUDA-11.4.1	foss/2021b
2.8.4		foss/2021b
2.8.4	-CUDA-11.4.1	foss/2021b
2.9.1		foss/2022a
2.9.1	-CUDA-11.7.0	foss/2022a
2.11.0		foss/2022a
2.11.0	-CUDA-11.7.0	foss/2022a
2.13.0		foss/2022b, foss/2023a

tensorflow-compression

TensorFlow Compression (TFC) contains data compression tools for TensorFlow.

homepage: https://github.com/tensorflow/compression

version	versionsuffix	toolchain
2.11.0	-CUDA-11.7.0	foss/2022a

TensorFlow-Datasets

TensorFlow Datasets is a collection of datasets ready to use, with TensorFlow or other Python ML frameworks, such as Jax. All datasets are exposed as tf.data.Datasets , enabling easy-to-use and high-performance input pipelines.

homepage: https://www.tensorflow.org/datasets

version	versionsuffix	toolchain
4.7.0	-CUDA-11.3.1	foss/2021a
4.8.3	-CUDA-11.4.1	foss/2021b

TensorFlow-Graphics

Tensorflow Graphics provides a set of differentiable graphics and geometry layers (e.g. cameras, reflectance models, spatial transformations, mesh convolutions) and 3D viewer functionalities (e.g. 3D TensorBoard) that can be used to train and debug your machine learning models of choice.

homepage: https://github.com/tensorflow/graphics

version	versionsuffix	toolchain
2021.12.3	-CUDA-11.4.1	foss/2021b

tensorflow-probability

TensorFlow Probability (TFP) is a library for probabilistic reasoning and statistical analysis.

homepage: https://www.tensorflow.org/probability

version	versionsuffix	toolchain
0.9.0	-Python-3.7.4	foss/2019b
0.12.1		foss/2020b, fosscuda/2020b
0.14.0		foss/2021a
0.16.0		foss/2021b
0.19.0		foss/2022a
0.19.0	-CUDA-11.7.0	foss/2022a
0.20.0		foss/2023a

TensorRT

NVIDIA TensorRT is a platform for high-performance deep learning inference

homepage: https://developer.nvidia.com/tensorrt

version	versionsuffix	toolchain
4.0.1.6	-Python-2.7.15	fosscuda/2018b
8.6.1	-CUDA-11.7.0	foss/2022a

terastructure

TeraStructure is a new algorithm to fit Bayesian models of genetic variation in human populations on tera-sample-sized data sets (10^12 observed genotypes, i.e., 1M individuals at 1M SNPs). This package provides a scalable, multi-threaded C++ implementation that can be run on a single computer.

homepage: https://github.com/StoreyLab/terastructure

version	toolchain
1.0	GCC/8.3.0

termcolor

Termcolor is a header-only C++ library for printing colored messages to the terminal.

homepage: https://termcolor.readthedocs.io/

version	toolchain
2.0.0	system

Tesla-Deployment-Kit

The Tesla Deployment Kit is a set of tools provided primarily for the NVIDIA Tesla range of GPUs. They aim to empower users to better manage their NVIDIA GPUs by providing a broad range of functionalities. The kit contains: * NVIDIA Management Library (NVML), * Tesla Deployment Kit - Linux Edition (Aug 1st, 2013)

homepage: https://developer.nvidia.com/tesla-deployment-kit

version	toolchain
5.319.43	system

tesseract

Tesseract is an optical character recognition engine

homepage: https://github.com/tesseract-ocr/tesseract

version	toolchain
4.0.0	GCCcore/7.3.0
4.1.0	GCCcore/10.3.0, GCCcore/8.2.0
5.3.0	GCCcore/11.3.0

testpath

Test utilities for code working with files and commands

homepage: https://github.com/jupyter/testpath

version	versionsuffix	toolchain
0.3	-Python-2.7.11	foss/2016a, intel/2016a
0.3	-Python-2.7.12	foss/2016b, intel/2016b
0.3	-Python-3.5.1	foss/2016a
0.3	-Python-3.5.2	intel/2016b

TetGen

A Quality Tetrahedral Mesh Generator and a 3D Delaunay Triangulator

homepage: http://wias-berlin.de/software/index.jsp?id=TetGen

version	toolchain
1.5.0	GCCcore/6.4.0
1.6.0	GCCcore/10.2.0

TEToolkit

Tools for estimating differential enrichment of Transposable Elements and other highly repetitive regions

homepage: http://hammelllab.labsites.cshl.edu/software/#TEToolkit

version	versionsuffix	toolchain
1.5.1	-Python-2.7.11	foss/2016a

TEtranscripts

TEtranscripts and TEcount takes RNA-seq (and similar data) and annotates reads to both genes & transposable elements. TEtranscripts then performs differential analysis using DESeq2.

homepage: https://github.com/mhammell-laboratory/TEtranscripts

version	toolchain
2.2.0	foss/2020a

texinfo

Texinfo is the official documentation format of the GNU project.

homepage: https://www.gnu.org/software/texinfo/

version	toolchain
4.13a	system
5.2	GCC/4.8.2
6.4	GCCcore/5.4.0
6.5	GCCcore/6.4.0, GCCcore/7.3.0
6.6	GCCcore/8.2.0
6.7	GCCcore/10.2.0, GCCcore/8.3.0, GCCcore/9.3.0
6.8	GCCcore/11.2.0
7.0.2	GCCcore/11.3.0
7.1	GCCcore/12.3.0

texlive

TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript text intertwined with TeX commands in a plain text file. You then run TeX to produce formatted output, such as a PDF file. Thus, in contrast to standard word processors, your document is a separate file that does not pretend to be a representation of the final typeset output, and so can be easily edited and manipulated.

homepage: https://tug.org

version	toolchain
20200406	GCCcore/8.3.0
20210324	GCC/10.3.0, GCC/11.2.0
20220321	GCC/11.2.0
20230313	GCC/11.3.0, GCC/12.3.0

Text-CSV

Text-CSV parser

homepage: https://metacpan.org/pod/Text::CSV

version	versionsuffix	toolchain
1.33	-Perl-5.22.1	foss/2016a

TFEA

Transcription Factor Enrichment Analysis

homepage: https://github.com/Dowell-Lab/TFEA

version	versionsuffix	toolchain
1.1.4	-muMerge-1.1.0	foss/2020b

Theano

Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.

homepage: https://deeplearning.net/software/theano

version	versionsuffix	toolchain
0.8.2	-Python-2.7.11	foss/2016a
0.8.2	-Python-3.5.1	foss/2016a
0.8.2	-Python-3.5.2	intel/2016b
0.9.0	-Python-2.7.13	intel/2017a
0.9.0	-Python-3.6.1	intel/2017a
1.0.0	-Python-2.7.14	intel/2017b
1.0.0	-Python-3.6.3	intel/2017b
1.0.1	-Python-3.6.3	foss/2017b, intel/2017b
1.0.2	-Python-2.7.14	fosscuda/2017b, intelcuda/2017b
1.0.2	-Python-2.7.15	fosscuda/2018b
1.0.2	-Python-3.6.3	fosscuda/2017b, intelcuda/2017b
1.0.2	-Python-3.6.4	foss/2018a, intel/2018a
1.0.3	-Python-3.6.6	foss/2018b, fosscuda/2018b
1.0.4		foss/2019a, fosscuda/2019a
1.0.4	-Python-3.6.4	foss/2018a
1.0.4	-Python-3.6.6	foss/2018b, fosscuda/2018b
1.0.4	-Python-3.7.4	foss/2019b, fosscuda/2019b, intel/2019b
1.0.4	-Python-3.8.2	foss/2020a
1.1.2	-PyMC	foss/2020b, foss/2021b, fosscuda/2020b, intel/2020b, intel/2021b

ThemisPy

A header-only C++ library for L-BFGS and L-BFGS-B algorithms

homepage: https://github.com/aeb/ThemisPy

version	toolchain
0.3.0	foss/2021a

THetA

Tumor Heterogeneity Analysis (THetA) and THetA2 are algorithms that estimate the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data.

homepage: https://github.com/raphael-group/THetA

version	versionsuffix	toolchain
0.7	-Python-2.7.15	foss/2018b

thirdorder

A Python script to help create input files for computing anhamonic interatomic force constants, harnessing the symmetries of the system to minimize the number of required DFT calculations. A second mode of operation allows the user to build the third-order IFC matrix from the results of those runs.

homepage: https://bitbucket.org/sousaw/thirdorder/

version	toolchain
1.1.1	foss/2022a

thurstonianIRT

Fit Thurstonian IRT models in R using Stan, lavaan, or Mplus

homepage: https://github.com/paul-buerkner/thurstonianIRT

version	versionsuffix	toolchain
0.9.0	-R-3.6.0	foss/2019a

TiCCutils

TiCC utils is a collection of generic C++ software which is used in a lot of programs produced at Tilburg centre for Cognition and Communication (TiCC) at Tilburg University and Centre for Dutch Language and Speech at University of Antwerp.

homepage: https://github.com/LanguageMachines/ticcutils

version	toolchain
0.11	foss/2016a
0.21	iimpi/2019a, intel/2018b

tidybayes

Compose data for and extract, manipulate, and visualize posterior draws from Bayesian models ('JAGS', 'Stan', 'rstanarm', 'brms', 'MCMCglmm', 'coda', ...) in a tidy data format.

homepage: https://cran.r-project.org/package=tidybayes

version	versionsuffix	toolchain
2.1.1	-R-4.0.0	foss/2020a

tidymodels

tidymodels is a 'meta-package' for modeling and statistical analysis that shares the underlying design philosophy, grammar, and data structures of the tidyverse.

homepage: https://tidymodels.tidymodels.org

version	versionsuffix	toolchain
0.1.0	-R-4.0.0	foss/2020a
1.1.0		foss/2022b

Tika

The Apache Tika toolkit detects and extracts metadata and text from over a thousand different file types (such as PPT, XLS, and PDF).

homepage: https://tika.apache.org/

version	toolchain
1.16	system

TiMBL

TiMBL (Tilburg Memory Based Learner) is an open source software package implementing several memory-based learning algorithms, among which IB1-IG, an implementation of k-nearest neighbor classification with feature weighting suitable for symbolic feature spaces, and IGTree, a decision-tree approximation of IB1-IG. All implemented algorithms have in common that they store some representation of the training set explicitly in memory. During testing, new cases are classified by extrapolation from the most similar stored cases.

homepage: http://ilk.uvt.nl/timbl/

version	toolchain
6.4.7	foss/2016a
6.4.13	iimpi/2019a, intel/2018b

time

The `time' command runs another program, then displays information about the resources used by that program, collected by the system while the program was running.

homepage: https://www.gnu.org/software/time/

version	toolchain
1.7	system
1.9	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/7.3.0, GCCcore/8.3.0, GCCcore/9.3.0

timm

timm is a library containing SOTA computer vision models, layers, utilities, optimizers, schedulers, data-loaders, augmentations, and training/evaluation scripts. It comes packaged with >700 pretrained models, and is designed to be flexible and easy to use.

homepage: https://huggingface.co/docs/timm

version	versionsuffix	toolchain
0.6.13	-CUDA-11.7.0	foss/2022a
0.9.7	-CUDA-11.7.0	foss/2022a

TINKER

The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.

homepage: https://dasher.wustl.edu/tinker

version	toolchain
8.6.1	foss/2018b
8.7.2	foss/2019b
8.8.1	foss/2020a

tiny-cuda-nn

is a small, self-contained framework for training and querying neural networks. Most notably, it contains a lightning fast "fully fused" multi-layer perceptron (technical paper), a versatile multiresolution hash encoding (technical paper), as well as support for various other input encodings, losses, and optimizers.

homepage: https://github.com/NVlabs/tiny-cuda-nn

version	versionsuffix	toolchain
1.6	-CUDA-11.7.0	foss/2022a

TinyDB

TinyDB is a lightweight document oriented database optimized for your happiness :) It's written in pure Python and has no external dependencies. The target are small apps that would be blown away by a SQL-DB or an external database server.

homepage: https://tinydb.readthedocs.io/

version	toolchain
3.15.2	GCCcore/8.3.0

TinyXML

TinyXML is a simple, small, minimal, C++ XML parser that can be easily integrating into other programs. It reads XML and creates C++ objects representing the XML document. The objects can be manipulated, changed, and saved again as XML.

homepage: https://sourceforge.net/projects/tinyxml

version	toolchain
2.6.2	GCCcore/11.2.0, GCCcore/11.3.0

Tk

Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages.

homepage: https://www.tcl.tk/

version	versionsuffix	toolchain
8.6.3	-no-X11	GCC/4.8.4, GCC/4.9.2
8.6.4		iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25
8.6.4	-libX11-1.6.3	intel/2016a
8.6.4	-no-X11	GCC/4.9.3-2.25, GNU/4.9.3-2.25, foss/2016a, gimkl/2.11.5, intel/2016.02-GCC-4.9, intel/2016a
8.6.5		GCC/5.4.0-2.26, GCCcore/6.3.0, foss/2016.04, foss/2016a, foss/2016b, iccifort/2016.3.210-GCC-5.4.0-2.26, intel/2016b
8.6.6		foss/2017a, intel/2017a
8.6.7		foss/2017b, fosscuda/2017b, intel/2017b, intelcuda/2017b
8.6.8		GCCcore/6.4.0, GCCcore/7.3.0, foss/2018a, iomkl/2018a
8.6.9		GCCcore/8.2.0, GCCcore/8.3.0
8.6.10		GCCcore/10.2.0, GCCcore/9.3.0
8.6.11		GCCcore/10.3.0, GCCcore/11.2.0
8.6.12		GCCcore/11.3.0, GCCcore/12.2.0
8.6.13		GCCcore/12.3.0, GCCcore/13.2.0

Tkinter

Tkinter module, built with the Python buildsystem

homepage: https://python.org/

version	versionsuffix	toolchain
2.7.13	-Python-2.7.13	foss/2017a, intel/2017a
2.7.14	-Python-2.7.14	foss/2017b, foss/2018a, fosscuda/2017b, intel/2017b, intel/2018a, intelcuda/2017b
2.7.15		GCCcore/8.2.0
2.7.15	-Python-2.7.15	foss/2018b, fosscuda/2018b, intel/2018b
2.7.16		GCCcore/8.3.0
2.7.18		GCCcore/10.2.0, GCCcore/11.2.0, GCCcore/9.3.0
3.6.1	-Python-3.6.1	foss/2017a, intel/2017a
3.6.2	-Python-3.6.2	foss/2017b
3.6.3	-Python-3.6.3	foss/2017b, fosscuda/2017b, intel/2017b, intelcuda/2017b
3.6.4	-Python-3.6.4	foss/2018a, intel/2018a, iomkl/2018.02, iomkl/2018a
3.6.6	-Python-3.6.6	foss/2018b, fosscuda/2018b, intel/2018b, iomkl/2018b
3.7.2		GCCcore/8.2.0
3.7.4		GCCcore/8.3.0
3.8.2		GCCcore/9.3.0
3.8.6		GCCcore/10.2.0
3.9.5		GCCcore/10.3.0
3.9.6		GCCcore/11.2.0
3.10.4		GCCcore/11.3.0
3.10.8		GCCcore/12.2.0
3.11.3		GCCcore/12.3.0
3.11.5		GCCcore/13.2.0

TM-align

This package unifies protein structure alignment and RNA structure alignment into the standard TM-align program for single chain structure alignment, MM-align program for multi-chain structure alignment, and TM-score program for sequence dependent structure superposition.

homepage: https://zhanglab.ccmb.med.umich.edu/RNA-align/TMalign/

version	toolchain
20180426	foss/2018b, intel/2019a
20190822	GCC/11.3.0

tMAE

Package containing functions to: perform a negative binomial test on allele-specific counts add gnomAD minor allele frequencies MAplot (FC vs total counts) of allele-specific counts and results allelic counts (ALT vs REF)

homepage: https://github.com/mumichae/tMAE

version	versionsuffix	toolchain
1.0.0	-R-4.0.3	foss/2020b
1.0.1	-R-4.1.2	foss/2021b

tmap

tmap is a very fast visualization library for large, high-dimensional data sets. Currently, tmap is available for Python. tmap's graph layouts are based on the OGDF library.

homepage: https://tmap.gdb.tools

version	toolchain
20220502	GCC/11.2.0

tmux

tmux is a terminal multiplexer: it enables a number of terminals to be created, accessed, and controlled from a single screen. tmux may be detached from a screen and continue running in the background, then later reattached.

homepage: https://github.com/tmux/tmux/

version	toolchain
1.9a	GCC/4.9.2
2.2	GCCcore/4.9.3
2.3	GCC/5.4.0-2.26, system
3.1c	GCCcore/8.3.0
3.2	GCCcore/10.2.0, GCCcore/9.3.0
3.2a	GCCcore/10.3.0, GCCcore/11.2.0, system
3.3a	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, system

TN93

This is a simple program meant to compute pairwise distances between aligned nucleotide sequences in sequential FASTA format using the Tamura Nei 93 distance.

homepage: https://github.com/veg/tn93

version	toolchain
1.0.7	GCCcore/10.3.0

TOBIAS

TOBIAS is a collection of command-line bioinformatics tools for performing footprinting analysis on ATAC-seq data.

homepage: https://github.com/loosolab/TOBIAS

version	toolchain
0.12.12	foss/2021b
0.14.0	foss/2020b

ToFu

Tomography for Fusion.

homepage: https://github.com/ToFuProject/tofu

version	versionsuffix	toolchain
1.3.17	-Python-2.7.14	foss/2018a
1.3.17	-Python-3.6.4	foss/2018a
1.4.0	-Python-2.7.14	foss/2018a, intel/2018a
1.4.0	-Python-3.6.4	foss/2018a, intel/2018a
1.4.1	-Python-3.6.4	foss/2018a, intel/2018a
1.5.0		foss/2020b, intel/2020b

Togl

A Tcl/Tk widget for OpenGL rendering.

homepage: https://sourceforge.net/projects/togl/

version	toolchain
2.0	GCCcore/10.2.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/8.3.0

toil

A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.

homepage: https://github.com/DataBiosphere/toil

version	toolchain
5.8.0	foss/2021a

tokenizers

Fast State-of-the-Art Tokenizers optimized for Research and Production

homepage: https://github.com/huggingface/tokenizers

version	toolchain
0.12.1	GCCcore/10.3.0
0.13.3	GCCcore/12.2.0

Tombo

Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.

homepage: https://github.com/nanoporetech/tombo

version	versionsuffix	toolchain
1.5.1	-Python-3.7.4	foss/2019b

TOML-Fortran

TOML parser for Fortran projects

homepage: https://github.com/toml-f/toml-f

version	toolchain
0.2.2	GCC/10.2.0, iccifort/2020.4.304
0.3.1	GCC/11.2.0, GCC/11.3.0
0.4.1	GCC/12.2.0, intel-compilers/2022.2.1

TOPAS

TOPAS wraps and extends the Geant4 Simulation Toolkit to make advanced Monte Carlo simulation of all forms of radiotherapy easier to use for medical physicists.

homepage: https://www.topasmc.org

version	toolchain
3.9	foss/2022b

topaz

Particle picking software for single particle cryo-electron microscopy using convolutional neural networks and positive-unlabeled learning. Includes methods for micrograph denoising.

homepage: http://cb.csail.mit.edu/cb/topaz/

version	versionsuffix	toolchain
0.2.5		foss/2021a
0.2.5	-CUDA-11.3.1	foss/2021a
0.2.5.20230926	-CUDA-11.7.0	foss/2022a

TopHat

TopHat is a fast splice junction mapper for RNA-Seq reads.

homepage: http://ccb.jhu.edu/software/tophat/

version	versionsuffix	toolchain
2.1.0	-Python-2.7.14	intel/2018a
2.1.1		foss/2016a, foss/2016b, foss/2017b, intel/2017a, intel/2017b
2.1.2		foss/2018b, gompi/2019b, iimpi/2019b
2.1.2	-Python-2.7.18	GCC/10.2.0, GCC/11.2.0, GCC/11.3.0, gompi/2020a, iimpi/2020a

torchaudio

Data manipulation and transformation for audio signal processing, powered by PyTorch

homepage: https://github.com/pytorch/audio

version	versionsuffix	toolchain
0.5.0	-Python-3.7.4-PyTorch-1.4.0	foss/2019b, fosscuda/2019b
0.12.0	-PyTorch-1.12.0	foss/2022a
0.12.0	-PyTorch-1.12.0-CUDA-11.7.0	foss/2022a

torchdata

TorchData is a prototype library of common modular data loading primitives for easily constructing flexible and performant data pipelines."

homepage: https://github.com/pytorch/data

version	versionsuffix	toolchain
0.3.0	-PyTorch-1.11.0-CUDA-11.3.1	foss/2021a

torchinfo

" Torchinfo provides information complementary to what is provided by print(your_model) in PyTorch, similar to Tensorflow's model.summary() API to view the visualization of the model, which is helpful while debugging your network.

homepage: https://github.com/TylerYep/torchinfo

version	versionsuffix	toolchain
1.5.2	-PyTorch-1.7.1	foss/2020b, fosscuda/2020b

torchsampler

A (PyTorch) imbalanced dataset sampler for oversampling low classes and undersampling high frequent ones.

homepage: https://github.com/ufoym/imbalanced-dataset-sampler

version	versionsuffix	toolchain
0.1.2		foss/2022a
0.1.2	-CUDA-11.7.0	foss/2022a

torchtext

Data loaders and abstractions for text and NLP

homepage: https://github.com/pytorch/text

version	versionsuffix	toolchain
0.5.0	-PyTorch-1.4.0-Python-3.7.4	fosscuda/2019b
0.7.0	-Python-3.7.4-PyTorch-1.6.0	foss/2019b, fosscuda/2019b
0.8.1	-PyTorch-1.7.1	fosscuda/2020b
0.9.1	-PyTorch-1.8.1	fosscuda/2020b
0.10.0	-PyTorch-1.9.0	fosscuda/2020b
0.14.1	-PyTorch-1.12.0	foss/2022a

torchvf

TorchVF is a unifying Python library for using vector fields for efficient proposal-free instance segmentation.

homepage: https://github.com/ryanirl/torchvf

version	versionsuffix	toolchain
0.1.3		foss/2022a
0.1.3	-CUDA-11.7.0	foss/2022a

torchvision

Datasets, Transforms and Models specific to Computer Vision

homepage: https://github.com/pytorch/vision

version	versionsuffix	toolchain
0.2.0	-Python-3.6.4	intel/2018a
0.2.0	-Python-3.6.4-CUDA-9.1.85	foss/2018a
0.2.2	-Python-3.6.6	foss/2018b, fosscuda/2018b
0.3.0	-Python-3.7.2	foss/2019a
0.4.2	-PyTorch-1.3.1	fosscuda/2020b
0.4.2	-Python-3.7.4	foss/2019b, fosscuda/2019b
0.5.0	-Python-3.7.4-PyTorch-1.4.0	fosscuda/2019b
0.7.0	-Python-3.7.4-PyTorch-1.6.0	foss/2019b, fosscuda/2019b
0.7.0	-Python-3.7.4-PyTorch-1.6.0-imkl	fosscuda/2019b
0.8.2	-PyTorch-1.7.1	foss/2020b, fosscuda/2020b
0.8.2	-Python-3.7.4-PyTorch-1.7.1	fosscuda/2019b
0.9.1	-PyTorch-1.8.1	fosscuda/2020b
0.9.1	-Python-3.7.4-PyTorch-1.8.1	fosscuda/2019b
0.10.0	-PyTorch-1.9.0	fosscuda/2020b
0.11.1		foss/2021a
0.11.1	-CUDA-11.3.1	foss/2021a
0.11.3		foss/2021a
0.11.3	-CUDA-11.3.1	foss/2021a
0.12.0	-PyTorch-1.11.0-CUDA-11.3.1	foss/2021a
0.13.1		foss/2022a
0.13.1	-CUDA-11.7.0	foss/2022a
0.14.1		foss/2022b
0.16.0		foss/2023a

tornado

Tornado is a Python web framework and asynchronous networking library.

homepage: https://github.com/tornadoweb/tornado

version	toolchain
6.3.2	GCCcore/12.3.0

TotalView

TotalView is a GUI-based source code defect analysis tool that gives you unprecedented control over processes and thread execution and visibility into program state and variables. It allows you to debug one or many processes and/or threads in a single window with complete control over program execution. This allows you to set breakpoints, stepping line by line through the code on a single thread, or with coordinated groups of processes or threads, and run or halt arbitrary sets of processes or threads. You can reproduce and troubleshoot difficult problems that can occur in concurrent programs that take advantage of threads, OpenMP, MPI, GPUs or coprocessors.

homepage: http://www.roguewave.com/products/totalview.aspx

version	versionsuffix	toolchain
8.11.0-0	-linux-x86-64	system
8.11.0-2	-linux-x86-64	system
8.12.0-0	-linux-x86-64	system

tox

tox aims to automate and standardize testing in Python

homepage: https://tox.wiki

version	toolchain
3.25.1	GCCcore/10.2.0, GCCcore/11.3.0

tqdm

A fast, extensible progress bar for Python and CLI

homepage: https://github.com/tqdm/tqdm

version	versionsuffix	toolchain
4.24.0	-Python-2.7.15	foss/2018b
4.24.0	-Python-3.5.1	foss/2016a
4.29.0	-Python-3.6.4	intel/2018a
4.32.1		GCCcore/8.2.0
4.41.1		GCCcore/8.3.0
4.41.1	-Python-3.6.6	foss/2018b, intel/2018b
4.47.0		GCCcore/9.3.0
4.51.0	-Python-3.8.2	intel/2020a
4.56.2		GCCcore/10.2.0
4.60.0		GCCcore/10.2.0
4.61.1		GCCcore/10.3.0
4.61.2		GCCcore/10.3.0
4.62.3		GCCcore/11.2.0
4.64.0		GCCcore/11.3.0
4.64.1		GCCcore/12.2.0
4.66.1		GCCcore/12.3.0
4.66.2		GCCcore/13.2.0

Tracer

Tracer is a graphical tool for visualization and diagnostics of MCMC output.

homepage: https://github.com/beast-dev/tracer

version	toolchain
1.7.1	GCCcore/8.2.0

TranscriptClean

TranscriptClean is a Python program that corrects mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome.

homepage: https://github.com/mortazavilab/TranscriptClean

version	toolchain
2.0.2	foss/2020b

TransDecoder

TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

homepage: https://github.com/TransDecoder/TransDecoder/wiki

version	versionsuffix	toolchain
2.1.0	-Perl-5.24.1	intel/2017a
5.5.0		GCC/11.3.0

Transformers

State-of-the-art Natural Language Processing for PyTorch and TensorFlow 2.0

homepage: https://github.com/huggingface/transformers

version	versionsuffix	toolchain
4.2.1	-Python-3.8.2	foss/2020a
4.20.1		foss/2021a
4.21.1		foss/2021b
4.24.0		foss/2022a
4.29.2		foss/2022a
4.30.2		foss/2022b

Transrate

Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly.

homepage: http://hibberdlab.com/transrate/

version	toolchain
1.0.3	system

travis

Travis CI Client (CLI and Ruby library)

homepage: https://github.com/travis-ci/travis.rb

version	versionsuffix	toolchain
1.8.2	-Ruby-2.3.1	system
1.8.4	-Ruby-2.3.3	system

TRAVIS-Analyzer

TRAVIS is a free tool for analyzing and visualizing trajectories from all kinds of Molecular Dynamics or Monte Carlo simulations.

homepage: http://www.travis-analyzer.de/

version	toolchain
210521	GCC/10.3.0
220729	GCC/11.3.0

treatSens

Utilities to investigate sensitivity to unmeasured confounding in parametric models with either binary or continuous treatment.

homepage: https://github.com/vdorie/treatSens

version	versionsuffix	toolchain
3.0-20201002	-R-4.0.0	foss/2020a

TreeMix

TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations.

homepage: http://bitbucket.org/nygcresearch/treemix

version	toolchain
1.13	GCC/10.3.0, GCC/11.2.0, intel/2018a

TreeShrink

TreeShrink is an algorithm for detecting abnormally long branches in one or more phylogenetic trees.

homepage: https://github.com/uym2/TreeShrink

version	versionsuffix	toolchain
1.3.2	-Python-3.7.2	GCC/8.2.0-2.31.1

TRF

Tandem Repeats Finder: a program to analyze DNA sequences.

homepage: https://tandem.bu.edu/trf/trf.html

version	versionsuffix	toolchain
4.09	-linux64	system
4.09.1		GCC/10.3.0, GCCcore/10.2.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/9.3.0

Triangle

Triangle generates exact Delaunay triangulations, constrained Delaunay triangulations, conforming Delaunay triangulations, Voronoi diagrams, and high-quality triangular meshes. The latter can be generated with no small or large angles, and are thus suitable for finite element analysis.

homepage: http://www.cs.cmu.edu/~quake/triangle.html

version	toolchain
1.6	GCCcore/6.4.0, GCCcore/9.3.0, foss/2016a, foss/2018a, intel/2016b, intel/2017a, intel/2018a

Trilinos

The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages.

homepage: https://trilinos.org

version	versionsuffix	toolchain
12.12.1	-Python-2.7.14	foss/2017b, intel/2017b
12.12.1	-Python-3.6.4	foss/2018a, intel/2018a
12.12.1	-Python-3.7.4	foss/2019b
13.4.1		foss/2022a
13.4.1	-zoltan	foss/2022a

Trim_Galore

Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing).

homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

version	versionsuffix	toolchain
0.4.2		foss/2016b
0.4.4		foss/2016b, intel/2017a
0.5.0		foss/2018b
0.5.0	-Python-3.6.6	intel/2018b
0.6.0	-Python-2.7.15	foss/2018b
0.6.0	-Python-3.6.6	foss/2018b
0.6.1	-Python-2.7.15	foss/2018b
0.6.1	-Python-3.6.6	foss/2018b
0.6.2	-Java-11	GCCcore/8.2.0
0.6.2	-Python-2.7.15	foss/2018b
0.6.2	-Python-3.6.6	foss/2018b
0.6.5	-Java-11-Python-3.7.4	GCCcore/8.3.0
0.6.6	-Python-2.7.18	GCC/10.2.0
0.6.6	-Python-3.8.2	GCCcore/9.3.0
0.6.7		GCCcore/10.3.0
0.6.10		GCCcore/11.2.0, GCCcore/11.3.0

trimAl

A tool for automated alignment trimming in large-scale phylogenetic analyses

homepage: http://trimal.cgenomics.org/

version	toolchain
1.4.1	GCC/8.2.0-2.31.1, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.3.0, GCCcore/9.3.0, intel/2018a

trimesh

Trimesh is a Python (2.7- 3.3+) library for loading and using triangular meshes with an emphasis on watertight meshes. The goal of the library is to provide a fully featured Trimesh object which allows for easy manipulation and analysis, in the style of the excellent Polygon object in the Shapely library.

homepage: https://trimsh.org/

version	toolchain
3.17.1	foss/2022a
3.21.5	gfbf/2022b

Trimmomatic

Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.

homepage: http://www.usadellab.org/cms/?page=trimmomatic

version	versionsuffix	toolchain
0.32	-Java-1.7.0_80	system
0.36	-Java-1.8.0_92	system
0.38	-Java-1.8	system
0.38	-Java-1.8.0_162	system
0.39	-Java-1.8	system
0.39	-Java-11	system
0.39	-Java-17	system

Trinity

Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.

homepage: https://trinityrnaseq.github.io

version	versionsuffix	toolchain
2.2.0		foss/2016a
2.4.0		foss/2017a
2.5.1		intel/2017a, intel/2017b
2.6.6		intel/2018a
2.8.4		foss/2018b
2.8.5		iccifort/2019.1.144-GCC-8.2.0-2.31.1
2.8.5	-Java-11	GCC/8.3.0
2.9.1		foss/2020b
2.9.1	-Python-2.7.16	foss/2019b
2.9.1	-Python-3.7.4	foss/2019b
2.10.0	-Python-3.7.4	foss/2019b
2.15.1		foss/2021b, foss/2022a

Trinotate

Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Trinotate makes use of a number of different well referenced methods for functional annotation including homology search to known sequence data (BLAST+/SwissProt), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain prediction (signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg databases). All functional annotation data derived from the analysis of transcripts is integrated into a SQLite database which allows fast efficient searching for terms with specific qualities related to a desired scientific hypothesis or a means to create a whole annotation report for a transcriptome.

homepage: https://github.com/Trinotate/Trinotate/wiki

version	toolchain
4.0.1	foss/2022a

Triplexator

Triplexator is a tool for detecting nucleic acid triple helices and triplex features in nucleotide sequences using the canonical triplex-formation rules.

homepage: https://github.com/Gurado/triplexator

version	toolchain
1.3.3	GCC/11.2.0

TRIQS

TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems.

homepage: https://triqs.github.io/triqs

version	versionsuffix	toolchain
2.2.0	-Python-2.7.15	foss/2019a
2.2.1	-Python-2.7.15	foss/2019a
3.0.0	-Python-3.8.2	foss/2020a
3.1.1		foss/2022a
3.2.0		foss/2023a

TRIQS-cthyb

TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems. cthyb = continuous-time hybridisation-expansion quantum Monte Carlo The TRIQS-based hybridization-expansion solver allows to solve the generic problem of a quantum impurity embedded in a conduction bath for an arbitrary local interaction vertex. The “impurity” can be any set of orbitals, on one or several atoms.

homepage: https://triqs.github.io/cthyb/

version	versionsuffix	toolchain
2.2.0	-Python-2.7.15	foss/2019a
3.0.0	-Python-3.8.2	foss/2020a
3.1.0		foss/2022a
3.2.1		foss/2023a

TRIQS-dft_tools

TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems. This TRIQS-based-based application is aimed at ab-initio calculations for correlated materials, combining realistic DFT band-structure calculation with the dynamical mean-field theory. Together with the necessary tools to perform the DMFT self-consistency loop for realistic multi-band problems, the package provides a full-fledged charge self-consistent interface to the Wien2K package. In addition, if Wien2k is not available, it provides a generic interface for one-shot DFT+DMFT calculations, where only the single-particle Hamiltonian in orbital space has to be provided.

homepage: https://triqs.github.io/dft_tools/

version	versionsuffix	toolchain
2.2.0	-Python-2.7.15	foss/2019a
3.0.0	-Python-3.8.2	foss/2020a
3.1.0		foss/2022a
3.2.0		foss/2023a

TRIQS-tprf

TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems. TPRF is a TRIQS-based two-particle response function tool box that implements basic operations for higher order response functions such as inversion, products, the random phase approximation, the bethe salpeter equation (in the local vertex approximation), etc.. The aim is to provide efficient (C++/OpenMP/MPI) implementations of the basic operations needed to compute the two-particle response in the different two-particle channels (particle-hole, particle-particle).

homepage: https://triqs.github.io/tprf

version	versionsuffix	toolchain
2.2.0	-Python-2.7.15	foss/2019a
3.0.0	-Python-3.8.2	foss/2020a
3.1.1		foss/2022a
3.2.1		foss/2023a

Triton

Triton is a language and compiler for parallel programming. It aims to provide a Python-based programming environment for productively writing custom DNN compute kernels capable of running at maximal throughput on modern GPU hardware.

homepage: https://triton-lang.org/

version	versionsuffix	toolchain
1.1.1	-CUDA-11.7.0	foss/2022a

tRNAscan-SE

tRNAscan-SE is the most widely employed tool for identifying and annotating tRNA genes in genomes.

homepage: http://trna.ucsc.edu/tRNAscan-SE/

version	toolchain
2.0.12	GCC/11.2.0, foss/2022b

TRUST

Tcr Receptor Utilities for Solid Tissue (TRUST) is a computational tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from solid tissues, including tumors.

homepage: https://bitbucket.org/liulab/trust

version	versionsuffix	toolchain
3.0.2	-Python-2.7.14	intel/2018a

TRUST4

Tcr Receptor Utilities for Solid Tissue (TRUST) is a computational tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from solid tissues, including tumors. TRUST4 performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining region 3 (CDR3) and reports consensus of BCR/TCR sequences. TRUST4 then realigns the contigs to IMGT reference gene sequences to report the corresponding information. TRUST4 supports both single-end and paired-end sequencing data with any read length.

homepage: https://github.com/liulab-dfci/TRUST4

version	toolchain
1.0.5.1	system
1.0.6	GCC/11.2.0
1.0.7	GCC/11.3.0

Trycycler

Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes.

homepage: https://github.com/rrwick/Trycycler

version	versionsuffix	toolchain
0.3.3	-Python-3.8.2	foss/2020a
0.5.2		foss/2021a
0.5.3		foss/2021b

tseriesEntropy

Implements an Entropy measure of dependence based on the Bhattacharya-Hellinger-Matusita distance. Can be used as a (nonlinear) autocorrelation/crosscorrelation function for continuous and categorical time series. The package includes tests for serial dependence and nonlinearity based on it. Some routines have a parallel version that can be used in a multicore/cluster environment. The package makes use of S4 classes.

homepage: https://cran.r-project.org/web/packages/tseriesEntropy/index.html

version	versionsuffix	toolchain
0.6-0	-R-4.2.1	foss/2022a

tsne

Python library containing T-SNE algorithms.

homepage: https://github.com/danielfrg/tsne

version	versionsuffix	toolchain
0.1.8	-Python-2.7.16	intel/2019b

turbinesFoam

turbinesFoam is a library for simulating wind and marine hydrokinetic turbines in OpenFOAM using the actuator line method.

homepage: https://github.com/turbinesFoam/turbinesFoam

version	versionsuffix	toolchain
20220516	-OpenFOAM-8	foss/2020a

TurboVNC

TurboVNC is a derivative of VNC (Virtual Network Computing) that is tuned to provide peak performance for 3D and video workloads.

homepage: https://www.turbovnc.org

version	toolchain
2.2.3	GCCcore/8.2.0
3.0.1	GCCcore/11.3.0

TVB

The Virtual Brain will deliver the first open simulation of the human brain based on individual large-scale connectivity.

homepage: http://thevirtualbrain.org

version	versionsuffix	toolchain
1.4.1	-Python-2.7.11	intel/2016a
1.5	-Python-2.7.11	intel/2016a

tvb-data

The Virtual Brain Project (TVB Project) has the purpose of offering some modern tools to the Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains. Various demonstration data for use with TVB.

homepage: http://www.thevirtualbrain.org/

version	versionsuffix	toolchain
1.5	-Python-2.7.11	intel/2016a
20150915	-Python-2.7.11	intel/2016a

TVB-deps

Bundle of dependency Python packages for TVB (The Virtual Brain)

homepage: https://thevirtualbrain.org

version	versionsuffix	toolchain
20160618	-Python-2.7.11	intel/2016a

tvb-framework

The Virtual Brain Project (TVB Project) has the purpose of offering some modern tools to the Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains. TVB Scientific Library is the most important scientific contribution of TVB Project.

homepage: http://www.thevirtualbrain.org/

version	versionsuffix	toolchain
1.5	-Python-2.7.11	intel/2016a
20150921	-Python-2.7.11	intel/2016a

tvb-library

The Virtual Brain Project (TVB Project) has the purpose of offering some modern tools to the Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains. TVB Scientific Library is the most important scientific contribution of TVB Project.

homepage: http://www.thevirtualbrain.org/

version	versionsuffix	toolchain
1.5	-Python-2.7.11	intel/2016a
20150922	-Python-2.7.11	intel/2016a

TWL-NINJA

Nearly Infinite Neighbor Joining Application.

homepage: https://github.com/TravisWheelerLab/NINJA

version	toolchain
0.97-cluster_only	GCC/10.2.0
0.98-cluster_only	GCC/11.3.0

TXR

TXR is a pragmatic, convenient tool ready to take on your daily hacking challenges with its dual personality: its whole-document pattern matching and extraction language for scraping information from arbitrary text sources, and its powerful data-processing language to slice through problems like a hot knife through butter. Many tasks can be accomplished with TXR "one liners" directly from your system prompt.

homepage: https://www.nongnu.org/txr/

version	toolchain
291	GCCcore/12.2.0

typing-extensions

Typing Extensions – Backported and Experimental Type Hints for Python

homepage: https://github.com/python/typing/blob/master/typing_extensions/README.rst

version	versionsuffix	toolchain
3.7.4.3		GCCcore/10.2.0
3.7.4.3	-Python-3.7.4	GCCcore/8.3.0
3.7.4.3	-Python-3.8.2	GCCcore/9.3.0
3.10.0.0		GCCcore/10.3.0
3.10.0.2		GCCcore/11.2.0
4.3.0		GCCcore/11.3.0
4.4.0		GCCcore/10.3.0
4.9.0		GCCcore/12.2.0, GCCcore/12.3.0
4.10.0		GCCcore/13.2.0

U

UCC - UCC-CUDA - UCLUST - UCX - UCX-CUDA - ucx-py - UCX-ROCm - udocker - UDUNITS - UFL - Ultralytics - umap-learn - UMI-tools - umi4cPackage - umis - UNAFold - uncertainties - uncertainty-calibration - unicore-uftp - Unicycler - Unidecode - unifdef - UniFrac - unimap - units - unixODBC - unrar - UnZip - UQTk - USEARCH - UShER - USPEX - utf8proc - util-linux

UCC

UCC (Unified Collective Communication) is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes.

homepage: https://www.openucx.org/

version	toolchain
1.0.0	GCCcore/11.3.0
1.1.0	GCCcore/12.2.0
1.2.0	GCCcore/12.3.0, GCCcore/13.2.0

UCC-CUDA

UCC (Unified Collective Communication) is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes. This module adds the UCC CUDA support.

homepage: https://www.openucx.org/

version	versionsuffix	toolchain
1.0.0	-CUDA-11.7.0	GCCcore/11.3.0
1.1.0	-CUDA-12.0.0	GCCcore/12.2.0
1.2.0	-CUDA-12.1.1	GCCcore/12.3.0

UCLUST

UCLUST: Extreme high-speed sequence clustering, alignment and database search.

homepage: https://www.drive5.com/usearch/index.html

version	versionsuffix	toolchain
1.2.22q	-i86linux64	system

UCX

Unified Communication X An open-source production grade communication framework for data centric and high-performance applications

homepage: http://www.openucx.org/

version	versionsuffix	toolchain
1.3.1		GCCcore/6.4.0, GCCcore/7.3.0
1.5.0		GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0
1.5.0rc1	-hpcx	GCCcore/8.2.0
1.5.1		GCCcore/8.2.0
1.6.1		GCCcore/8.3.0
1.8.0		GCCcore/9.3.0
1.8.0	-CUDA-11.0.2	GCCcore/9.3.0
1.9.0		GCCcore/10.2.0
1.9.0	-CUDA-11.1.1	GCCcore/10.2.0
1.9.0	-CUDA-11.2.1	GCCcore/10.2.0
1.10.0		GCCcore/10.3.0
1.11.0		GCCcore/11.2.0
1.11.2		GCCcore/11.2.0
1.12.1		GCCcore/11.3.0
1.13.1		GCCcore/12.2.0
1.14.0		GCCcore/12.2.0
1.14.1		GCCcore/12.3.0
1.15.0		GCCcore/13.2.0
1.16.0-rc4		GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

UCX-CUDA

Unified Communication X An open-source production grade communication framework for data centric and high-performance applications This module adds the UCX CUDA support.

homepage: http://www.openucx.org/

version	versionsuffix	toolchain
1.10.0	-CUDA-11.3.1	GCCcore/10.3.0
1.11.0	-CUDA-11.4.1	GCCcore/11.2.0
1.11.2	-CUDA-11.4.1	GCCcore/11.2.0
1.11.2	-CUDA-11.5.2	GCCcore/11.2.0
1.12.1	-CUDA-11.7.0	GCCcore/11.3.0
1.13.1	-CUDA-12.0.0	GCCcore/12.2.0
1.14.1	-CUDA-12.1.1	GCCcore/12.3.0
1.15.0	-CUDA-12.4.0	GCCcore/13.2.0

ucx-py

UCX-Py is the Python interface for UCX, a low-level high-performance networking library. UCX and UCX-Py supports several transport methods including InfiniBand and NVLink while still using traditional networking protocols like TCP.

homepage: https://ucx-py.readthedocs.io

version	toolchain
0.21.0	foss/2020b

UCX-ROCm

Unified Communication X An open-source production grade communication framework for data centric and high-performance applications This module adds the UCX ROCm support.

homepage: http://www.openucx.org/

version	versionsuffix	toolchain
1.11.2	-ROCm-4.5.0	GCCcore/11.2.0

udocker

A basic user tool to execute simple docker containers in batch or interactive systems without root privileges.

homepage: https://github.com/indigo-dc/udocker

version	versionsuffix	toolchain
1.1.1	-Python-2.7.14	foss/2017b
1.1.3	-Python-2.7.14	intel/2018a

UDUNITS

UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.

homepage: https://www.unidata.ucar.edu/software/udunits/

version	toolchain
2.2.20	foss/2016a, intel/2016b
2.2.24	intel/2017a
2.2.25	foss/2017b, intel/2017b
2.2.26	GCCcore/10.2.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0, foss/2018a, foss/2018b, foss/2020a, intel/2017b, intel/2018a, intel/2018b, iomkl/2018b
2.2.28	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

UFL

The Unified Form Language (UFL) is a domain specific language for declaration of finite element discretizations of variational forms. More precisely, it defines a flexible interface for choosing finite element spaces and defining expressions for weak forms in a notation close to mathematical notation.

homepage: https://bitbucket.org/fenics-project/ufl

version	versionsuffix	toolchain
2018.1.0	-Python-3.6.4	foss/2018a
2019.1.0	-Python-3.7.4	foss/2019b

Ultralytics

Ultralytics YOLOv8 is a cutting-edge, state-of-the-art (SOTA) model that builds upon the success of previous YOLO versions and introduces new features and improvements to further boost performance and flexibility. YOLOv8 is designed to be fast, accurate, and easy to use, making it an excellent choice for a wide range of object detection and tracking, instance segmentation, image classification and pose estimation tasks.

homepage: https://github.com/ultralytics/ultralytics

version	versionsuffix	toolchain
8.0.92	-CUDA-11.7.0	foss/2022a

umap-learn

Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction.

homepage: https://umap-learn.readthedocs.io/en/latest/

version	toolchain
0.4.6	foss/2020b, fosscuda/2020b
0.5.3	foss/2020b, foss/2021a, foss/2021b, foss/2022a
0.5.5	foss/2023a

UMI-tools

Tools for handling Unique Molecular Identifiers in NGS data sets

homepage: https://umi-tools.readthedocs.io

version	versionsuffix	toolchain
1.0.0	-Python-3.6.6	foss/2018b
1.0.1	-Python-3.7.4	foss/2019b
1.0.1	-Python-3.8.2	foss/2020a
1.1.4		foss/2023a

umi4cPackage

umi4cPackage is a processing and analysis pipeline for UMI-4C experiment.

homepage: https://github.com/tanaylab/umi4cpackage

version	versionsuffix	toolchain
20200116	-R-4.0.0	foss/2020a

umis

Package for estimating UMI counts in Transcript Tag Counting data.

homepage: https://github.com/vals/umis

version	toolchain
1.0.3	intel/2019a

UNAFold

The UNAFold package contains several programs for performing energy minimization and partition function calculations on nucleic acid sequences.

homepage: http://mfold.rna.albany.edu/?q=DINAMelt/software

version	versionsuffix	toolchain
3.8	-Perl-5.24.1	intel/2017a

uncertainties

Transparent calculations with uncertainties on the quantities involved (aka error propagation); fast calculation of derivatives

homepage: http://uncertainties-python-package.readthedocs.io

version	toolchain
3.1.7	foss/2021b, foss/2023a

uncertainty-calibration

Python library to measure the calibration error of models, including confidence intervals computed by Bootstrap resampling, and code to recalibrate models.

homepage: https://github.com/p-lambda/verified_calibration

version	toolchain
0.0.9	foss/2021b

unicore-uftp

UNICORE Java-based client for UFTP

homepage: https://sourceforge.net/projects/unicore/

version	versionsuffix	toolchain
1.4.2	-Java-11	system

Unicycler

Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline.

homepage: https://github.com/rrwick/Unicycler

version	versionsuffix	toolchain
0.4.7	-Python-3.7.2	foss/2019a
0.4.8	-Python-3.8.2	gompi/2020a
0.4.9		gompi/2021a
0.5.0		gompi/2021b

Unidecode

Python library for lossy ASCII transliterations of Unicode text (port of Text::Unidecode Perl module)

homepage: https://github.com/avian2/unidecode

version	versionsuffix	toolchain
1.1.1	-Python-3.7.4	GCCcore/8.3.0
1.3.6		GCCcore/11.3.0

unifdef

unifdef - selectively remove C preprocessor conditionals The unifdef utility selectively processes conditional C preprocessor and the additional text that they delimit, while otherwise leaving the file alone.

homepage: https://github.com/fanf2/unifdef

version	toolchain
2.12	GCCcore/11.3.0

UniFrac

UniFrac is the de facto repository for high-performance phylogenetic diversity calculations. The methods in this repository are based on an implementation of the Strided State UniFrac algorithm which is faster, and uses less memory than Fast UniFrac. Strided State UniFrac supports Unweighted UniFrac, Weighted UniFrac, Generalized UniFrac, Variance Adjusted UniFrac and meta UniFrac, in both double and single precision (fp32). This repository also includes Stacked Faith (manuscript in preparation), a method for calculating Faith's PD that is faster and uses less memory than the Fast UniFrac-based reference implementation.

homepage: https://github.com/biocore/unifrac-binaries

version	toolchain
1.3.2	foss/2022a

unimap

Unimap is a fork of minimap2 optimized for assembly-to-reference alignment. It integrates the minigraph chaining algorithm and can align through long INDELs (up to 100kb by default) much faster than minimap2. Unimap is a better fit for resolving segmental duplications and is recommended over minimap2 for alignment between high-quality assemblies. Unimap does not replace minimap2 for other types of alignment. It drops the support of multi-part index and short-read mapping. Its long-read alignment is different from minimap2 but is not necessarily better. Unimap is more of a specialized minimap2 at the moment.

homepage: https://github.com/lh3/unimap

version	toolchain
0.1	GCCcore/10.2.0, GCCcore/11.3.0

units

GNU Units converts quantities expressed in various systems of measurement to their equivalents in other systems of measurement. Like many similar programs, it can handle multiplicative scale changes. It can also handle nonlinear conversions such as Fahrenheit to Celsius or wire gauge, and it can convert from and to sums of units, such as converting between meters and feet plus inches.

homepage: https://www.gnu.org/software/units/

version	toolchain
2.19	GCCcore/8.2.0

unixODBC

unixODBC provides a uniform interface between application and database driver

homepage: https://www.unixodbc.org

version	toolchain
2.3.7	foss/2018b
2.3.11	foss/2022b

unrar

RAR is a powerful archive manager.

homepage: https://www.rarlab.com/

version	toolchain
5.6.1	GCCcore/7.3.0
5.7.3	GCCcore/8.2.0
6.0.2	GCCcore/10.2.0

UnZip

UnZip is an extraction utility for archives compressed in .zip format (also called "zipfiles"). Although highly compatible both with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's own Zip program, our primary objectives have been portability and non-MSDOS functionality.

homepage: http://www.info-zip.org/UnZip.html

version	toolchain
6.0	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.1.0, GCCcore/13.2.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0, system

UQTk

The UQ Toolkit (UQTk) is a collection of libraries and tools for the quantification of uncertainty in numerical model predictions.

homepage: https://www.sandia.gov/UQToolkit/

version	versionsuffix	toolchain
3.1.0	-Python-3.7.4	intel/2019b

USEARCH

USEARCH is a unique sequence analysis tool which offers search and clustering algorithms that are often orders of magnitude faster than BLAST.

homepage: http://www.drive5.com/usearch/index.html

version	versionsuffix	toolchain
5.2.236	-i86linux32	system
5.2.236-6.1.544	-i86linux32	system
6.1.544	-i86linux32	system
11.0.667	-i86linux32	system

UShER

UShER is now a package consisting of a family of programs for rapid phylogenetic analyses, particularly suitable for the SARS-CoV-2 genomes.

homepage: https://github.com/yatisht/usher

version	toolchain
0.4.1	gompi/2020b
0.5.0	gompi/2021b

USPEX

USPEX (Universal Structure Predictor: Evolutionary Xtallography... and in Russian "uspekh" means "success" - owing to the high success rate and many useful results produced by this method) is a method developed by the Oganov laboratory since 2004. The problem of crystal structure prediction is very old and does, in fact, constitute the central problem of theoretical crystal chemistry. USPEX can also be used for finding low-energy metastable phases, as well as stable structures of nanoparticles, surface reconstructions, molecular packings in organic crystals, and for searching for materials with desired physical (mechanical, electronic) properties. The USPEX code is based on an efficient evolutionary algorithm developed by A.R. Oganov's group, but also has options for using alternative methods (random sampling, metadynamics, corrected particle swarm optimization algorithms). USPEX is interfaced with many ab initio codes, such as VASP, SIESTA, GULP, Quantum Espresso, CP2K, CASTEP, LAMMPS, and so on.

homepage: http://uspex-team.org/uspex/overview

version	versionsuffix	toolchain
9.4.4	-Python-2.7.12	intel/2016b

utf8proc

utf8proc is a small, clean C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 encoding.

homepage: https://github.com/JuliaStrings/utf8proc

version	toolchain
2.2.0	GCCcore/6.4.0
2.3.0	GCCcore/8.2.0
2.5.0	GCCcore/10.2.0, GCCcore/8.3.0, GCCcore/9.3.0
2.6.1	GCCcore/10.3.0, GCCcore/11.2.0
2.7.0	GCCcore/11.3.0
2.8.0	GCCcore/12.2.0, GCCcore/12.3.0

util-linux

Set of Linux utilities

homepage: https://www.kernel.org/pub/linux/utils/util-linux

version	toolchain
2.27.1	foss/2016a, intel/2016a
2.28	foss/2016a, intel/2016a
2.28.1	intel/2016b
2.29	foss/2016b, intel/2016b
2.29.2	GCCcore/6.3.0, intel/2017a
2.30	GCCcore/6.4.0
2.30.1	GCCcore/6.3.0, foss/2017a
2.31	GCCcore/6.4.0
2.31.1	GCCcore/6.4.0
2.32	GCCcore/6.4.0, GCCcore/7.3.0
2.32.1	GCCcore/7.3.0
2.33	GCCcore/8.2.0
2.34	GCCcore/8.3.0
2.35	GCCcore/9.3.0
2.36	GCCcore/10.2.0, GCCcore/10.3.0
2.37	GCCcore/11.2.0
2.38	GCCcore/11.3.0
2.38.1	GCCcore/12.2.0
2.39	GCCcore/12.3.0, GCCcore/13.2.0

V

V8 - vaeda - Vala - Valgrind - Vamb - Vampir - Vampire - VarDict - variant_tools - VariantMetaCaller - VarScan - vartools - VASP - VAtools - vawk - VBZ-Compression - VCF-kit - vcflib - vcfnp - VCFtools - vConTACT2 - VEGAS - velocyto - Velvet - VEP - verifyBamID - VERSE - VESTA - ViennaRNA - Vim - VirSorter - VirSorter2 - virtualenv - VirtualGL - Virtuoso-opensource - visdom - vispr - VisPy - vitessce-python - vitessceR - VMD - VMTK - voltools - vorbis-tools - Voro++ - vsc-base - vsc-install - vsc-mympirun - vsc-mympirun-scoop - vsc-processcontrol - VSCode - VSEARCH - vt - VTK - VTune - VV - VXL

V8

R interface to Google's open source JavaScript engine

homepage: https://cran.r-project.org/web/packages/V8/

version	versionsuffix	toolchain
2.2	-R-3.5.1	foss/2018b
2.3	-R-3.6.0	foss/2019a, intel/2019a
3.2.0	-R-3.6.2	foss/2019b
3.4.0	-R-4.0.0	foss/2020a

vaeda

vaeda (variaitonal auto-encoder (vae) for doublet annotation (da)) is a Python package for doublet annotation in single cell RNA-sequencing.

homepage: https://github.com/kostkalab/vaeda

version	toolchain
0.0.30	foss/2022a

Vala

Vala is a programming language using modern high level abstractions without imposing additional runtime requirements and without using a different ABI compared to applications and libraries written in C.

homepage: https://wiki.gnome.org/Projects/Vala

version	toolchain
0.52.4	GCCcore/10.3.0
0.56.14	GCCcore/12.3.0

Valgrind

Valgrind: Debugging and profiling tools

homepage: https://valgrind.org

version	toolchain
3.11.0	foss/2016a, intel/2016a
3.13.0	foss/2017b, foss/2018a, intel/2017a, intel/2017b, intel/2018a
3.14.0	foss/2018b
3.16.1	gompi/2019b, gompi/2020a, gompi/2020b, iimpi/2020a
3.17.0	gompi/2021a
3.18.1	gompi/2021b, iimpi/2021b
3.19.0	gompi/2022a
3.20.0	gompi/2022a
3.21.0	gompi/2022b, gompi/2023a

Vamb

Vamb is a metagenomic binner which feeds sequence composition information from a contig catalogue and co-abundance information from BAM files into a variational autoencoder and clusters the latent representation.

homepage: https://github.com/RasmussenLab/vamb

version	versionsuffix	toolchain
3.0.9	-CUDA-11.5.2	foss/2021b

Vampir

The Vampir software tool provides an easy-to-use framework that enables developers to quickly display and analyze arbitrary program behavior at any level of detail. The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data.

homepage: http://www.vampir.eu

version	versionsuffix	toolchain
8.4.1		system
8.4.1	-demo	system

Vampire

The Vampire Theorem Prover.

homepage: https://vprover.github.io/

version	toolchain
4.5.1	GCCcore/10.2.0

VarDict

VarDict is an ultra sensitive variant caller for both single and paired sample variant calling from BAM files.

homepage: https://github.com/AstraZeneca-NGS/VarDict

version	versionsuffix	toolchain
1.5.7	-Perl-5.28.0	foss/2018b

variant_tools

Variant tools is a software tool for the manipulation, annotation, selection, simulation, and analysis of variants in the context of next-gen sequencing analysis. Unlike some other tools used for Next-Gen sequencing analysis, variant tools is project based and provides a whole set of tools to manipulate and analyze genetic variants.

homepage: https://vatlab.github.io/vat-docs/

version	versionsuffix	toolchain
3.1.3	-Python-3.7.4	foss/2019b

VariantMetaCaller

VariantMetaCaller automatically integrates variant calling pipelines into a better performing overall model that also predicts accurate variant probabilities.

homepage: http://bioinformatics.mit.bme.hu/VariantMetaCaller/

version	toolchain
1.0	intel/2017a

VarScan

Variant calling and somatic mutation/CNV detection for next-generation sequencing data

homepage: https://github.com/dkoboldt/varscan

version	versionsuffix	toolchain
2.3.6	-Java-1.7.0_80	system
2.4.1	-Java-1.7.0_80	system
2.4.4	-Java-1.8	system
2.4.4	-Java-11	system

vartools

Command line utility that provides tools for processing and analyzing astronomical time series data.

homepage: https://www.astro.princeton.edu/~jhartman/vartools.html

version	toolchain
1.35	foss/2016b, intel/2016b

VASP

The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.

homepage: https://www.vasp.at

version	toolchain
5.4.1	intel/2016.02-GCC-4.9
6.3.2	nvofbf/2022.07

VAtools

VAtools is a python package that includes several tools to annotate VCF files with data from other tools.

homepage: https://vatools.readthedocs.io/en/latest/

version	versionsuffix	toolchain
3.0.1	-Python-3.6.6	foss/2018b

vawk

An awk-like VCF parser

homepage: https://github.com/cc2qe/vawk

version	versionsuffix	toolchain
0.0.1	-Python-2.7.18	GCCcore/10.2.0

VBZ-Compression

VBZ compression HDF5 plugin for nanopolish

homepage: https://github.com/nanoporetech/vbz_compression

version	toolchain
1.0.1	gompi/2020b
1.0.3	gompi/2022a

VCF-kit

VCF-kit is a command-line based collection of utilities for performing analysis on Variant Call Format (VCF) files.

homepage: https://github.com/AndersenLab/VCF-kit

version	versionsuffix	toolchain
0.1.6	-Python-2.7.15	intel/2018b

vcflib

vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended to concisely describe reference-indexed genetic variations between individuals.

homepage: https://github.com/vcflib/vcflib

version	versionsuffix	toolchain
1.0.2		GCC/10.2.0, GCC/10.3.0
1.0.2	-Python-3.8.2	GCC/9.3.0
1.0.3	-R-4.1.0	foss/2021a
1.0.3	-R-4.1.2	foss/2021b
1.0.9	-R-4.2.1	foss/2022a
1.0.9	-R-4.3.2	gfbf/2023a

vcfnp

Load data from a VCF (variant call format) file into numpy arrays, and (optionally) from there into an HDF5 file.

homepage: https://github.com/alimanfoo/vcfnp

version	versionsuffix	toolchain
2.3.0	-Python-2.7.11	foss/2016a

VCFtools

The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.

homepage: https://vcftools.github.io

version	versionsuffix	toolchain
0.1.14	-Perl-5.22.1	foss/2016a, intel/2016a
0.1.15	-Perl-5.24.0	foss/2016b
0.1.15	-Perl-5.26.0	foss/2017b, intel/2017b
0.1.15	-Perl-5.26.1	foss/2018a
0.1.16		GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/11.3.0, GCC/12.2.0, GCC/12.3.0, GCC/8.3.0, GCC/9.3.0, iccifort/2019.5.281
0.1.16	-Perl-5.28.0	foss/2018b, intel/2018b

vConTACT2

vConTACT2 is a tool to perform guilt-by-contig-association classification of viral genomic sequence data.

homepage: https://bitbucket.org/MAVERICLab/vcontact2

version	toolchain
0.11.3	foss/2022a

VEGAS

VEGAS (Versatile Gene-based Association Study) is a free program for performing gene-based tests for association using the results from genetic association studies

homepage: http://gump.qimr.edu.au/VEGAS/

version	toolchain
0.8.27	system

velocyto

Velocyto is a library for the analysis of RNA velocity.

homepage: https://velocyto.org/velocyto.py/

version	versionsuffix	toolchain
0.17.17		foss/2021a, foss/2022a
0.17.17	-Python-3.8.2	intel/2020a

Velvet

Sequence assembler for very short reads

homepage: https://github.com/dzerbino/velvet/

version	versionsuffix	toolchain
1.2.10	-mt-kmer_191	GCC/11.2.0, GCC/8.3.0, foss/2018a, foss/2018b, foss/2023a
1.2.10	-mt-kmer_37	intel/2017a

VEP

Variant Effect Predictor (VEP) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently used routines in VEP.

homepage: https://www.ensembl.org/info/docs/tools/vep

version	versionsuffix	toolchain
93.4	-Perl-5.26.1	intel/2018a
94.0	-Perl-5.28.0	foss/2018b
94.5	-Perl-5.26.0	foss/2017b, intel/2017b
95.0	-Perl-5.28.0	foss/2018b
96.0	-Perl-5.28.1	foss/2019a
103.1		GCC/10.2.0
105		GCC/11.2.0
107		GCC/11.3.0
111		GCC/12.2.0

verifyBamID

verifyBamID is a software that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples. verifyBamID can detect sample contamination and swaps when external genotypes are available. When external genotypes are not available, verifyBamID still robustly detects sample swaps.

homepage: http://csg.sph.umich.edu/kang/verifyBamID/index.html

version	toolchain
1.1.3	foss/2016a

VERSE

A versatile and efficient RNA-Seq read counting tool

homepage: https://github.com/qinzhu/VERSE

version	toolchain
0.1.5	foss/2016b

VESTA

VESTA is a 3D visualization program for structured models, volumetric data such as electron/nuclear densities, and crystal morphologies.

homepage: http://www.jp-minerals.org/vesta

version	versionsuffix	toolchain
3.5.8	-gtk3	system

ViennaRNA

The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.

homepage: https://www.tbi.univie.ac.at/RNA/

version	versionsuffix	toolchain
2.2.3		intel/2016b
2.3.4		foss/2016b
2.3.5		intel/2017a
2.4.10	-Python-2.7.15	foss/2018b, intel/2018b
2.4.11	-Python-3.6.6	foss/2018b
2.4.14	-Python-3.6.6	foss/2018b
2.5.0		foss/2021b
2.5.1		foss/2021b

Vim

Vim is an advanced text editor that seeks to provide the power of the de-facto Unix editor 'Vi', with a more complete feature set.

homepage: http://www.vim.org

version	versionsuffix	toolchain
8.0	-Python-2.7.11	foss/2016a
8.1.0483	-Python-2.7.15	foss/2018b
8.1.1209	-Python-3.7.2	GCCcore/8.2.0
9.0.0950		GCCcore/11.3.0
9.0.1434		GCCcore/12.2.0
9.1.0004		GCCcore/12.3.0

VirSorter

VirSorter: mining viral signal from microbial genomic data.

homepage: https://github.com/simroux/VirSorter

version	versionsuffix	toolchain
1.0.6		foss/2021b
20160601	-Perl-5.22.1	foss/2016a

VirSorter2

VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes.

homepage: https://github.com/jiarong/VirSorter2

version	toolchain
2.2.4	foss/2021b, foss/2022a

virtualenv

A tool for creating isolated virtual python environments.

homepage: https://github.com/pypa/virtualenv

version	toolchain
20.23.1	GCCcore/12.3.0
20.24.6	GCCcore/13.2.0

VirtualGL

VirtualGL is an open source toolkit that gives any Linux or Unix remote display software the ability to run OpenGL applications with full hardware acceleration.

homepage: https://virtualgl.org/

version	toolchain
2.6.1	foss/2018b
2.6.2	GCCcore/9.3.0
3.0	GCC/11.2.0
3.1	GCC/12.3.0

Virtuoso-opensource

Virtuoso is a high-performance and scalable Multi-Model RDBMS, Data Integration Middleware, Linked Data Deployment, and HTTP Application Server Platform.

homepage: https://github.com/openlink/virtuoso-opensource

version	toolchain
7.2.6.1	GCC/10.3.0

visdom

A flexible tool for creating, organizing, and sharing visualizations of live, rich data. Supports Torch and Numpy.

homepage: https://github.com/fossasia/visdom

version	toolchain
0.2.4	foss/2022a

vispr

VISPR - A visualization framework for CRISPR data.

homepage: https://pypi.org/project/vispr/

version	toolchain
0.4.14	foss/2022a

VisPy

VisPy is a high-performance interactive 2D/3D data visualization library leveraging the computational power of modern Graphics Processing Units (GPUs) through the OpenGL library to display very large datasets.

homepage: https://vispy.org

version	toolchain
0.6.6	foss/2020b, intel/2020b
0.12.2	foss/2022a, gfbf/2023a

vitessce-python

Python API and Jupyter widget facilitating interactive visualization of spatial single-cell data with Vitessce.

homepage: https://github.com/vitessce/vitessce-python

version	toolchain
20230222	foss/2022a

vitessceR

Vitessce is a visual integration tool for exploration of spatial single-cell experiments.

homepage: https://github.com/vitessce/vitessceR

version	versionsuffix	toolchain
0.99.0-20230110	-R-4.2.1	foss/2022a

VMD

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

homepage: https://www.ks.uiuc.edu/Research/vmd

version	versionsuffix	toolchain
1.9.3	-Python-2.7.12	intel/2016b
1.9.3	-Python-2.7.14	foss/2017b, intel/2018a
1.9.3	-Python-2.7.15	intel/2018b
1.9.4a43	-Python-3.7.4	fosscuda/2019b
1.9.4a51		foss/2020b, fosscuda/2020b
1.9.4a57		foss/2022a

VMTK

vmtk is a collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels.

homepage: https://vmtk.org

version	versionsuffix	toolchain
1.4.0	-Python-3.7.4	foss/2019b

voltools

CUDA-accelerated numpy 3D affine transformations

homepage: https://github.com/the-lay/voltools

version	toolchain
0.4.2	foss/2020b

vorbis-tools

Command-line tools for creating and playing Ogg Vorbis files.

homepage: https://xiph.org/vorbis/

version	toolchain
1.4.2	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0

Voro++

Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles.

homepage: http://math.lbl.gov/voro++/

version	toolchain
0.4.6	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/6.4.0, GCCcore/9.3.0, foss/2016a, foss/2019b, intel/2016a, intel/2019b

vsc-base

Basic Python libraries used by UGent's HPC group

homepage: http://hpcugent.github.com/vsc-base/

version	versionsuffix	toolchain
1.6.9		system
1.7.3		system
2.0.4		system
2.1.2		system
2.4.2		system
2.4.17	-Python-2.7.11	intel/2016a
2.5.1		system
2.5.1	-Python-2.7.11	intel/2016a
2.5.1	-Python-2.7.12	intel/2016b
2.5.8		system
2.8.0		system
2.8.1		system
2.8.3		system

vsc-install

vsc-install provides shared setuptools functions and classes for Python libraries developed by UGent's HPC group

homepage: https://pypi.python.org/pypi/vsc-install

version	versionsuffix	toolchain
0.9.18	-Python-2.7.11	intel/2016a
0.10.6		system
0.10.6	-Python-2.7.11	intel/2016a
0.10.11	-Python-2.7.11	intel/2016a
0.10.11	-Python-2.7.12	intel/2016b
0.10.25		system
0.10.26		system
0.11.1		system
0.11.2		system

vsc-mympirun

mympirun is a tool to make it easier for users of HPC clusters to run MPI programs with good performance.

homepage: https://github.com/hpcugent/vsc-mympirun

version	versionsuffix	toolchain
3.2.1		system
3.3.0		system
3.4.2		system
3.4.2	-Python-2.7.11-vsc-base-2.4.17	intel/2016a
3.4.2	-Python-2.7.11-vsc-base-2.5.1	intel/2016a
3.4.2	-vsc-base-2.4.2	system
3.4.3	-Python-2.7.12	intel/2016b
4.0.0		system
4.0.0b0		system
4.0.1		system
4.0.2		system
4.1.4		system
4.1.5		system
4.1.6		system
4.1.8		system
4.1.9		system
5.1.0		system
5.2.0		system
5.2.2		system
5.2.3		system
5.2.4		system
5.2.5		system
5.2.6		system
5.2.7		system
5.2.9		system
5.2.10		system
5.2.11		system
5.3.0		system
5.3.1		system
5.4.0		system

vsc-mympirun-scoop

VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.

homepage: http://hpcugent.github.com/vsc-mympirun/

version	versionsuffix	toolchain
3.4.1	-Python-2.7.12	intel/2016b

vsc-processcontrol

vsc-processcontrol is a module to abstract process control like scheduler settings and affinity from actual implementations like vsc.affinity and psutil.

homepage: http://hpcugent.github.com/vsc-processcontrol/

version	versionsuffix	toolchain
1.0		system
1.0	-vsc-base-2.1.2	system

VSCode

Visual Studio Code is a lightweight but powerful source code editor which runs on your desktop and is available for Windows, macOS and Linux. It comes with built-in support for JavaScript, TypeScript and Node.js and has a rich ecosystem of extensions for other languages and runtimes (such as C++, C#, Java, Python, PHP, Go, .NET). Begin your journey with VS Code with these introductory videos.

homepage: https://code.visualstudio.com/

version	toolchain
1.85.0	system

VSEARCH

VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads.

homepage: https://github.com/torognes/vsearch

version	toolchain
2.9.1	foss/2018b
2.13.4	iccifort/2019.1.144-GCC-8.2.0-2.31.1
2.15.0	GCC/9.3.0
2.18.0	GCC/10.2.0
2.21.1	GCC/10.3.0
2.22.1	GCC/11.3.0
2.25.0	GCC/12.3.0

vt

A tool set for short variant discovery in genetic sequence data.

homepage: http://genome.sph.umich.edu/wiki/Vt

version	toolchain
0.57721	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, GCC/9.3.0, foss/2018b

VTK

The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.

homepage: https://www.vtk.org

version	versionsuffix	toolchain
6.3.0	-Python-2.7.11	foss/2016a, intel/2016a
6.3.0	-Python-2.7.12	foss/2016b, intel/2016b
7.0.0	-Python-2.7.12	intel/2016b
7.1.0	-Python-2.7.12	intel/2016b
7.1.1	-Python-2.7.13	intel/2017a
8.0.1	-Python-2.7.14	foss/2017b, intel/2017b
8.1.0	-Python-2.7.14	foss/2018a, intel/2018a
8.1.0	-Python-3.6.4	foss/2018a, intel/2018a
8.1.1	-Python-2.7.14	intel/2018a
8.1.1	-Python-2.7.15	foss/2018b
8.1.1	-Python-3.6.6	foss/2018b, fosscuda/2018b
8.2.0		foss/2021a
8.2.0	-Python-2.7.15	foss/2019a
8.2.0	-Python-2.7.16	foss/2019b
8.2.0	-Python-3.7.2	foss/2019a, intel/2019a
8.2.0	-Python-3.7.4	foss/2019b
8.2.0	-Python-3.8.2	foss/2020a, fosscuda/2020a, intel/2020a
9.0.1		foss/2020b, foss/2021a, fosscuda/2020b
9.1.0		foss/2021b
9.2.0.rc2		foss/2022a
9.2.2		foss/2022a
9.2.6		foss/2022b
9.3.0		foss/2023a

VTune

Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.

homepage: https://software.intel.com/en-us/vtune

version	toolchain
2013_update6	system
2013_update8	system
2013_update9	system
2013_update10	system
2013_update11	system
2013_update12	system
2016_update3	system
2017	system
2017_update1	system
2017_update2	system
2017_update3	system
2018_update1	system
2018_update2	system
2018_update3	system
2019_update2	system
2019_update3	system
2019_update5	system
2020_update3	system
2021.6.0	system
2021.9.0	system
2022.0.0	system
2022.2.0	system
2022.3.0	system
2023.2.0	system

VV

VV is an open-source and cross platform image viewer, designed for fast and simple visualization of spatio-temporal images: 2D, 2D+t, 3D and 3D+t (or 4D) images. Only the command-line (clitk) tools are build.

homepage: https://www.creatis.insa-lyon.fr/rio/vv

version	versionsuffix	toolchain
2018.09.19	-Python-3.6.6	foss/2018b

VXL

A multi-platform collection of C++ software libraries for Computer Vision and Image Understanding.

homepage: https://sf.net/projects/vxl

version	toolchain
1.18.0	foss/2018a

W

waLBerla - wandb - Wannier90 - WannierTools - Wayland - Waylandpp - WCSLIB - WCT - wcwidth - webin-cli - WebKitGTK+ - WebSocket++ - WEKA - WFA2 - wget - wgsim - WHAM - WhatsHap - wheel - WIEN2k - WildMagic - Winnowmap - WisecondorX - WISExome - wkhtmltopdf - worker - wpebackend-fdo - WPS - wrapt - WRF - WRF-Fire - wrf-python - WSClean - wtdbg2 - wxPropertyGrid - wxPython - wxWidgets

waLBerla

Widely applicable Lattics-Boltzmann from Erlangen is a block-structured high-performance framework for multiphysics simulations

homepage: https://walberla.net/index.html

version	toolchain
6.1	foss/2021a, foss/2022b

wandb

CLI and Python API for Weights and Biases (wandb), a tool for visualizing and tracking your machine learning experiments.

homepage: https://www.wandb.com/

version	versionsuffix	toolchain
0.8.30	-Python-3.7.4	gcccuda/2019b
0.13.4		GCCcore/11.3.0
0.13.6		GCC/11.3.0
0.16.1		GCC/12.3.0

Wannier90

A tool for obtaining maximally-localised Wannier functions

homepage: http://www.wannier.org

version	versionsuffix	toolchain
1.2		intel/2016.02-GCC-4.9
2.0.1		intel/2016.02-GCC-4.9, intel/2016a
2.0.1.1	-abinit	intel/2018b
2.1.0		foss/2017b, intel/2017a, intel/2017b
3.0.0		intel/2018b
3.1.0		foss/2020b, foss/2021a, foss/2021b, foss/2022a, foss/2023a, gomkl/2021a, gomkl/2023a, intel/2020a, intel/2020b, intel/2021a, intel/2021b, intel/2022a, intel/2022b, intel/2023a

WannierTools

WannierTools is an open source software that studies the physical properties of given tight-binding model.

homepage: http://www.wanniertools.com

version	toolchain
2.3.0	intel/2018a
2.5.1	intel/2020b

Wayland

Wayland is a project to define a protocol for a compositor to talk to its clients as well as a library implementation of the protocol. The compositor can be a standalone display server running on Linux kernel modesetting and evdev input devices, an X application, or a wayland client itself. The clients can be traditional applications, X servers (rootless or fullscreen) or other display servers.

homepage: https://wayland.freedesktop.org/

version	toolchain
1.20.0	GCCcore/11.3.0
1.21.0	GCCcore/11.2.0, GCCcore/11.3.0
1.22.0	GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

Waylandpp

Wayland is an object oriented display protocol, which features request and events. Requests can be seen as method calls on certain objects, whereas events can be seen as signals of an object. This makes the Wayland protocol a perfect candidate for a C++ binding. The goal of this library is to create such a C++ binding for Wayland using the most modern C++ technology currently available, providing an easy to use C++ API to Wayland.

homepage: https://github.com/NilsBrause/waylandpp

version	toolchain
1.0.0	GCCcore/11.2.0, GCCcore/11.3.0

WCSLIB

The FITS "World Coordinate System" (WCS) standard defines keywords and usage that provide for the description of astronomical coordinate systems in a FITS image header.

homepage: https://www.atnf.csiro.au/people/mcalabre/WCS/

version	toolchain
7.11	GCC/11.2.0, GCC/11.3.0, GCC/13.2.0

WCT

NOAA's Weather and Climate Toolkit (WCT) is free, platform independent software distributed from NOAA's National Centers for Environmental Information (NCEI). The WCT allows the visualization and data export of weather and climate data, including Radar, Satellite and Model data. The WCT also provides access to weather/climate web services provided from NCEI and other organizations.

homepage: https://www.ncdc.noaa.gov/wct/index.php

version	versionsuffix	toolchain
4.6.0	-Java-11	system

wcwidth

wcwidth is a low-level Python library to simplify Terminal emulation.

homepage: https://github.com/jquast/wcwidth

version	versionsuffix	toolchain
0.1.7	-Python-2.7.11	foss/2016a
0.1.7	-Python-2.7.12	foss/2016b, intel/2016b
0.1.7	-Python-3.5.1	foss/2016a
0.1.7	-Python-3.5.2	intel/2016b

webin-cli

The Webin command line submission interface can be used to validate, upload and submit files to the European Nucleotide Archive (ENA)

homepage: https://github.com/enasequence/webin-cli

version	toolchain
1.8.9	system

WebKitGTK+

WebKitGTK+ is a full-featured port of the WebKit rendering engine, suitable for projects requiring any kind of web integration, from hybrid HTML/CSS applications to full-fledged web browsers. It offers WebKit's full functionality and is useful in a wide range of systems from desktop computers to embedded systems like phones, tablets, and televisions.

homepage: https://webkitgtk.org/

version	toolchain
2.24.1	GCC/8.2.0-2.31.1
2.27.4	GCC/10.3.0, GCC/8.3.0
2.37.1	GCC/11.2.0
2.40.4	GCC/11.3.0

WebSocket++

WebSocket++ is an open source (BSD license) header only C++ library that implements RFC6455 The WebSocket Protocol.

homepage: https://www.zaphoyd.com/websocketpp/

version	toolchain
0.8.1	gompi/2019a

WEKA

Weka is a collection of machine learning algorithms for data mining tasks. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization. It is also well-suited for developing new machine learning schemes.

homepage: http://www.cs.waikato.ac.nz/ml/weka/index.html

version	versionsuffix	toolchain
3.6.12	-Java-1.7.0_80	system
3.7.0	-Java-1.7.0_80	system

WFA2

The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process.

homepage: https://github.com/smarco/WFA2-lib

version	toolchain
2.3.3	GCCcore/11.3.0
2.3.4	GCCcore/12.3.0

wget

GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non-interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.

homepage: https://www.gnu.org/software/wget

version	toolchain
1.17.1	foss/2016a, foss/2016b
1.19.4	GCCcore/6.4.0
1.20.1	GCCcore/7.3.0, GCCcore/8.3.0
1.20.3	GCCcore/10.2.0, GCCcore/9.3.0
1.21.1	GCCcore/10.3.0
1.21.2	GCCcore/11.2.0
1.21.3	GCCcore/11.3.0
1.21.4	GCCcore/13.2.0

wgsim

Wgsim is a small tool for simulating sequence reads from a reference genome.

homepage: https://github.com/lh3/wgsim/

version	toolchain
20111017	GCC/10.2.0, GCC/11.2.0

WHAM

An implementation of WHAM: the Weighted Histogram Analysis Method

homepage: http://membrane.urmc.rochester.edu/?page_id=126

version	versionsuffix	toolchain
2.0.9.1		intel/2019a
2.0.9.1	-kj_mol	intel/2019a
2.0.10.2		intel/2020a
2.0.10.2	-kj_mol	intel/2020a

WhatsHap

WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads.

homepage: https://whatshap.readthedocs.io

version	toolchain
1.1	foss/2020b, foss/2021a
1.4	foss/2021b
1.7	foss/2022a
2.1	foss/2022b
2.2	foss/2023a

wheel

A built-package format for Python.

homepage: https://pypi.python.org/pypi/wheel

version	versionsuffix	toolchain
0.29.0	-Python-2.7.11	foss/2016a
0.29.0	-Python-3.5.1	foss/2016a
0.30.0	-Python-2.7.14	foss/2017b, fosscuda/2017b, intel/2017b, intelcuda/2017b
0.30.0	-Python-3.6.3	foss/2017b, fosscuda/2017b, intel/2017b, intelcuda/2017b
0.30.0	-Python-3.6.4	foss/2018a, intel/2018a
0.31.0	-Python-2.7.14	fosscuda/2018a, intel/2018a
0.31.0	-Python-3.6.4	foss/2018a, fosscuda/2018a
0.31.1	-Python-2.7.15	fosscuda/2018b
0.31.1	-Python-3.6.6	foss/2018b, fosscuda/2018b

WIEN2k

The program package WIEN2k allows to perform electronic structure calculations of solids using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave ((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. WIEN2k is an all-electron scheme including relativistic effects and has many features.

homepage: http://www.wien2k.at/

version	toolchain
17.1	foss/2018a, gimkl/2017a, intel/2018a
18.1	foss/2018a, gimkl/2017a, intel/2018a
19.1	intel/2019a
19.2	intel/2020b
21.1	intel/2021a, intel/2021b
23.2	intel/2021b

WildMagic

Wild Magic 5.17

homepage: https://www.geometrictools.com/index.html

version	toolchain
5.17	GCCcore/10.3.0, foss/2018b

Winnowmap

Winnowmap is a long-read mapping algorithm, and a result of our exploration into superior minimizer sampling techniques.

homepage: https://github.com/marbl/Winnowmap

version	toolchain
1.0	GCC/8.3.0

WisecondorX

WisecondorX -- an evolved WISECONDOR

homepage: https://github.com/CenterForMedicalGeneticsGhent/WisecondorX

version	versionsuffix	toolchain
1.1.6	-Python-3.8.2	foss/2020a

WISExome

A within-sample comparison approach to detect copy number variations in whole exome sequencing data

homepage: https://github.com/VUmcCGP/wisexome

version	versionsuffix	toolchain
20180517	-Python-2.7.14	intel/2018a

wkhtmltopdf

wkhtmltopdf and wkhtmltoimage are open source (LGPLv3) command line tools to render HTML into PDF and various image formats using the Qt WebKit rendering engine. These run entirely headless and do not require a display or display service.

homepage: http://wkhtmltopdf.org/

version	versionsuffix	toolchain
0.12.3	-Linux-x86_64	system

worker

The Worker framework has been developed to help deal with parameter exploration experiments that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.

homepage: https://github.com/gjbex/worker

version	versionsuffix	toolchain
1.6.4		intel/2016a
1.6.5		intel/2016a
1.6.6		intel/2016b
1.6.7	-intel-2016b	system
1.6.7	-intel-2017a	system
1.6.7	-intel-2017b	system
1.6.8	-intel-2018a	system
1.6.8	-intel-2018b	system
1.6.11		intel/2019b
1.6.12		foss/2019a, foss/2021b
1.6.13		iimpi/2021b, iimpi/2022b

wpebackend-fdo

WPE WebKit allows embedders to create simple and performant systems based on Web platform technologies. It is a WebKit port designed with flexibility and hardware acceleration in mind, leveraging common 3D graphics APIs for best performance.

homepage: https://wpewebkit.org/

version	toolchain
1.13.1	GCCcore/11.2.0
1.14.1	GCCcore/11.3.0

WPS

WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs.

homepage: http://www.wrf-model.org

version	versionsuffix	toolchain
3.8.0	-dmpar	intel/2016a
3.9.1	-dmpar	foss/2020b
4.0.1	-dmpar	intel/2018b
4.0.2	-dmpar	foss/2018b
4.1	-dmpar	intel/2019b
4.2	-dmpar	foss/2020b
4.3.1	-dmpar	foss/2021a
4.4	-dmpar	foss/2022a

wrapt

The aim of the wrapt module is to provide a transparent object proxy for Python, which can be used as the basis for the construction of function wrappers and decorator functions.

homepage: https://pypi.org/project/wrapt/

version	toolchain
1.15.0	foss/2022a, gfbf/2022b, gfbf/2023a, intel/2022a

WRF

The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs.

homepage: https://www.wrf-model.org

version	versionsuffix	toolchain
3.8.0	-dmpar	intel/2016a, intel/2016b
3.9.1.1	-dmpar	foss/2020a, foss/2020b, intel/2020a, intel/2020b
4.0.1	-dmpar	intel/2018b
4.0.2	-dmpar	foss/2018b
4.1.3	-dm+sm	intel/2019b
4.1.3	-dmpar	foss/2019b, foss/2020a, intel/2019b
4.2.2	-dmpar	foss/2020b
4.3	-dmpar	foss/2021a
4.4	-dmpar	foss/2022a
4.4.1	-dmpar	foss/2022b

WRF-Fire

WRF-Fire combines the Weather Research and Forecasting model (WRF) with a fire code implementing a surface fire behavior model, called SFIRE, based on semi-empirical formulas calculate the rate of spread of the fire line (the interface between burning and unignited fuel) based on fuel properties, wind velocities from WRF, and terrain slope. The fire spread is implemented by the level set method.

homepage: http://www.openwfm.org/wiki/WRF-SFIRE

version	versionsuffix	toolchain
20170221	-dmpar	intel/2016b

wrf-python

A collection of diagnostic and interpolation routines for use with output from the Weather Research and Forecasting (WRF-ARW) Model.

homepage: https://wrf-python.readthedocs.io

version	versionsuffix	toolchain
1.2.0	-Python-3.6.4	intel/2018a
1.3.1	-Python-3.6.6	intel/2018b
1.3.4.1		foss/2023a

WSClean

WSClean (w-stacking clean) is a fast generic widefield imager. It implements several gridding algorithms and offers fully-automated multi-scale multi-frequency deconvolution.

homepage: https://wsclean.readthedocs.io/

version	toolchain
3.4	foss/2022a, foss/2023b

wtdbg2

Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output.

homepage: https://github.com/ruanjue/wtdbg2

version	toolchain
2.3	GCC/7.3.0-2.30
2.5	GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/9.3.0

wxPropertyGrid

wxPropertyGrid is a property sheet control for wxWidgets. In other words, it is a specialized two-column grid for editing properties such as strings, numbers, flagsets, string arrays, and colours.

homepage: http://wxpropgrid.sourceforge.net/

version	toolchain
1.4.15	GCC/4.9.2

wxPython

Wraps the wxWidgets C++ toolkit and provides access to the user interface portions of the wxWidgets API, enabling Python applications to have a native GUI on Windows, Macs or Unix systems, with a native look and feel and requiring very little (if any) platform specific code.

homepage: https://www.wxpython.org/

version	versionsuffix	toolchain
3.0.2.0	-Python-2.7.11	foss/2016a, intel/2016a
3.0.2.0	-Python-2.7.12	intel/2016b
3.0.2.0	-Python-2.7.13	intel/2017a
3.0.2.0	-Python-2.7.14	intel/2017b
3.0.2.0	-Python-2.7.15	foss/2018b
4.0.4	-Python-2.7.15	GCC/8.2.0-2.31.1
4.0.4	-Python-3.7.2	GCC/8.2.0-2.31.1
4.0.7.post2	-Python-3.7.4	GCC/8.3.0
4.1.1		foss/2021a
4.2.0		foss/2021b
4.2.1		foss/2022a

wxWidgets

wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux and other platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform's native API rather than emulating the GUI.

homepage: https://www.wxwidgets.org

version	toolchain
3.0.3	foss/2018a
3.0.4	GCC/8.2.0-2.31.1
3.1.3	GCC/8.3.0
3.1.4	GCC/10.2.0
3.1.5	GCC/10.3.0, GCC/11.2.0
3.2.0	GCC/11.2.0
3.2.1	GCC/11.3.0
3.2.2.1	GCC/12.2.0, GCC/12.3.0

X

X11 - x13as - x264 - x265 - XALT - xarray - XBeach - xbitmaps - xcb-proto - xcb-util - xcb-util-image - xcb-util-keysyms - xcb-util-renderutil - xcb-util-wm - xCell - XCFun - xclip - XCrySDen - xdotool - Xerces-C++ - xESMF - xextproto - xf86vidmodeproto - XGBoost - XGrafix - xineramaproto - XKeyboardConfig - XlsxWriter - XMDS2 - Xmipp - xmitgcm - XML-Compile - XML-LibXML - XML-Parser - xmlf90 - XMLSec - XMLStarlet - xonsh - XOOPIC - xorg-macros - xpdf - XPLOR-NIH - xprop - xproto - XSD - XTandem - xtb - xtensor - xtrans - Xvfb - xxd - xxHash - XZ

X11

The X Window System (X11) is a windowing system for bitmap displays

homepage: https://www.x.org

version	toolchain
20160819	GCCcore/5.4.0, foss/2016b, intel/2016b
20170129	GCCcore/6.3.0, gimkl/2017a
20170314	GCCcore/6.3.0
20171023	GCCcore/6.4.0
20180131	GCCcore/6.4.0
20180604	GCCcore/7.3.0
20190311	GCCcore/8.2.0
20190717	GCCcore/8.3.0
20200222	GCCcore/9.3.0
20201008	GCCcore/10.2.0
20210518	GCCcore/10.3.0
20210802	GCCcore/11.2.0
20220504	GCCcore/11.3.0
20221110	GCCcore/12.2.0
20230603	GCCcore/12.3.0
20231019	GCCcore/13.2.0

x13as

X-13ARIMA-SEATS is seasonal adjustment software produced, distributed, and maintained by the Census Bureau. Features of X-13ARIMA-SEATS include: - Extensive time series modeling and model selection capabilities for linear regression models with ARIMA errors (regARIMA models); - The capability to generate ARIMA model-based seasonal adjustment using a version of the SEATS software originally developed by Victor Gómez and Agustín Maravall at the Bank of Spain, as well as nonparametric adjustments from the X-11 procedure; - Diagnostics of the quality and stability of the adjustments achieved under the options selected; - The ability to efficiently process many series at once.

homepage: https://www.census.gov/data/software/x13as.About_X-13.html

version	toolchain
1-1-b59	GCCcore/10.2.0, GCCcore/11.2.0

x264

x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL.

homepage: https://www.videolan.org/developers/x264.html

version	toolchain
20160114	gimkl/2.11.5, intel/2016a
20160430	foss/2016a, intel/2016a
20160614	foss/2016b, intel/2016b
20170406	gimkl/2017a
20170721	GCCcore/6.4.0
20170913	intel/2017a
20171217	foss/2017b, intel/2017b
20180128	GCCcore/6.4.0
20180325	GCCcore/6.4.0
20181203	GCCcore/7.3.0
20190413	GCCcore/8.2.0
20190925	GCCcore/8.3.0
20191217	GCCcore/9.3.0
20201026	GCCcore/10.2.0
20210414	GCCcore/10.3.0
20210613	GCCcore/11.2.0
20220620	GCCcore/11.3.0
20230226	GCCcore/12.2.0, GCCcore/12.3.0
20231019	GCCcore/13.2.0

x265

x265 is a free software library and application for encoding video streams into the H.265 AVC compression format, and is released under the terms of the GNU GPL.

homepage: https://x265.org/

version	toolchain
2.4	foss/2016b
2.5	intel/2017a
2.6	GCCcore/6.4.0, intel/2017b
2.7	GCCcore/6.4.0
2.9	GCCcore/7.3.0
3.0	GCCcore/8.2.0
3.2	GCCcore/8.3.0
3.3	GCCcore/10.2.0, GCCcore/9.3.0
3.5	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0

XALT

XALT 2 is a tool to allow a site to track user executables and library usage on a cluster. When installed it can tell a site what are the top executables by Node-Hours or by the number of users or the number of times it is run. XALT 2 also tracks library usage as well. XALT 2 can also track package use by R, MATLAB or Python. It tracks both MPI and non-MPI programs.

homepage: https://github.com/xalt/xalt

version	toolchain
2.8.4	system

xarray

xarray (formerly xray) is an open source project and Python package that aims to bring the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the core pandas data structures.

homepage: https://github.com/pydata/xarray

version	versionsuffix	toolchain
0.9.5	-Python-2.7.13	intel/2017a
0.9.5	-Python-3.6.1	intel/2017a
0.9.6	-Python-2.7.13	intel/2017a
0.10.0	-Python-2.7.14	intel/2017b
0.10.0	-Python-3.6.3	intel/2017b
0.10.3	-Python-3.6.4	intel/2018a
0.10.4	-Python-3.6.4	intel/2018a
0.10.8	-Python-3.6.4	intel/2018a
0.12.1	-Python-3.6.6	foss/2018b, intel/2018b
0.13.0	-Python-3.7.2	intel/2019a
0.15.1	-Python-3.7.4	foss/2019b, intel/2019b
0.16.1	-Python-3.8.2	foss/2020a, intel/2020a
0.16.2		foss/2020b, fosscuda/2020b, intel/2020b
0.19.0		foss/2021a
0.20.1		foss/2021b, intel/2021b
2022.6.0		foss/2022a, intel/2022a
2022.9.0		foss/2022a
2023.4.2		gfbf/2022b
2023.9.0		gfbf/2023a

XBeach

XBeach is a two-dimensional model for wave propagation, long waves and mean flow, sediment transport and morphological changes of the nearshore area, beaches, dunes and backbarrier during storms.

homepage: https://oss.deltares.nl/web/xbeach

version	toolchain
20230831	gompi/2022a

xbitmaps

provides bitmaps for x

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.1.1	foss/2016a, intel/2016a, system
1.1.2	system

xcb-proto

The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.

homepage: https://xcb.freedesktop.org/

version	toolchain
1.11	system
1.13	system

xcb-util

The xcb-util package provides additional extensions to the XCB library, many that were previously found in Xlib, but are not part of core X protocol

homepage: http://xcb.freedesktop.org/

version	toolchain
0.4.0	foss/2016a, intel/2016a

xcb-util-image

The xcb-util-image package provides additional extensions to the XCB library.

homepage: http://xcb.freedesktop.org/

version	toolchain
0.4.0	foss/2016a, intel/2016a

xcb-util-keysyms

The xcb-util-keysyms package contains a library for handling standard X key constants and conversion to/from keycodes.

homepage: http://xcb.freedesktop.org/

version	toolchain
0.4.0	foss/2016a, intel/2016a

xcb-util-renderutil

The xcb-util-renderutil package provides additional extensions to the XCB library.

homepage: http://xcb.freedesktop.org/

version	toolchain
0.3.9	foss/2016a, intel/2016a

xcb-util-wm

The xcb-util-wm package contains libraries which provide client and window-manager helpers for EWMH and ICCCM.

homepage: http://xcb.freedesktop.org/

version	toolchain
0.4.1	foss/2016a, intel/2016a

xCell

xCell is a gene signatures-based method learned from thousands of pure cell types from various sources.

homepage: https://github.com/dviraran/xCell

version	versionsuffix	toolchain
1.12	-R-3.5.1	foss/2018b

XCFun

XCFun is a library of DFT exchange-correlation (XC) functionals. It is based on automatic differentiation and can therefore generate arbitrary order derivatives of these functionals.

homepage: http://dftlibs.org/xcfun/

version	versionsuffix	toolchain
2.1.0		GCCcore/9.3.0
2.1.1		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.3.0, GCCcore/12.2.0
20180122	-Python-2.7.14	intel/2017b
20190127	-Python-3.7.2	foss/2019a

xclip

xclip is a command line utility that is designed to run on any system with an X11 implementation.

homepage: https://github.com/astrand/xclip

version	toolchain
0.13	GCCcore/11.3.0

XCrySDen

XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. It also possesses some tools for analysis of properties in reciprocal space such as interactive selection of k-paths in the Brillouin zone for the band-structure plots, and visualisation of Fermi surfaces.

homepage: http://www.xcrysden.org/

version	toolchain
1.5.60	intel/2019a
1.6.2	foss/2019b, foss/2020b, foss/2022a, intel/2019b, intel/2021b, intel/2022a

xdotool

xdotool lets you simulate keyboard input and mouse activity, move and resize windows, etc. It does this using X11’s XTEST extension and other Xlib functions.

homepage: https://github.com/jordansissel/xdotool

version	toolchain
3.20211022.1	GCCcore/11.3.0

Xerces-C++

Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs.

homepage: https://xerces.apache.org/xerces-c/

version	toolchain
3.1.4	GCCcore/6.4.0
3.2.0	GCCcore/7.3.0
3.2.2	GCCcore/8.2.0, GCCcore/8.3.0
3.2.3	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/9.3.0
3.2.4	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0
3.2.5	GCCcore/13.2.0

xESMF

xESMF: Universal Regridder for Geospatial Data

homepage: https://xesmf.readthedocs.io

version	versionsuffix	toolchain
0.3.0		intel/2020b
0.3.0	-Python-3.8.2	foss/2020a

xextproto

XExtProto protocol headers.

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
7.3.0	foss/2016a, gimkl/2.11.5, intel/2016a, intel/2017b

xf86vidmodeproto

X11 XFree86 video mode extension protocol headers.

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
2.3.1	foss/2016a, intel/2016a

XGBoost

XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, flexible and portable.

homepage: https://github.com/dmlc/xgboost

version	versionsuffix	toolchain
0.6a2	-Python-2.7.12	intel/2016b
0.6a2	-Python-3.5.2	intel/2016b
0.6a2	-Python-3.6.1	intel/2017a
0.72.1	-Python-2.7.14	intel/2017b
0.90	-Python-3.7.4	foss/2019b
1.2.0	-Python-3.8.2	foss/2020a
1.5.0		foss/2021a
1.7.1		foss/2022a
1.7.2		foss/2022a
1.7.2	-CUDA-11.7.0	foss/2022a
2.0.2		gfbf/2023a
20171120	-Java-1.8.0_152	intel/2017b

XGrafix

A graphics library and controller for physics simulation programs. 3-d surface plots, scatter plots, 2-d line plots.

homepage: https://ptsg.egr.msu.edu/

version	toolchain
2.41	GCCcore/9.3.0

xineramaproto

X protocol and ancillary headers for xinerama

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.2.1	foss/2016a, intel/2016a

XKeyboardConfig

The non-arch keyboard configuration database for X Window. The goal is to provide the consistent, well-structured, frequently released open source of X keyboard configuration data for X Window System implementations (free, open source and commercial). The project is targeted to XKB-based systems.

homepage: http://www.freedesktop.org/wiki/Software/XKeyboardConfig/

version	toolchain
2.17	foss/2016a, intel/2016a

XlsxWriter

A Python module for creating Excel XLSX files

homepage: https://xlsxwriter.readthedocs.io/

version	toolchain
1.4.0	GCCcore/10.2.0
1.4.4	GCCcore/10.3.0
3.0.2	GCCcore/11.2.0
3.0.8	GCCcore/11.3.0
3.1.2	GCCcore/12.2.0
3.1.3	GCCcore/12.3.0
3.1.9	GCCcore/13.2.0

XMDS2

The purpose of XMDS2 is to simplify the process of creating simulations that solve systems of initial-value first-order partial and ordinary differential equations.

homepage: http://www.xmds.org/

version	versionsuffix	toolchain
2.2.3	-Python-2.7.15	foss/2018b

Xmipp

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents an unified interface for both biologists and developers. Scipion allows to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on.

homepage: https://github.com/I2PC/scipion/wiki

version	versionsuffix	toolchain
3.19.04-Apollo	-Python-2.7.15	foss/2019a, fosscuda/2019a
3.22.07-Helios		foss/2022a
3.22.07-Helios	-CUDA-11.7.0	foss/2022a

xmitgcm

xmitgcm is a python package for reading MITgcm binary MDS files into xarray data structures. By storing data in dask arrays, xmitgcm enables parallel, out-of-core analysis of MITgcm output data.

homepage: https://github.com/MITgcm/xmitgcm

version	toolchain
0.5.2	foss/2022a

XML-Compile

Perl module for compilation based XML processing

homepage: https://metacpan.org/pod/XML::Compile

version	toolchain
1.63	GCCcore/11.2.0, GCCcore/12.2.0

XML-LibXML

Perl binding for libxml2

homepage: https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod

version	versionsuffix	toolchain
2.0132	-Perl-5.24.0	foss/2016b, intel/2016b
2.0132	-Perl-5.24.1	intel/2017a
2.0132	-Perl-5.26.0	foss/2017b, intel/2017b
2.0132	-Perl-5.26.1	GCCcore/6.4.0
2.0132	-Perl-5.28.0	GCCcore/7.3.0
2.0200	-Perl-5.28.1	GCCcore/8.2.0
2.0201		GCCcore/8.3.0
2.0205		GCCcore/9.3.0
2.0206		GCCcore/10.2.0
2.0207		GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0
2.0208		GCCcore/12.2.0
2.0209		GCCcore/12.3.0

XML-Parser

This is a Perl extension interface to James Clark's XML parser, expat.

homepage: https://search.cpan.org/~toddr/XML-Parser-2.46/

version	versionsuffix	toolchain
2.41	-Perl-5.20.3	intel/2016a
2.44	-Perl-5.22.1	foss/2016a, intel/2016a
2.44_01	-Perl-5.24.0	GCCcore/4.9.3, GCCcore/5.4.0, foss/2016b, gimkl/2017a, intel/2016b
2.44_01	-Perl-5.24.1	GCCcore/6.3.0, intel/2017a
2.44_01	-Perl-5.26.0	GCCcore/6.4.0
2.44_01	-Perl-5.26.1	GCCcore/6.4.0
2.44_01	-Perl-5.28.0	GCCcore/7.3.0
2.46	-Perl-5.32.1	GCCcore/10.3.0
2.46	-Perl-5.34.1	GCCcore/11.3.0
2.46	-Perl-5.36.1	GCCcore/12.3.0

xmlf90

A fast XML parser and generator in Fortran

homepage: https://gitlab.com/siesta-project/libraries/xmlf90

version	toolchain
1.5.3	foss/2016b, foss/2017a
1.5.4	GCC/10.2.0, GCC/10.3.0, GCC/11.2.0, iccifort/2019.5.281, iccifort/2020.4.304, intel-compilers/2021.2.0, intel-compilers/2021.4.0
1.5.6	GCC/11.3.0

XMLSec

XML Security Library is a C library based on LibXML2, supporting major XML security standards.

homepage: https://www.aleksey.com/xmlsec/index.html

version	toolchain
1.2.26	GCCcore/6.4.0

XMLStarlet

Command line XML tool

homepage: http://xmlstar.sourceforge.net

version	toolchain
1.6.1	GCCcore/6.4.0, foss/2016a

xonsh

Xonsh is a Python-ish, BASHwards-looking shell language and command prompt.

homepage: https://xon.sh/

version	toolchain
0.3.2	intel/2016a

XOOPIC

XOOPIC is a two-dimensional 3-velocity particle-in-cell simulator. It can handle electrostatic and electromagnetic models, has a large variety of boundary conditions, supports multiple gasses and gas chemistry, and is easily reconfigurable via an input file.

homepage: https://github.com/rinku-mishra/xoopic

version	toolchain
20210302	foss/2020a

xorg-macros

X.org macros utilities.

homepage: https://gitlab.freedesktop.org/xorg/util/macros

version	toolchain
1.19.0	foss/2016a, foss/2016b, gimkl/2.11.5, intel/2016a, intel/2016b
1.19.1	GCCcore/6.3.0, GCCcore/6.4.0
1.19.2	GCCcore/10.2.0, GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.2.0, GCCcore/9.3.0
1.19.3	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0
1.20.0	GCCcore/12.3.0, GCCcore/13.2.0

xpdf

Xpdf was first released in 1995. It was written, and is still developed, by Derek Noonburg. Xpdf is a free PDF viewer and toolkit, including a text extractor, image converter, HTML converter, and more. Most of the tools are available as open source.

homepage: https://www.xpdfreader.com/

version	toolchain
4.04	GCCcore/12.3.0

XPLOR-NIH

A System for X-ray Crystallography and NMR

homepage: https://nmr.cit.nih.gov/xplor-nih/

version	versionsuffix	toolchain
3.4	-Linux_x86_64	system

xprop

The xprop utility is for displaying window and font properties in an X server. One window or font is selected using the command line arguments or possibly in the case of a window, by clicking on the desired window. A list of properties is then given, possibly with formatting information.

homepage: https://www.x.org/wiki/

version	versionsuffix	toolchain
1.2.2		GCCcore/5.4.0, GCCcore/6.4.0, foss/2016a, foss/2016b, intel/2016a, intel/2016b, intel/2017a
1.2.2	-X11-20180131	GCCcore/6.4.0
1.2.3		GCCcore/7.3.0
1.2.4		GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
1.2.5		GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0
1.2.6		GCCcore/12.3.0

xproto

X protocol and ancillary headers

homepage: https://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
7.0.28	foss/2016a, gimkl/2.11.5, intel/2016a
7.0.29	intel/2016a
7.0.31	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.3.0, GCCcore/13.2.0, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.3.0, GCCcore/9.3.0

XSD

CodeSynthesis XSD is an open-source, cross-platform W3C XML Schema to C++ data binding compiler.

homepage: https://www.codesynthesis.com/products/xsd/

version	toolchain
4.0.0	GCCcore/8.2.0

XTandem

X!Tandem open source is software that can match tandem mass spectra with peptide sequences, in a process that has come to be known as protein identification.

homepage: https://www.thegpm.org/tandem

version	toolchain
17.02.01.4	GCC/6.4.0-2.28, iccifort/2017.4.196-GCC-6.4.0-2.28

xtb

xtb - An extended tight-binding semi-empirical program package.

homepage: https://xtb-docs.readthedocs.io

version	versionsuffix	toolchain
6.2.2-hotfix	-Python-3.6.3	intel/2017b
6.2.3		foss/2019b
6.4.1		foss/2021b, intel/2021a
6.5.0		foss/2021b
6.5.1		foss/2022a
6.6.0		foss/2022a, intel/2022a
6.6.1		gfbf/2023a

xtensor

xtensor is a C++ library meant for numerical analysis with multi-dimensional array expressions.

homepage: https://github.com/xtensor-stack/xtensor

version	toolchain
0.24.0	foss/2021b

xtrans

xtrans includes a number of routines to make X implementations transport-independent; at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet.

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.3.5	GCCcore/11.3.0, foss/2016a, gimkl/2.11.5, intel/2016a

Xvfb

Xvfb is an X server that can run on machines with no display hardware and no physical input devices. It emulates a dumb framebuffer using virtual memory.

homepage: https://www.x.org/releases/X11R7.6/doc/man/man1/Xvfb.1.xhtml

version	toolchain
1.20.8	GCCcore/8.2.0, GCCcore/8.3.0
1.20.9	GCCcore/10.2.0, GCCcore/9.3.0
1.20.11	GCCcore/10.3.0
1.20.13	GCCcore/11.2.0
21.1.3	GCCcore/11.3.0
21.1.6	GCCcore/12.2.0
21.1.8	GCCcore/12.3.0
21.1.9	GCCcore/13.2.0

xxd

xxd is part of the VIM package and this will only install xxd, not vim! xxd converts to/from hexdumps of binary files.

homepage: https://www.vim.org

version	toolchain
8.2.4220	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0
9.0.1696	GCCcore/12.2.0
9.0.2112	GCCcore/12.3.0

xxHash

xxHash is an extremely fast non-cryptographic hash algorithm, working at RAM speed limit.

homepage: https://cyan4973.github.io/xxHash

version	toolchain
0.8.0	GCCcore/11.2.0
0.8.1	GCCcore/10.2.0, GCCcore/11.3.0, GCCcore/12.2.0
0.8.2	GCCcore/12.3.0

XZ

xz: XZ utilities

homepage: https://tukaani.org/xz/

version	versionsuffix	toolchain
5.0.5		GCC/4.8.2
5.2.0		GCC/4.9.2
5.2.2		GCC/4.9.2, GCC/5.4.0-2.26, GCCcore/4.9.3, GCCcore/5.4.0, foss/2016.04, foss/2016a, foss/2016b, intel/2016a, intel/2016b
5.2.2	-gettext-0.19.7	foss/2016a, intel/2016a
5.2.3		GCCcore/6.3.0, GCCcore/6.4.0, gimkl/2017a
5.2.4		GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.2.0
5.2.5		GCCcore/10.1.0, GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/9.3.0
5.2.7		GCCcore/12.2.0
5.4.2		GCCcore/12.3.0, GCCcore/13.1.0
5.4.4		GCCcore/13.2.0

Y

YACS - Yade - yaff - Yambo - yaml-cpp - YANK - YAPS - Yasm - YAXT - Yices - YODA - yt

YACS

YACS was created as a lightweight library to define and manage system configurations, such as those commonly found in software designed for scientific experimentation. These "configurations" typically cover concepts like hyperparameters used in training a machine learning model or configurable model hyperparameters, such as the depth of a convolutional neural network.

homepage: https://github.com/rbgirshick/yacs

version	toolchain
0.1.8	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/8.3.0

Yade

Yade is an extensible open-source framework for discrete numerical models, focused on Discrete Element Method. The computation parts are written in c++ using flexible object model, allowing independent implementation of new alogrithms and interfaces. Python is used for rapid and concise scene construction, simulation control, postprocessing and debugging.

homepage: https://yade-dem.org/doc/

version	versionsuffix	toolchain
1.20.0	-Python-2.7.11	foss/2016a, intel/2016a
2016.06a	-Python-2.7.12	foss/2016b, intel/2016b
2017.01a	-Python-2.7.12	intel/2016b
2018.02b	-Python-2.7.14	intel/2018a

yaff

Yaff stands for 'Yet another force field'. It is a pythonic force-field code.

homepage: https://molmod.github.io/yaff/

version	versionsuffix	toolchain
1.0.develop.2.15	-Python-2.7.12-HDF5-1.8.18	intel/2016b
1.1.2	-Python-2.7.13	intel/2017a
1.1.3	-Python-2.7.13	intel/2017a
1.4.2	-Python-2.7.14	foss/2018a, intel/2017b, intel/2018a
1.4.2	-Python-3.6.3	intel/2017b
1.4.5	-Python-2.7.15	intel/2018b
1.5.0	-Python-2.7.15	intel/2018b
1.5.0	-Python-3.7.2	intel/2019a
1.6.0		foss/2020b, foss/2023a
1.6.0	-Python-3.7.2	intel/2019a
1.6.0	-Python-3.7.4	foss/2019b, intel/2019b
1.6.0	-Python-3.8.2	foss/2020a, intel/2020a

Yambo

Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf.

homepage: http://www.yambo-code.org

version	toolchain
3.4.2	intel/2016.02-GCC-4.9
5.0.4	intel/2021a
5.1.2	intel/2021b

yaml-cpp

yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec

homepage: https://github.com/jbeder/yaml-cpp

version	toolchain
0.6.3	GCCcore/8.3.0
0.7.0	GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0

YANK

A GPU-accelerated Python framework for exploring algorithms for alchemical free energy calculations

homepage: http://getyank.org/

version	versionsuffix	toolchain
0.25.2	-Python-3.8.2	intel/2020a

YAPS

YAPS - Yet Another Positioning Solver

homepage: https://github.com/baktoft/yaps

version	versionsuffix	toolchain
1.1.0	-R-3.5.1	foss/2018b
1.1.0	-R-3.6.0	intel/2019a

Yasm

Yasm: Complete rewrite of the NASM assembler with BSD license

homepage: http://www.tortall.net/projects/yasm/

version	toolchain
1.3.0	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0, foss/2016a, foss/2016b, foss/2017a, gimkl/2.11.5, gimkl/2017a, intel/2016a, intel/2016b, intel/2017a

YAXT

Yet Another eXchange Tool

homepage: https://www.dkrz.de/redmine/projects/yaxt

version	toolchain
0.5.1	intel/2016b, intel/2017a, intel/2017b
0.6.0	intel/2018a, intel/2018b, iomkl/2018b
0.6.2	foss/2018b, gompi/2019b, iimpi/2019b
0.9.0	gompi/2020b
0.9.1	gompi/2021a
0.9.2	iimpi/2021b
0.9.2.1	gompi/2021b
0.10.0	gompi/2022b

Yices

Yices 2 is an SMT solver that decides the satisfiability of formulas containing uninterpreted function symbols with equality, real and integer arithmetic, bitvectors, scalar types, and tuples. Yices 2 supports both linear and nonlinear arithmetic.

homepage: https://yices.csl.sri.com/index.html

version	toolchain
2.6.2	GCCcore/10.2.0
2.6.4	GCCcore/12.2.0

YODA

Yet more Objects for (High Energy Physics) Data Analysis

homepage: https://yoda.hepforge.org/

version	toolchain
1.9.7	GCC/11.3.0
1.9.9	GCC/12.3.0

yt

yt is an open-source, permissively-licensed python package for analyzing and visualizing volumetric data.

homepage: https://yt-project.org

version	toolchain
4.3.0	foss/2022a

Z

Z3 - zarr - Zeo++ - ZeroMQ - zeus-mcmc - zfp - Zgoubi - ZIMPL - zingeR - Zip - zlib - zlib-ng - zlibbioc - Zopfli - ZPAQ - zsh - zstd - zUMIs

Z3

Z3 is a theorem prover from Microsoft Research.

homepage: https://github.com/Z3Prover/z3

version	versionsuffix	toolchain
4.8.9		GCCcore/8.3.0, GCCcore/9.3.0
4.8.10		GCCcore/10.2.0
4.8.10	-Python-3.8.6	GCCcore/10.2.0
4.8.11		GCCcore/10.3.0
4.8.11	-Python-3.9.5	GCCcore/10.3.0
4.8.12		GCCcore/11.2.0
4.8.12	-Python-3.9.6	GCCcore/11.2.0
4.8.16		GCCcore/11.3.0
4.8.16	-Python-3.10.4	GCCcore/11.3.0
4.10.2		GCCcore/11.3.0
4.10.2	-Python-3.10.4	GCCcore/11.3.0
4.12.2		GCCcore/12.2.0, GCCcore/12.3.0
4.12.2	-Python-3.10.8	GCCcore/12.2.0
4.13.0		GCCcore/13.2.0

zarr

Zarr is a Python package providing an implementation of compressed, chunked, N-dimensional arrays, designed for use in parallel computing.

homepage: https://zarr.readthedocs.io/en/stable/

version	versionsuffix	toolchain
2.1.4	-Python-2.7.13	foss/2017a
2.4.0	-Python-3.8.2	foss/2020a
2.8.1		foss/2020b
2.10.1		foss/2021a
2.13.3		foss/2021b, foss/2022a
2.16.0		foss/2022b

Zeo++

Zeo++ is a software package for analysis of crystalline porous materials. Zeo++ can be used to perform geometry-based analysis of structure and topology of the void space inside a material, to assemble or alternate structures as well as to generate structure representations to be used in structure similarity calculations. Zeo++ can be used to either analyze a single structure or perform high-throughput analysis of a large database.

homepage: https://www.zeoplusplus.org/

version	toolchain
0.3	intel-compilers/2023.1.0

ZeroMQ

ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems.

homepage: https://www.zeromq.org/

version	toolchain
4.1.4	foss/2016a, intel/2016a
4.1.5	intel/2016b
4.2.0	foss/2016b, intel/2016b
4.2.2	foss/2017a, foss/2017b, fosscuda/2017b, intel/2017a, intel/2017b, intelcuda/2017b
4.2.5	foss/2018a, foss/2018b, fosscuda/2018b, intel/2018a, intel/2018b
4.3.2	GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
4.3.3	GCCcore/10.2.0
4.3.4	GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0
4.3.5	GCCcore/13.2.0

zeus-mcmc

Zeus is a Python implementation of the Ensemble Slice Sampling method.

homepage: https://zeus-mcmc.readthedocs.io

version	toolchain
2.5.4	foss/2022a

zfp

zfp is a compressed format for representing multidimensional floating-point and integer arrays. zfp provides compressed-array classes that support high throughput read and write random access to individual array elements. zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications that read and write large data sets to and from disk.

homepage: https://github.com/LLNL/zfp

version	toolchain
0.5.5	GCCcore/10.2.0
1.0.0	GCCcore/10.3.0, GCCcore/11.3.0, GCCcore/9.3.0

Zgoubi

Zgoubi is a ray-tracing code in use for charged particle beam dynamics simulations. It can simulate beam dynamics in a large variety of machines and optical systems.

homepage: https://zgoubi.sourceforge.io

version	toolchain
6.0.2	GCCcore/10.3.0

ZIMPL

ZIMPL is a little language to translate the mathematical model of a problem into a linear or nonlinear (mixed-) integer mathematical program expressed in .lp or .mps file format which can be read and (hopefully) solved by a LP or MIP solver.

homepage: https://zimpl.zib.de/

version	toolchain
3.3.4	GCCcore/11.3.0

zingeR

Zero-Inflated Negative binomial Gene Expression in R

homepage: https://github.com/statOmics/zingeR

version	versionsuffix	toolchain
20180131	-R-3.5.1	foss/2018b

Zip

Zip is a compression and file packaging/archive utility. Although highly compatible both with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives have been portability and other-than-MSDOS functionality

homepage: http://www.info-zip.org/Zip.html

version	toolchain
3.0	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.2.0, GCCcore/11.3.0, GCCcore/12.2.0, GCCcore/12.3.0, GCCcore/13.2.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0

zlib

zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.

homepage: http://www.zlib.net/

version	toolchain
1.2.7	GCC/4.8.1, GCC/4.8.2
1.2.8	GCC/4.8.2, GCC/4.8.3, GCC/4.8.4, GCC/4.9.2, GCC/4.9.2-binutils-2.25, GCC/4.9.3, GCC/4.9.3-2.25, GCC/4.9.3-binutils-2.25, GCC/5.1.0-binutils-2.25, GCCcore/4.9.2, GCCcore/4.9.3, GCCcore/4.9.4, GCCcore/5.3.0, GCCcore/5.4.0, GCCcore/6.1.0, GCCcore/6.2.0, GCCcore/6.3.0, GNU/4.9.3-2.25, foss/2016.04, foss/2016a, gimkl/2.11.5, intel/2016.02-GCC-4.9, intel/2016a, intel/2016b, intel/2017.01, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25, system
1.2.10	system
1.2.11	FCC/4.5.0, GCCcore/10.1.0, GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.1.0, GCCcore/11.2.0, GCCcore/5.4.0, GCCcore/5.5.0, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.1.0, GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/7.4.0, GCCcore/8.1.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/8.4.0, GCCcore/9.1.0, GCCcore/9.2.0, GCCcore/9.3.0, GCCcore/9.4.0, GCCcore/system, gimkl/2017a, system
1.2.12	GCCcore/11.3.0, GCCcore/12.1.0, GCCcore/12.2.0, GCCcore/9.5.0, system
1.2.13	GCCcore/11.4.0, GCCcore/12.3.0, GCCcore/13.1.0, GCCcore/13.2.0, system

zlib-ng

zlib data compression library for the next generation systems

homepage: https://github.com/zlib-ng/zlib-ng

version	toolchain
2.0.5	GCCcore/10.2.0
2.0.6	GCCcore/10.3.0
2.0.7	GCCcore/11.3.0

zlibbioc

This package uses the source code of zlib-1.2.5 to create libraries for systems that do not have these available via other means.

homepage: https://bioconductor.org/packages/release/bioc/html/zlibbioc.html

version	versionsuffix	toolchain
1.18.0	-R-3.2.3	intel/2016a
1.20.0	-R-3.3.1	intel/2016b

Zopfli

Zopfli Compression Algorithm is a compression library programmed in C to perform very good, but slow, deflate or zlib compression.

homepage: https://github.com/google/zopfli

version	toolchain
1.0.3	GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/11.3.0

ZPAQ

zpaq is a free and open source (GPL v3) incremental, journaling command-line archiver for Windows, Linux and Mac OS/X

homepage: http://mattmahoney.net/dc/zpaq.html

version	toolchain
7.00	GCC/4.8.2

zsh

Zsh is a shell designed for interactive use, although it is also a powerful scripting language.

homepage: https://www.zsh.org/

version	toolchain
5.1.1	GNU/4.9.3-2.25
5.2	foss/2016b
5.8	GCC/8.3.0, system
5.9	system

zstd

Zstandard is a real-time compression algorithm, providing high compression ratios. It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. It also offers a special mode for small data, called dictionary compression, and can create dictionaries from any sample set.

homepage: https://facebook.github.io/zstd

version	toolchain
1.3.4	foss/2016b
1.4.0	GCCcore/7.3.0, GCCcore/8.2.0, foss/2018b
1.4.4	GCCcore/8.3.0, GCCcore/9.3.0
1.4.5	GCCcore/10.2.0
1.4.9	GCCcore/10.3.0
1.5.0	GCCcore/11.2.0
1.5.2	GCCcore/11.3.0, GCCcore/12.2.0
1.5.5	GCCcore/12.3.0, GCCcore/13.2.0

zUMIs

A fast and flexible pipeline to process RNA sequencing data with UMIs.

homepage: https://github.com/sdparekh/zUMIs

version	versionsuffix	toolchain
2.9.7	-R-4.3.2	foss/2023a