List of supported software¶

EasyBuild 4.5.2 supports 2622 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¶

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/8.2.0-2.31.1`, `intel/2018b`

A¶

ABAQUS - ABINIT - ABRA2 - ABRicate - abTEM - ABySS - ack - ACT - ACTC - ada - AdapterRemoval - ADDA - ADF - ADIOS - adjustText - ADMIXTURE - ADOL-C - Advisor - AFNI - AGFusion - aiohttp - ALADIN - Albacore - alevin-fry - ALFA - alleleCount - Allinea - ALLPATHS-LG - almosthere - Alpha - AlphaFold - ALPS - alsa-lib - Amara - amask - Amber - AmberMini - AmberTools - AMD-LibM - AMD-RNG - AMD-SecureRNG - AMD-uProf - AMOS - AMPHORA2 - AMPL-MP - amplimap - AmrPlusPlus - Anaconda2 - Anaconda3 - aNCI - andi - ANGEL - angsd - ANIcalculator - Annif - annovar - ANSYS - ANSYS_CFD - ant - antiSMASH - ANTLR - ANTs - anvio - any2fasta - AOCC - AOMP - APBS - apex - APR - APR-util - ARAGORN - Arb - arcasHLA - ARCH - Archive-Zip - archspec - ARGoS - argtable - aria2 - Arlequin - Armadillo - ARPACK++ - arpack-ng - ArrayFire - Arriba - Arrow - arrow-R - ART - artic-ncov2019 - ARTS - ArviZ - ARWEN - ASAP - ASAP3 - ASE - ASHS - Aspera-CLI - Aspera-Connect - assimp - Assimulo - ASTRID - astropy - at-spi2-atk - at-spi2-core - ATK - ATLAS - atomate - AtomPAW - atools - atropos - ATSAS - attr - attrdict - augur - AUGUSTUS - Austin - AUTO-07p - Autoconf - Autoconf-archive - AutoDock - AutoDock-GPU - AutoDock-Vina - AutoGeneS - AutoGrid - Automake - AutoMap - autopep8 - Autotools - awscli

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`

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`		`intel/2020a`
`9.4.1`		`foss/2020b`, `intel/2020a`, `intel/2020b`
`9.4.2`		`foss/2021a`, `intel/2021a`
`9.6.2`		`intel/2021a`, `intel/2021b`

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`

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`

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`

ACT¶

ACT is a Java application for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyse regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. It can read complete EMBL, GENBANK and GFF entries or sequences in FASTA or raw format.

homepage: https://sanger-pathogens.github.io/Artemis/ACT/

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

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/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`

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`

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`

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`

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`

aiohttp¶

” Async http client/server framework

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

version	versionsuffix	toolchain
`3.5.4`	`-Python-3.6.6`	`foss/2018b`

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`

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`

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`

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`

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`

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

homepage: https://deepmind.com/research/case-studies/alphafold

version	toolchain
`2.0.0`	`foss/2020b`, `fosscuda/2020b`
`2.0.1`	`foss/2020b`, `fosscuda/2020b`
`2.1.1`	`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`

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: http://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`

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`

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`

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`

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`

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`

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¶

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`

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`

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`

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`

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: http://www.ansys.com

version	toolchain
`15.0`	`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`

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/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`

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`

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/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 12.0

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`

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/8.2.0`, `GCCcore/9.3.0`

APR-util¶

Apache Portable Runtime (APR) util libraries.

homepage: http://apr.apache.org/

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

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`

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`

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`

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`

argtable¶

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

homepage: http://argtable.sourceforge.net/

version	toolchain
`2.13`	`GCCcore/10.3.0`, `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`

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`

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`

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`

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`

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`

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`

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`

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`

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`

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`

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`

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`

astropy¶

The Astropy Project is a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages.

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`		`intelcuda/2020b`
`4.3.1`		`foss/2021a`, `intel/2021a`

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`

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`

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`

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`

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`

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`

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`

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`, `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`

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`

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`

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`

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`

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`

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`

B¶

BabelStream - babl - Bader - BAGEL - BAli-Phy - bam-readcount - BAMM - BamM - BAMSurgeon - bamtofastq - BamTools - BamUtil - Bandage - barrnap - basemap - Bash - bashplotlib - bat - BatMeth2 - BayesAss - BayeScan - BayeScEnv - BayesTraits - Bazel - bbcp - bbFTP - BBMap - bc - BCALM - bcbio-gff - BCEL - BCFtools - bcgTree - bcl2fastq2 - bcolz - BDBag - beagle-lib - Beast - BeautifulSoup - BEDOPS - BEDTools - BEEF - behave - BerkeleyGW - BFAST - BFC - bgen - bgen-reader - bibtexparser - BiG-SCAPE - BinSanity - binutils - Bio-DB-HTS - Bio-EUtilities - Bio-SamTools - Bio-SearchIO-hmmer - bioawk - 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 - Blosc - Blosc2 - bmtagger - bnpy - BOINC - bokeh - BoltzTraP - Bonito - Bonmin - Bonnie++ - Boost - Boost.Python - boost_histogram - boto3 - Bottleneck - Bowtie - Bowtie2 - Bpipe - bpp - bpytop - Bracken - BRAKER - BreakDancer - breseq - Brotli - Brotli-python - Brunsli - bsddb3 - BSMAPz - Bsoft - BSseeker2 - BuDDy - BUFRLIB - buildenv - Bullet - BUSCO - BUStools - BWA - bwa-meth - bwakit - bwidget - BWISE - bx-python - BXH_XCEDE_TOOLS - byacc - byobu - bzip2

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`

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`

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/9.3.0`, `foss/2018b`

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/2016b`

BamM¶

BamM is a c library, wrapped in python, that parses BAM files

homepage: http://ecogenomics.github.io/BamM/

version	versionsuffix	toolchain
`1.7.3`	`-Python-2.7.12`	`foss/2016b`
`1.7.3`	`-Python-2.7.14`	`foss/2018a`

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`

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`

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`

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`

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`

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`

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`

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: http://www.evolution.reading.ac.uk/BayesTraitsV1.html

version	versionsuffix	toolchain
`1.0-linux32`		`system`
`2.0`	`-Beta-Linux64`	`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`

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`		`iccifort/2020.1.217`
`38.90`		`GCC/10.2.0`, `GCC/9.3.0`

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`

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`

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`

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/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`

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`

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/8.2.0-2.31.1`, `GCC/9.3.0`, `gcccuda/2019b`

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: http://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`

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`

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`

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`, `iccifort/2020.4.304`

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`

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`

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`

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`

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`

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`

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`
`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`

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`, `foss/2018b`

biobambam2¶

Tools for processing BAM files

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

version	toolchain
`2.0.87`	`intel/2018a`

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`
`3.2.8`	`foss/2021a`

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`

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`

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`
`1.78`		`foss/2020b`, `fosscuda/2020b`, `intel/2020b`
`1.78`	`-Python-3.8.2`	`foss/2020a`, `intel/2020a`
`1.79`		`foss/2021a`, `foss/2021b`

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`

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`	`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+¶

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`, `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`

BLAT¶

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

homepage: http://genome.ucsc.edu/FAQ/FAQblat.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`

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`

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`
`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`	`GCCcore/10.2.0`, `GCCcore/10.3.0`

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/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`

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`

Blosc2¶

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

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

version	toolchain
`2.0.3`	`GCCcore/10.2.0`

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`

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`
`2.4.1`		`foss/2021a`

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`

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++¶

Bonnie++-1.97: Enhanced performance Test of Filesystem I/O

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

version	toolchain
`1.97`	`foss/2016a`

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`
`1.76.0`		`GCC/10.3.0`, `intel-compilers/2021.2.0`
`1.77.0`		`GCC/11.2.0`, `intel-compilers/2021.4.0`

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`

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`

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/11.2.0`

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`

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`

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: http://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`

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`

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`

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`

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/8.3.0`

Brotli-python¶

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

version	toolchain
`1.0.9`	`GCCcore/10.3.0`

Brunsli¶

Brunsli is a lossless JPEG repacking library.

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

version	toolchain
`0.1`	`GCCcore/10.2.0`

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`

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`

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`

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 <this module name>

homepage: None

version	versionsuffix	toolchain
`default`		`FCC/4.5.0`, `Fujitsu/21.05`, `foss/2017b`, `foss/2018b`, `foss/2019b`, `foss/2020a`, `foss/2020b`, `foss/2021a`, `fosscuda/2019b`, `fosscuda/2020a`, `fosscuda/2020b`, `intel/2016b`, `intel/2017a`, `intel/2019b`, `intel/2020a`, `intel/2020b`, `intel/2021a`, `intelcuda/2019b`, `intelcuda/2020a`, `intelcuda/2020b`
`default`	`-CUDA-11.3.1`	`foss/2021a`

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`
`5.0.0`		`foss/2020b`
`5.1.2`		`foss/2020b`

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`

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`, `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`

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`

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`

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`

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/8.3.0, GCCcore/9.3.0, system

C¶

c-ares - C3D - cadaver - CaDiCaL - CAFE5 - Caffe - cairo - cairomm - Calcam - Calendrical - Calib - CAMPARI - Cantera - canu - Canvas - CAP3 - CapnProto - Cargo - Carma - carputils - Cartopy - CaSpER - CastXML - Catch2 - CatMAP - causallift - causalml - CaVEMan - CAVIAR - Cbc - CBLAS - ccache - CCfits - CCL - cclib - cctools - CD-HIT - CDAT - cdbfasta - cddlib - cDNA_Cupcake - CDO - cdsapi - cell2location - CellMix - CellRanger - CellRanger-ARC - CellRanger-ATAC - CellRank - Centrifuge - Cereal - CESM-deps - CFDEMcoupling - CFITSIO - cftime - CGAL - cget - Cgl - CGmapTools - CGNS - CharLS - CHARMM - charmm - CHASE - Check - check - CheckM - Cheetah - CheMPS2 - CHERAB - chewBBACA - chi2comb - Chimera - ChimPipe - Chromaprint - cicero - CIF2Cell - CIRCexplorer - CIRCexplorer2 - Circos - CIRI - CIRI-long - cisTEM - CITE-seq-Count - Clang - Clang-AOMP - Clang-Python-bindings - CLAPACK - CLEASE - CLHEP - CLISP - ClonalFrameML - CLooG - Clp - Clustal-Omega - ClustalW2 - Cluster-Buster - ClusterShell - CMake - CMSeq - CNT-ILP - CNVkit - CNVnator - Co-phylog - CoCoALib - code-server - CODEX2 - Cogent - Coin - CoinUtils - Commet - CompareM - COMSOL - Con3F - CONCOCT - configparser - configurable-http-proxy - ConnectomeWorkbench - Control-FREEC - CoordgenLibs - Coot - core-counter - Coreutils - corner - coverage - cowsay - CP2K - CPB - CPLEX - CppUnit - cppy - cpu_features - cram - cramtools - CrayCCE - CrayGNU - CrayIntel - CrayPGI - crb-blast - CREST - CRF++ - CRISPR-DAV - CRISPResso2 - cromwell - CrossMap - CrossTalkZ - CRPropa - cryoDRGN - CryptoMiniSat - CSB - CSBDeep - CSBLAST - cscope - csvkit - ctags - ctffind - Cube - CubeGUI - CubeLib - CubeWriter - CUDA - CUDAcore - cuDNN - Cufflinks - CUnit - CuPy - cURL - custodian - cutadapt - cuTENSOR - CVS - CVXOPT - CVXPY - cxxopts - cysignals - Cython - cytoolz - cytosim - cyvcf2

c-ares¶

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

homepage: https://c-ares.haxx.se

version	toolchain
`1.17.2`	`GCCcore/10.3.0`

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`

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`

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`

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`

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`		`GCCcore/10.3.0`, `GCCcore/11.2.0`

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`

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`

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`

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`

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`

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`

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`

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`

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`

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`

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/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`

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`

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`

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`

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`

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`

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`

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`

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`

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`

Centrifuge¶

Classifier for metagenomic sequences

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

version	toolchain
`1.0.3`	`foss/2018b`
`1.0.4`	`gompi/2020b`
`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`

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`, `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`

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`

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-3.7.4`	`foss/2019b`, `intel/2019b`
`4.14.3`		`gompi/2021a`, `gompi/2021b`
`4.14.3`	`-Python-3.8.2`	`gompi/2020a`, `iimpi/2020a`
`5.2`		`gompi/2020b`

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`

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`

CHARMM¶

CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile and widely used molecular simulation program with broad application to many-particle systems.

homepage: http://www.charmm.org

version	toolchain
`37b2`	`foss/2016a`, `intel/2016a`

charmm¶

CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile and widely used molecular simulation program with broad application to many-particle systems. charmm provides all the functionality of CHARMM except its performance enhancements.

homepage: http://www.charmm.org

version	toolchain
`43b2`	`foss/2017b`, `intel/2017b`

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
`0.15.2`	`GCCcore/10.2.0`, `GCCcore/10.3.0`, `GCCcore/9.3.0`

check¶

homepage: https://libcheck.github.io/check/

version	toolchain
`0.12.0`	`GCCcore/6.4.0`

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`

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`

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`

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`

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`

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`

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`

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`

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`

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/9.3.0`

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`

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`

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`
`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`

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`

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`

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`

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`

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`

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/10.3.0`, `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`, `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: Finding dense clusters of motifs in DNA sequences

homepage: https://github.com/weng-lab/cluster-buster/

version	toolchain
`20160106`	`intel/2016a`

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`
`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`

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`

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`

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`

CoCoALib¶

CoCoALib is a free GPL3 C++ library for doing Computations in Commutative Algebra.

homepage: http://cocoa.dima.unige.it/cocoalib

version	toolchain
`0.99601`	`GCC/8.2.0-2.31.1`
`0.99700`	`GCC/8.3.0`

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`

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`

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`

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`

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`

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.com

version	toolchain
`5.4.0.225`	`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`

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`

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`

ConnectomeWorkbench¶

Connectome Workbench is an open-source visualization and discovery tool used to explore data generated by the Human Connectome Project. The distribution includes wb_view, a GUI-based visualization platform, and wb_command, a command-line program for performing a variety of algorithmic tasks using volume, surface, and grayordinate data.

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`

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`

CoordgenLibs¶

Schrodinger-developed 2D Coordinate Generation

homepage: https://github.com/schrodinger/coordgenlibs

version	toolchain
`1.3.2`	`gompi/2019a`, `iimpi/2019a`

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`

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`

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`

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`

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`

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`

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`

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/10.3.0`, `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`

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`, `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`

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`

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`

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	toolchain
`0.3.2`	`fosscuda/2020b`

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`

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`

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`

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`

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`, `fosscuda/2019b`, `fosscuda/2020b`
`4.1.14`	`-CUDA-11.3.1`	`foss/2021a`

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¶

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`

CubeLib¶

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`

CubeWriter¶

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`

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`

CUDAcore¶

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`

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-11.4.1`	`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`, `gompi/2019a`

CUnit¶

Automated testing framework for C.

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

version	toolchain
`2.1-3`	`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`

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`

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`	`-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`

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`

CVS¶

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`

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`

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`

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`

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`
`3.0a5`		`GCCcore/10.2.0`

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`

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 - Dalton - damageproto - dammit - DANPOS2 - DAS_Tool - dask - datamash - davix - DB - DB_File - DBD-mysql - DBG2OLC - DBus - dbus-glib - dcm2niix - DCMTK - dd - deal.II - deap - decona - deconf - DeconICA - deepdiff - DeepSurv - deepTools - Delly - DeMixT - DendroPy - destiny - detonate - DFA - DFT-D3 - DFT-D4 - DFTB+ - dftd3-lib - DGL - DIAL - DIAMOND - dicom2nifti - DicomBrowser - Diffutils - dijitso - dill - DIRAC - distributed - DistributedStream - DL_POLY_4 - DL_POLY_Classic - dlib - dm-reverb - dm-tree - DMCfun - DMTCP - DOLFIN - Doris - DosageConvertor - dotNET-Core-Runtime - dotNET-SDK - double-conversion - DoubletFinder - Doxygen - Drake - dRep - DROP - dropEst - DSA - dSFMT - DSRC - Dsuite - dtcmp - dtcwt - DualSPHysics - DUBStepR - dune-core - dune-fem - dxpy - DyMat

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`

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`

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`

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`
`2021.9.1`		`foss/2021a`

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`

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/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`

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`
`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`

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: http://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`

dbus-glib¶

D-Bus is a message bus system, a simple way for applications to talk to one another.

homepage: http://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`

dcm2niix¶

dcm2niix is a 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`

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`

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`	`intel/2019a`

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://deepdiff.readthedocs.io/en/latest/

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`

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`

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`

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`

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`
`4.5.2`	`-Python-2.7.18`	`GCCcore/10.2.0`

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`

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`	`intel/2017b`

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: http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english

version	toolchain
`3.2.0`	`GCC/8.3.0`, `iccifort/2020.4.304`, `intel-compilers/2021.2.0`, `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`

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`

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`

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`

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`

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`

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`

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`

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`

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`

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`

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`

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`

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`

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`

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`

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`

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`

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`

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`
`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`

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`

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`

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`

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`

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`

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`

dxpy¶

DNAnexus Platform API bindings for Python

homepage: http://autodoc.dnanexus.com/

version	versionsuffix	toolchain
`0.266.1`	`-Python-2.7.14`	`intel/2018a`

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`

E¶

E-ANTIC - ea-utils - earthengine-api - EasyBuild - EasyQC - ecCodes - eccodes-python - ED2 - edlib - EggLib - eggnog-mapper - eht-imaging - Eigen - EIGENSOFT - einops - elastix - elbencho - ELFIO - elfutils - Elk - ELPA - ELPH - elprep - ELSI - ELSI-RCI - Emacs - EMAN2 - EMBOSS - Embree - emcee - EMU - enaBrowserTool - enchant - EnsEMBLCoreAPI - entrypoints - EPD - EPIC - epiScanpy - EricScript - ESL-Bundle - ESMF - ESMPy - ESMValTool - eSpeak-NG - Essentia - ETE - ETSF_IO - eudev - EvidentialGene - evmix - ExaBayes - ExaML - Excel-Writer-XLSX - ExifTool - exiv2 - Exonerate - expat - expect - expecttest - eXpress - Extrae

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/videlec/e-antic

version	toolchain
`0.1.2`	`GCC/8.2.0-2.31.1`
`0.1.5`	`GCC/8.3.0`

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`

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`

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`

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`

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`

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`

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`

EggLib¶

EggLib is a C++/Python library and program package for evolutionary genetics and genomics.

homepage: http://egglib.sourceforge.net/

version	toolchain
`2.1.10`	`intel/2016a`

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`

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`

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/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`

elastix¶

elastix: a toolbox for rigid and nonrigid registration of images.

homepage: http://elastix.isi.uu.nl/

version	toolchain
`4.9.0`	`foss/2018a`

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`

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`

ELPA¶

Eigenvalue SoLvers for Petaflop-Applications .

homepage: https://elpa.rzg.mpg.de

version	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`

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`		`intel/2019b`
`2.5.0`	`-PEXSI`	`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`

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`, `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`

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://dfm.io/emcee

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`

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`

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`

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`

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`

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`