List of supported software

EasyBuild 4.5.0 supports 2506 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

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 - ALFA - alleleCount - Allinea - ALLPATHS-LG - almosthere - Alpha - AlphaFold - ALPS - alsa-lib - Amara - amask - Amber - AmberMini - AmberTools - AMD-LibM - AMD-RNG - AMD-SecureRNG - AMOS - AMPHORA2 - AMPL-MP - amplimap - AmrPlusPlus - Anaconda2 - Anaconda3 - aNCI - andi - angsd - 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 - ART - artic-ncov2019 - ARTS - ArviZ - ARWEN - ASAP3 - ASE - ASHS - Aspera-CLI - Aspera-Connect - assimp - Assimulo - ASTRID - astropy - at-spi2-atk - at-spi2-core - ATK - ATLAS - atomate - AtomPAW - atools - ATSAS - attr - attrdict - augur - AUGUSTUS - AUTO-07p - Autoconf - Autoconf-archive - AutoDock - 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   intel/2021a

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

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

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

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 -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

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

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

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

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

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

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

homepage: https://www.anaconda.com

version toolchain
4.0.0 system
4.2.0 system
4.4.0 system
5.0.1 system
5.1.0 system
5.3.0 system
2018.12 system
2019.03 system
2019.07 system
2019.10 system
2020.02 system
2020.07 system
2020.11 system
2021.05 system

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

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

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

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

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/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/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

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://mbio-serv2.mbioekol.lu.se/ARAGORN/

version toolchain
1.2.38 foss/2016b, iccifort/2019.5.281

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

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

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 is 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   fosscuda/2020b, intel/2020b
0.17.1 -Python-3.8.2 foss/2020a, intel/2020a

arrow

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

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

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

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

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

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

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

AutoDock_Vina

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

homepage: http://vina.scripps.edu/index.html

version versionsuffix toolchain
1.1.2 _linux_x86 system

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

babl - Bader - BAGEL - BAli-Phy - bam-readcount - BAMM - BamM - BAMSurgeon - BamTools - BamUtil - Bandage - barrnap - basemap - Bash - bashplotlib - bat - BatMeth2 - BayesAss - BayeScan - BayeScEnv - BayesTraits - Bazel - bbcp - bbFTP - BBMap - bc - BCALM - 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 - biomart-perl - BioPerl - BioPP - Biopython - BioServices - BirdNET - biscuit - Bismark - Bison - bitarray - BLACS - BLASR - blasr_libcpp - BLAST - BLAST+ - BLAT - Blender - BLIS - Blitz++ - BlobTools - Blosc - bmtagger - bnpy - BOINC - bokeh - BoltzTraP - Bonito - Bonmin - Bonnie++ - Boost - Boost.Python - Bottleneck - Bowtie - Bowtie2 - Bpipe - bpp - bpytop - Bracken - BRAKER - BreakDancer - breseq - Brotli - bsddb3 - BSMAPz - Bsoft - BSseeker2 - BuDDy - BUFRLIB - buildenv - Bullet - BUSCO - BUStools - BWA - bwa-meth - bwakit - bwidget - BWISE - bx-python - BXH_XCEDE_TOOLS - byacc - byobu - bzip2

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

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

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/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

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

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/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

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, 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/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

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

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

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: http://www.bioinformatics.babraham.ac.uk/projects/bismark/

version toolchain
0.19.0 intel/2017b
0.20.1 foss/2018b, intel/2018b

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

bitarray

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

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

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

BLACS

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

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

version toolchain
1.1 gmvapich2/2016a

BLASR

The PacBio® long read aligner

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

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

blasr_libcpp

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

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

version toolchain
20170426 intel/2017a

BLAST

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

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

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

BLAST+

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

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

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

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

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

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

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

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

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

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

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

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/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/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 - Caffe - cairo - cairomm - Calendrical - Calib - CAMPARI - Cantera - canu - Canvas - CAP3 - CapnProto - Cargo - 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-Python-bindings - CLAPACK - CLHEP - CLISP - ClonalFrameML - CLooG - Clp - Clustal-Omega - ClustalW2 - Cluster-Buster - ClusterShell - CMake - CNT-ILP - CNVkit - CNVnator - Co-phylog - CoCoALib - code-server - CODEX2 - 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 - cram - cramtools - CrayCCE - CrayGNU - CrayIntel - CrayPGI - crb-blast - CREST - CRF++ - CRISPR-DAV - CRISPResso2 - 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 - 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

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

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

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

Cargo

The Rust package manager

homepage: https://crates.io/

version toolchain
0.13.0 foss/2016b

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/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

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/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

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

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
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

Check is a unit testing framework for C. It features a simple interface for defining unit tests, putting little in the way of the developer. Tests are run in a separate address space, so both assertion failures and code errors that cause segmentation faults or other signals can be caught. Test results are reportable in the following: Subunit, TAP, XML, and a generic logging format.

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

version toolchain
0.12.0 GCCcore/6.4.0

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 -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

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-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

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/10.3.0
3.21.1 GCCcore/11.2.0

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

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

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

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, 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

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

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

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

Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube graphical report explorer.

homepage: https://www.scalasca.org/software/cube-4.x/download.html

version toolchain
4.4.4 GCCcore/8.2.0, GCCcore/9.3.0
4.6 GCCcore/10.2.0, GCCcore/10.3.0

CubeLib

Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube general purpose C++ library component and command-line tools.

homepage: https://www.scalasca.org/software/cube-4.x/download.html

version toolchain
4.4.4 GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
4.6 GCCcore/10.2.0, GCCcore/10.3.0

CubeWriter

Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube high-performance C writer library component.

homepage: https://www.scalasca.org/software/cube-4.x/download.html

version toolchain
4.4.3 GCCcore/10.2.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.3.0
4.6 GCCcore/10.2.0, GCCcore/10.3.0

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

CUDAcore

CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.

homepage: https://developer.nvidia.com/cuda-toolkit

version toolchain
11.0.2 system
11.1.1 system
11.2.1 system
11.2.2 system
11.3.0 system

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

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/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
1.2.4 -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

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

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 - dm-reverb - dm-tree - DMCfun - DMTCP - DOLFIN - Doris - DosageConvertor - dotNET-Core-Runtime - dotNET-SDK - double-conversion - DoubletFinder - Doxygen - Drake - DROP - dropEst - DSA - dSFMT - DSRC - Dsuite - dtcmp - dtcwt - dxpy

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

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://pypi.python.org/pypi/DendroPy/

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
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

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

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

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

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

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

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

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

dxpy

DNAnexus Platform API bindings for Python

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

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

E

E-ANTIC - ea-utils - earthengine-api - EasyBuild - EasyQC - ecCodes - eccodes-python - ED2 - edlib - EggLib - eggnog-mapper - Eigen - EIGENSOFT - elastix - elfutils - Elk - ELPA - ELPH - ELSI - ELSI-RCI - Emacs - EMAN2 - EMBOSS - emcee - EMU - enaBrowserTool - enchant - EnsEMBLCoreAPI - entrypoints - EPD - EPIC - EricScript - ESL-Bundle - ESMF - ESMPy - ESMValTool - eSpeak-NG - Essentia - ETE - ETSF_IO - eudev - EvidentialGene - evmix - ExaBayes - 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

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

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

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

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, intel/2019a

elastix

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

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

version toolchain
4.9.0 foss/2018a

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

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 foss/2020b, 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

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

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

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   foss/2016a
7.0.2   intel/2017b
7.1.0r   foss/2018b, foss/2019a, intel/2018a, intel/2018b, iomkl/2018b
8.0.0   foss/2019b, intel/2019b
8.0.1   foss/2020a, foss/2020b, intel/2020a, intel/2020b
8.1.1   foss/2021a, intel/2021a

ESMPy

Earth System Modeling Framework (ESMF) Python Interface

homepage: https://earthsystemmodeling.org/esmpy

version versionsuffix toolchain
8.0.0 -Python-3.7.4 intel/2019b
8.0.1   intel/2020b

ESMValTool

The Earth System Model eValuation Tool (ESMValTool) is a community diagnostics and performance metrics tool for the evaluation of Earth System Models (ESMs) that allows for routine comparison of single or multiple models, either against predecessor versions or against observations.

homepage: https://www.esmvaltool.org/

version versionsuffix toolchain
1.1.0 -Python-2.7.14 intel/2017b

eSpeak-NG

The eSpeak NG is a compact open source software text-to-speech synthesizer for Linux, Windows, Android and other operating systems. It supports more than 100 languages and accents. It is based on the eSpeak engine created by Jonathan Duddington.

homepage: https://github.com/espeak-ng/espeak-ng

version toolchain
1.50 gompi/2020a

Essentia

Open-source library and tools for audio and music analysis, description and synthesis

homepage: https://essentia.upf.edu

version versionsuffix toolchain
2.1_beta5 -Python-2.7.15 foss/2019a

ETE

A Python framework for the analysis and visualization of trees

homepage: http://etetoolkit.org

version versionsuffix toolchain
3.0.0b36 -Python-2.7.12 intel/2016b
3.1.1 -Python-3.6.6 foss/2018b
3.1.2   foss/2020b
3.1.2 -Python-3.8.2 foss/2020a

ETSF_IO

A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL.

homepage: http://www.etsf.eu/resources/software/libraries_and_tools

version toolchain
1.0.4 foss/2017b, foss/2018a, foss/2018b, intel/2017b, intel/2018a, intel/2018b

eudev

eudev is a fork of systemd-udev with the goal of obtaining better compatibility with existing software such as OpenRC and Upstart, older kernels, various toolchains and anything else required by users and various distributions.

homepage: https://wiki.gentoo.org/wiki/Project:Eudev

version toolchain
3.1.5 foss/2016a, gimkl/2.11.5, intel/2016a
3.2 GCCcore/4.9.3
3.2.2 GCCcore/6.4.0

EvidentialGene

EvidentialGene is a genome informatics project for “Evidence Directed Gene Construction for Eukaryotes”, for constructing high quality, accurate gene sets for animals and plants (any eukaryotes), being developed by Don Gilbert at Indiana University, gilbertd at indiana edu.

homepage: http://arthropods.eugenes.org/EvidentialGene/

version versionsuffix toolchain
2018.01.01 -Perl-5.24.1 intel/2017a

evmix

evmix: Extreme Value Mixture Modelling, Threshold Estimation and Boundary Corrected Kernel Density Estimation

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

version versionsuffix toolchain
2.6 -R-3.3.1 intel/2016b

ExaBayes

ExaBayes is a software package for Bayesian tree inference. It is particularly suitable for large-scale analyses on computer clusters

homepage: https://cme.h-its.org/exelixis/web/software/exabayes/

version toolchain
1.5 foss/2016b

Excel-Writer-XLSX

The Excel::Writer::XLSX module can be used to create an Excel file in the 2007+ XLSX format. Multiple worksheets can be added to a workbook and formatting can be applied to cells. Text, numbers, and formulas can be written to the cells.

homepage: https://metacpan.org/pod/Excel::Writer::XLSX

version toolchain
1.09 foss/2020b

ExifTool

Perl module (Image::ExifTool) and program (exiftool) to read EXIF information from images

homepage: https://owl.phy.queensu.ca/~phil/exiftool/

version toolchain
12.00 GCCcore/9.3.0

exiv2

Exiv2 is a Cross-platform C++ library and a command line utility to manage image metadata.

homepage: https://exiv2.org

version toolchain
0.27.4 GCCcore/10.3.0

Exonerate

Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics.

homepage: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate

version toolchain
2.4.0 GCC/10.2.0, GCC/10.3.0, GCC/6.4.0-2.28, GCC/8.3.0, foss/2016a, foss/2016b, iccifort/2017.4.196-GCC-6.4.0-2.28, iccifort/2019.1.144-GCC-8.2.0-2.31.1, iccifort/2019.5.281, intel/2017a

expat

Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags)

homepage: https://libexpat.github.io

version toolchain
2.1.0 GCC/4.9.2, foss/2016a, intel/2016a
2.1.1 foss/2016a, intel/2016a
2.2.0 GCCcore/4.9.3, GCCcore/5.4.0, GCCcore/6.3.0, foss/2016a, foss/2016b, gimkl/2017a, intel/2016b
2.2.4 GCCcore/6.4.0
2.2.5 GCCcore/6.4.0, GCCcore/7.3.0
2.2.6 GCCcore/8.2.0
2.2.7 GCCcore/8.3.0
2.2.9 FCC/4.5.0, GCCcore/10.2.0, GCCcore/10.3.0, GCCcore/9.3.0
2.4.1 GCCcore/11.2.0

expect

Expect is a tool for automating interactive applications such as telnet, ftp, passwd, fsck, rlogin, tip, etc. Expect really makes this stuff trivial. Expect is also useful for testing these same applications.

homepage: https://core.tcl.tk/expect/index

version toolchain
5.45.4 GCCcore/7.3.0, GCCcore/9.3.0

expecttest

This library implements expect tests (also known as “golden” tests). Expect tests are a method of writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and the test framework automatically populates the expected output. If the output of the test changes, you can rerun the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output.

homepage: https://github.com/ezyang/expecttest

version toolchain
0.1.3 GCCcore/10.3.0

eXpress

Streaming quantification for high-throughput sequencing

homepage: https://pachterlab.github.io/eXpress

version toolchain
1.5.1 intel/2017b

Extrae

Extrae is the core instrumentation package developed by the Performance Tools group at BSC. Extrae is capable of instrumenting applications based on MPI, OpenMP, pthreads, CUDA1, OpenCL1, and StarSs1 using different instrumentation approaches. The information gathered by Extrae typically includes timestamped events of runtime calls, performance counters and source code references. Besides, Extrae provides its own API to allow the user to manually instrument his or her application.

homepage: https://www.bsc.es/computer-sciences/performance-tools

version toolchain
3.4.1 foss/2017a
3.7.1 intel/2019a
3.8.0 gompi/2020b

F

f90cache - Faber - FabIO - faceswap - FALCON - FANN - fast5 - FASTA - fastahack - FastaIndex - FastANI - FastME - fastp - fastPHASE - fastq-pair - fastq-tools - FastQ_Screen - FastQC - fastqsplitter - FastQTL - fastqz - FastRFS - fastStructure - FastTree - FastViromeExplorer - FASTX-Toolkit - fatslim - fbm - FBPIC - FCC - FCM - fdict - FDS - fdstools - FDTD_Solutions - feh - FEniCS - fermi-lite - Ferret - festival - fetchMG - FFC - FFLAS-FFPACK - FFmpeg - ffmpi - ffnet - fftlib - FFTW - fgbio - FGSL - FHI-aims - FIAT - FIGARO - FigureGen - Fiji - file - filevercmp - Filtlong - find_circ - findhap - findutils - fineRADstructure - fineSTRUCTURE - Fiona - Firefox - FIRESTARTER - FireWorks - FIt-SNE - FIX - fixesproto - FLAC - FLAIR - FLANN - FLASH - Flask - flatbuffers - flatbuffers-python - FLEUR - flex - Flexbar - FlexiBLAS - FlexiDot - Flink - FLINT - flook - FLTK - FLUENT - Flye - FMILibrary - FMRIprep - fmt - FoldX - fontconfig - fontsproto - foss - fosscuda - FoX - FPM - fpocket - fqtrim - fqzcomp - FragGeneScan - FRANz - freebayes - FreeFEM - FreeFem++ - freeglut - FreeImage - FreeSASA - FreeSurfer - FreeTDS - freetype - freetype-py - FreeXL - freud-analysis - FriBidi - FRUIT - FRUIT_processor - FSL - FSLeyes - fsom - FTGL - Fujitsu - fullrmc - fumi_tools - FUNWAVE-TVD - FUSE - FuSeq - FusionCatcher - futhark - futile - future - fxtract

f90cache

f90cache is a compiler cache. It acts as a caching pre-processor to Fortran compilers, using the -E compiler switch and a hash to detect when a compilation can be satisfied from cache. This often results in a great speedup in common compilations.

homepage: http://people.irisa.fr/Edouard.Canot/f90cache/

version toolchain
0.96 system

Faber

Faber started as a clone of Boost.Build, to experiment with a new Python frontend. Meanwhile it has evolved into a new build system, which retains most of the features found in Boost.Build, but with (hopefully !) much simplified logic, in addition of course to using Python as scripting language, rather than Jam. The original bjam engine is still in use as scheduler, though at this point that is mostly an implementation detail.

homepage: https://stefanseefeld.github.io/faber

version toolchain
0.3 GCCcore/8.3.0

FabIO

FabIO is an I/O library for images produced by 2D X-ray detectors and written in Python. FabIO support images detectors from a dozen of companies (including Mar, Dectris, ADSC, Hamamatsu, Oxford, …), for a total of 20 different file formats (like CBF, EDF, TIFF, …) and offers an unified interface to their headers (as a python dictionary) and datasets (as a numpy ndarray of integers or floats).

homepage: http://www.silx.org

version versionsuffix toolchain
0.10.2 -Python-3.7.4 foss/2019b, fosscuda/2019b
0.11.0   foss/2020b

faceswap

Faceswap is a tool that utilizes deep learning to recognize and swap faces in pictures and videos.

homepage: https://github.com/deepfakes/faceswap

version versionsuffix toolchain
20180212 -Python-3.6.3 foss/2017b

FALCON

Falcon: a set of tools for fast aligning long reads for consensus and assembly

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

version versionsuffix toolchain
1.8.8   intel/2017b
1.8.8 -Python-2.7.16 intel/2019b

FANN

Fast Artificial Neural Network Library is a free open source neural network library, which implements multilayer artificial neural networks in C with support for both fully connected and sparsely connected networks.

homepage: http://leenissen.dk

version toolchain
2.2.0 GCCcore/6.4.0, intel/2018a

fast5

A lightweight C++ library for accessing Oxford Nanopore Technologies sequencing data.

homepage: http://simpsonlab.github.io/2017/02/27/packing_fast5/

version toolchain
0.6.5 system

FASTA

The FASTA programs find regions of local or global (new) similarity between protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence.

homepage: http://fasta.bioch.virginia.edu

version toolchain
36.3.5e foss/2016b

fastahack

Utilities for indexing and sequence extraction from FASTA files.

homepage: https://github.com/ekg/fastahack

version toolchain
1.0.0 GCCcore/10.2.0, GCCcore/9.3.0

FastaIndex

FastA index (.fai) handler compatible with samtools faidx

homepage: https://github.com/lpryszcz/FastaIndex

version versionsuffix toolchain
0.11rc7 -Python-2.7.14 intel/2017b

FastANI

FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.

homepage: https://github.com/ParBLiSS/FastANI

version toolchain
1.1 foss/2018b, intel/2018b
1.2 GCC/8.2.0-2.31.1, iccifort/2019.1.144-GCC-8.2.0-2.31.1
1.3 iccifort/2019.5.281
1.31 iccifort/2020.1.217
1.33 GCC/10.2.0, iccifort/2020.4.304

FastME

FastME: a comprehensive, accurate and fast distance-based phylogeny inference program.

homepage: http://www.atgc-montpellier.fr/fastme/

version toolchain
2.1.5 foss/2016a
2.1.6.1 GCC/10.2.0, GCC/8.3.0, iccifort/2019.5.281, intel/2018a, intel/2018b

fastp

A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.

homepage: https://github.com/OpenGene/fastp

version toolchain
0.19.7 foss/2018b
0.20.0 GCC/8.2.0-2.31.1, GCC/8.3.0, iccifort/2019.5.281

fastPHASE

fastPHASE: software for haplotype reconstruction, and estimating missing genotypes from population data Documentation: http://scheet.org/code/fastphase_doc_1.4.pdf

homepage: http://stephenslab.uchicago.edu/software.html#fastphase

version toolchain
1.4.8 system

fastq-pair

Match up paired end fastq files quickly and efficiently.

homepage: https://github.com/linsalrob/fastq-pair

version toolchain
1.0 GCCcore/8.2.0

fastq-tools

This package provides a number of small and efficient programs to perform common tasks with high throughput sequencing data in the FASTQ format. All of the programs work with typical FASTQ files as well as gzipped FASTQ files.

homepage: https://homes.cs.washington.edu/~dcjones/fastq-tools/

version toolchain
0.8 foss/2016b, foss/2018b
0.8.3 GCC/10.3.0

FastQ_Screen

FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.

homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/

version versionsuffix toolchain
0.11.3 -Perl-5.24.0 foss/2016b
0.11.4 -Perl-5.24.0 foss/2016b
0.12.0 -Perl-5.26.1 intel/2018a
0.13.0 -Perl-5.28.0 foss/2018b

FastQC

FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.

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