List of supported software

EasyBuild 4.0.1 supports 1725 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 intel/2018b

A

ABAQUS - ABINIT - ABySS - ack - ACML - ACT - ACTC - ada - AdapterRemoval - ADDA - ADF - adjustText - ADMIXTURE - ADOL-C - Advisor - AFNI - AGFusion - aiohttp - ALADIN - Albacore - ALFA - alleleCount - Allinea - ALLPATHS-LG - ALPS - amask - Amber - AmberMini - AmberTools - AMD-LibM - AMD-RNG - AMD-SecureRNG - AMOS - AMPL-MP - Anaconda2 - Anaconda3 - angsd - Annif - annovar - ANSYS - ANSYS_CFD - ant - ANTLR - ANTs - APBS - APR - APR-util - ARAGORN - Arb - ARCH - ARGoS - argtable - Armadillo - ARPACK++ - arpack-ng - ArrayFire - Arrow - ART - ARWEN - ASAP3 - ASE - ASHS - Aspera-CLI - Aspera-Connect - Assimulo - ASTRID - astropy - at-spi2-atk - at-spi2-core - ATK - ATLAS - atomate - AtomPAW - atools - ATSAS - AUGUSTUS - Autoconf - AutoDock - AutoDock_Vina - AutoGrid - Automake - 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

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: http://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

ABySS

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

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

version toolchain
1.9.0 foss/2016a
2.0.2 foss/2016b, foss/2018a, intel/2016b
2.0.3 foss/2017b, intel/2017b

ack

ack is a tool like grep, optimized for programmers

homepage: http://beyondgrep.com/

version toolchain
2.14 system

ACML

ACML provides a free set of thoroughly optimized and threaded math routines for HPC, scientific, engineering and related compute-intensive applications. ACML is ideal for weather modeling, computational fluid dynamics, financial analysis, oil and gas applications and more.

homepage: http://developer.amd.com/libraries/acml

version versionsuffix toolchain
4.4.0 -gfortran-64bit system
4.4.0 -gfortran-64bit-int64 system
4.4.0 -ifort-64bit system
4.4.0 -ifort-64bit-int64 system
5.2.0 -gfortran-64bit system
5.2.0 -gfortran-64bit-int64 system
5.2.0 -ifort-64bit system
5.2.0 -ifort-64bit-int64 system
5.3.0 -ifort-64bit system
5.3.1 -ifort-64bit system

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

version versionsuffix toolchain
18.0.2 -Java-11 system

ACTC

ACTC converts independent triangles into triangle strips or fans.

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

version toolchain
1.1 GCCcore/6.4.0, GCCcore/7.3.0, 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/%/(github_account)s/%(namelower)s

version toolchain
2.2.0 foss/2016b
2.2.2 foss/2018b
2.3.1 foss/2018b

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: http://www.scm.com/ADF/

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

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-3.7.2 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: http://software.genetics.ucla.edu/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

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

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

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

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

AmberMini

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

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

version toolchain
16.16.0 intel/2017b

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: http://ambermd.org/

version toolchain
17 intel/2017b, intel/2018a

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

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

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

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

AMPL-MP

An open-source library for mathematical programming.

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

version toolchain
3.1.0 GCCcore/6.4.0

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

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

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

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

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

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 -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: http://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

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

APR

Apache Portable Runtime (APR) libraries.

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

version toolchain
1.6.3 GCCcore/6.4.0, GCCcore/7.3.0, iomkl/2018a
1.7.0 GCCcore/8.2.0

APR-util

Apache Portable Runtime (APR) util libraries.

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

version toolchain
1.6.1 GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, 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

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: http://arblib.org

version toolchain
2.16.0 GCC/7.3.0-2.30, iccifort/2018.3.222-GCC-7.3.0-2.30

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

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/8.2.0, foss/2016b, foss/2018b, intel/2018a, intel/2018b

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
9.700.2   foss/2019a

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

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

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 intel/2018b
0.12.0 -Python-3.6.6 intel/2018b

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

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

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

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: http://asperasoft.com

version versionsuffix toolchain
3.7.2 .354.010c3b8 system
3.9.0 .1326.6985b21 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

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: http://www.astropy.org/

version versionsuffix toolchain
2.0.12 -Python-2.7.15 foss/2018b, intel/2018b
2.0.14   foss/2019a

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

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

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/stable/

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

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

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

AUGUSTUS

AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences

homepage: http://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

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: http://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/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, 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

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

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: http://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
1.16.1 GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0

Autotools

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

homepage: http://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

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

B

Bader - BAGEL - bam-readcount - BAMM - BamM - BamTools - BamUtil - Bandage - barrnap - basemap - Bash - bat - BayesAss - BayeScan - BayeScEnv - BayesTraits - Bazel - bbcp - bbFTP - BBMap - bc - BCALM - BCEL - BCFtools - bcgTree - bcl2fastq2 - bcolz - BDBag - beagle-lib - Beast - BeautifulSoup - BEDOPS - BEDTools - behave - BerkeleyGW - BFAST - BFC - binutils - Bio-DB-HTS - Bio-SamTools - bioawk - biobambam2 - biomart-perl - BioPerl - Biopython - biscuit - Bismark - Bison - bitarray - BLACS - BLASR - blasr_libcpp - BLAST - BLAST+ - BLAT - Blender - BLIS - Blitz++ - BlobTools - Blosc - bmtagger - bnpy - BOINC - bokeh - BoltzTraP - Bonmin - Bonnie++ - Boost - Boost.Python - Bottleneck - Bowtie - Bowtie2 - Bpipe - bpp-core - bpp-phyl - bpp-seq - BRAKER - BreakDancer - bsddb3 - buildenv - Bullet - BUSCO - BWA - bwakit - bwidget - BWISE - bx-python - BXH_XCEDE_TOOLS - byacc - bzip2

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

bam-readcount

Count DNA sequence reads in BAM files

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

version toolchain
0.8.0 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

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/8.2.0-2.31.1, foss/2017b, foss/2018a, foss/2018b, iccifort/2019.1.144-GCC-8.2.0-2.31.1, intel/2017b, intel/2018b

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 foss/2018b

basemap

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

homepage: http://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

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

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

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 foss/2016a

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: http://bazel.io/

version 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
0.29.1 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: http://doc.in2p3.fr/bbftp/

version toolchain
3.2.1 intel/2016a

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

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: http://commons.apache.org/proper/commons-bcel/

version versionsuffix toolchain
5.2 -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
1.6 foss/2016b, foss/2017b, intel/2017b
1.9 foss/2018a, foss/2018b, iccifort/2019.1.144-GCC-8.2.0-2.31.1, intel/2018b

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

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   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: http://bcolz.blosc.org/en/latest/

version versionsuffix toolchain
1.1.1 -Python-2.7.13 foss/2017a

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

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/8.2.0-2.31.1

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
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

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

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

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://github.com/arq5x/bedtools2

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, iccifort/2019.1.144-GCC-8.2.0-2.31.1

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: http://www.berkeleygw.org

version 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

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

binutils

binutils: GNU binary utilities

homepage: http://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

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 -Perl-5.28.1 GCC/8.2.0-2.31.1

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

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 foss/2018b

biobambam2

Tools for processing BAM files

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

version toolchain
2.0.87 intel/2018a

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: http://www.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

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: http://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
1.72 -Python-2.7.15 foss/2018b, intel/2018b
1.72 -Python-3.6.6 foss/2018b
1.73   foss/2019a, intel/2019a
1.73 -Python-3.6.6 foss/2018b

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 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: http://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/8.3.0, GCCcore/9.1.0, GCCcore/9.2.0, 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

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

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
2.2.31   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

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, 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

BLIS

AMD 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
1.2 -amd GCC/7.3.0-2.30

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: http://blitz.sourceforge.net/

version toolchain
0.10 GCCcore/6.4.0, foss/2016a

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: http://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

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

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: http://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

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

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   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, iimpi/2019a, iimpic/2019a
1.71.0   gompi/2019b

Boost.Python

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

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

version versionsuffix toolchain
1.65.1 -Python-2.7.14 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, iimpi/2019a

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

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, foss/2018b, iccifort/2019.1.144-GCC-8.2.0-2.31.1

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, iccifort/2019.1.144-GCC-8.2.0-2.31.1

Bpipe

Bpipe - a tool for running and managing bioinformatics pipelines

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

version toolchain
0.9.9.2 intel/2017a

bpp-core

Bio++ Core Library

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

version toolchain
2.4.1 GCC/8.2.0-2.31.1

bpp-phyl

Bio++ Phylogenetic Library

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

version toolchain
2.4.1 GCC/8.2.0-2.31.1

bpp-seq

Bio++ Sequence Library

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

version toolchain
2.4.1 GCC/8.2.0-2.31.1

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 toolchain
2.1.2 intel/2019a

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

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 -Python-2.7.15 fosscuda/2018b

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 toolchain
default foss/2017b, foss/2018b, intel/2016b, intel/2017a

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: http://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

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/8.2.0-2.31.1, foss/2017b, foss/2018a, foss/2018b, intel/2017b, intel/2018a, intel/2018b

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

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

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

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/8.3.0

C

C3D - cadaver - Caffe - cairo - cairomm - Calendrical - Cantera - canu - Canvas - CAP3 - CapnProto - Cargo - CastXML - Catch2 - CatMAP - causalml - CaVEMan - CBLAS - ccache - CCL - cclib - CD-HIT - cDNA_Cupcake - CDO - cdsapi - CellMix - CellRanger - Centrifuge - CESM-deps - CFITSIO - cftime - CGAL - cget - CGNS - CharLS - charmm - CHARMM - CHASE - CheckM - Cheetah - CheMPS2 - Chimera - ChimPipe - Chromaprint - CIRCexplorer - CIRCexplorer2 - Circos - CIRI - cisTEM - Clang - Clang-Python-bindings - CLAPACK - CLHEP - CLISP - ClonalFrameML - CLooG - Clustal-Omega - ClustalW2 - Cluster-Buster - ClusterShell - CMake - CNVkit - CNVnator - CODEX2 - Commet - Con3F - CONCOCT - configparser - configurable-http-proxy - ConnectomeWorkbench - Control-FREEC - Coot - core-counter - Coreutils - corner - coverage - cowsay - CP2K - CPB - CPLEX - CppUnit - cram - cramtools - CrayCCE - CrayGNU - CrayIntel - CrayPGI - crb-blast - CRF++ - CrossTalkZ - CryptoMiniSat - cscope - csvkit - ctags - ctffind - Cube - CubeGUI - CubeLib - CubeWriter - CUDA - cuDNN - Cufflinks - CUnit - cURL - custodian - cutadapt - CVS - CVXOPT - CVXPY - cysignals - Cython - cytosim - cyvcf2

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

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: http://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/8.2.0

cairomm

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

homepage: http://cairographics.org

version toolchain
1.12.2 GCCcore/6.4.0, GCCcore/7.3.0

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

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: http://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

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

CastXML

CastXML is a C-family abstract syntax tree XML output tool.

homepage: https://github.com/CastXML/CastXML

version toolchain
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

CatMAP

Catalyst Micro-kinetic Analysis Package for automated creation of micro-kinetic models used in catalyst screening.

homepage: http://catmap.readthedocs.io/

version versionsuffix toolchain
20170927 -Python-2.7.14 intel/2017b

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

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

CBLAS

C interface to the BLAS

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

version toolchain
20110120 foss/2016b

ccache

Cache for C/C++ compilers

homepage: http://ccache.samba.org/

version versionsuffix toolchain
3.2.5   system
3.3.1   system
3.3.3   system
3.3.4 -f90 system

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

cclib

cclib is a Python library that provides parsers for computational chemistry log files. It alsoprovides a platform to implement algorithms in a package-independent manner.

homepage: http://cclib.github.io/

version versionsuffix toolchain
1.5 -Python-3.5.2 foss/2016b

CD-HIT

CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.

homepage: http://weizhong-lab.ucsd.edu/cd-hit/

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   foss/2018b

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

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

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

Centrifuge

Classifier for metagenomic sequences

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

version toolchain
1.0.3 foss/2018b
1.0.4-beta foss/2018b

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: http://www.cesm.ucar.edu/models/cesm2/

version toolchain
2 foss/2018b, intel/2018b, iomkl/2018b

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

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: http://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

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

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

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

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

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

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

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

Cheetah

Cheetah is an open source template engine and code generation tool.

homepage: http://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
1.7.1 intel/2016a
1.7.2 intel/2016a
1.7-rc2 intel/2016a
1.8 intel/2016b
1.8.8 intel/2018b
1.8.9 foss/2018b, foss/2019a, intel/2018b, intel/2019a

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

CIRCexplorer

CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset.

homepage: http://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

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

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

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

Clang

C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library – use libstdc++ from GCC.

homepage: http://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

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

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: http://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

CLISP

Common Lisp is a high-level, general-purpose, object-oriented, dynamic, functional programming language.

homepage: http://www.clisp.org/

version toolchain
2.49 GCCcore/6.4.0

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

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 foss/2018b, intel/2018a, intel/2018b

ClustalW2

ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.

homepage: http://www.ebi.ac.uk/Tools/msa/clustalw2/

version toolchain
2.1 foss/2016b, foss/2018b, intel/2017b, intel/2018b

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: http://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: http://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
3.15.3 GCCcore/8.3.0

CNVkit

A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing.

homepage: http://github.com/etal/cnvkit

version versionsuffix toolchain
0.9.2 -Python-2.7.14 intel/2017b
0.9.6 -Python-3.7.2-R-3.6.0 foss/2019a

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

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

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

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

configparser

configparser is a Python library that brings the updated configparser from Python 3.5 to Python 2.6-3.5

homepage: http://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

ConnectomeWorkbench

Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project.

homepage: https://www.humanconnectome.org/software/connectome-workbench

version toolchain
1.2.2 system
1.3.2 foss/2017b, intel/2017b

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/8.2.0-2.31.1

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: http://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

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

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: http://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, intel/2017b, intel/2018a
6.1   foss/2019a, intel/2018a

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 toolchain
12.9 GCCcore/8.2.0

CppUnit

CppUnit is the C++ port of the famous JUnit framework for unit testing.

homepage: http://sourceforge.net/projects/cppunit/

version toolchain
1.12.1 GCCcore/6.4.0, foss/2016a

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 toolchain
0.6.9 intel/2017a

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

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

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

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 toolchain
1.0.4 GCCcore/8.2.0

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: http://grigoriefflab.janelia.org/ctffind4

version toolchain
4.1.13 foss/2019a, fosscuda/2019a

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

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

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/8.2.0

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 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
7.0.2 -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
7.6.2.24 -CUDA-10.1.243 system
7.6.4.38   gcccuda/2019a

CUnit

Automated testing framework for C.

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

version toolchain
2.1-3 GCCcore/6.4.0

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

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: http://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 -Python-2.7.15 foss/2018b
1.18 -Python-3.6.6 foss/2018b, intel/2018b
2.1 -Python-3.6.6 foss/2018b

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: http://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

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 toolchain
1.0.24 foss/2019a

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

The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.

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

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
0.29.10 -Python-2.7.14 foss/2017b, intel/2017b
0.29.10 -Python-3.6.3 foss/2017b, intel/2017b

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 - damageproto - dammit - DANPOS2 - DAS_Tool - dask - datamash - davix - DB - DB_File - DBD-mysql - DBG2OLC - DBus - dbus-glib - dcm2niix - DCMTK - deal.II - deap - deconf - DeconICA - deepdiff - DeepSurv - deepTools - Delly - DeMixT - DendroPy - destiny - detonate - DFT-D3 - DFTB+ - DIAL - DIAMOND - DicomBrowser - Diffutils - dill - distributed - DL_POLY_Classic - DMTCP - DOLFIN - Doris - dotNET-Core-Runtime - double-conversion - Doxygen - Drake - dropEst - DSA - DSRC - Dsuite - 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

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

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

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: http://dmc.web.cern.ch/projects/davix/home

version toolchain
0.6.6 intel/2017a

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

DB_File

Perl5 access to Berkeley DB version 1.x.

homepage: http://perldoc.perl.org/DB_File.html

version versionsuffix toolchain
1.835 -Perl-5.20.3 intel/2016a
1.835 -Perl-5.22.1 foss/2016a

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 -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

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, 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

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

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

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

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: http://deeptools.readthedocs.org/

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

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.

homepage: https://github.com/dellytools/delly

version versionsuffix toolchain
0.7.8 -linux_x86_64 system

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   intel/2019a
4.4.0 -Python-2.7.15 intel/2018b

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

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 intel/2019a

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

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

DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data.

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

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

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

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

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

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: https://github.com/dmtcp/dmtcp

version toolchain
2.4.5 system
2.5.0 foss/2016a
2.5.1 system
2.5.2 foss/2016b, foss/2018b

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

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

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

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

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: http://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

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

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

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

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

ea-utils - earthengine-api - EasyBuild - EasyQC - ecCodes - ED2 - EggLib - eggnog-mapper - Eigen - EIGENSOFT - elastix - Elk - ELPA - ELPH - Emacs - EMAN2 - EMBOSS - emcee - enaBrowserTool - enchant - entrypoints - EPD - EPIC - EricScript - ESMF - Essentia - ETE - ETSF_IO - eudev - EvidentialGene - evmix - ExaBayes - Exonerate - expat - expect - eXpress - Extrae

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

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 toolchain
2.7.3 intel/2018a
2.8.2 intel/2018a
2.9.2 intel/2018b, iomkl/2018b
2.12.5 gompi/2019a

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

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 (genes or proteins) using precomputed eggNOG-based orthology assignments

homepage: http://eggnog-mapper.embl.de

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

Eigen

Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.

homepage: http://eigen.tuxfamily.org/index.php?title=Main_Page

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 system

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/2019a, 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

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

ELPA

Eigenvalue SoLvers for Petaflop-Applications .

homepage: http://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

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

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: http://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

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
2.21a -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   foss/2016b, foss/2018b, intel/2017a, intel/2018b
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

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

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

ESMF

The Earth System Modeling Framework (ESMF) is software for building and coupling weather, climate, and related models.

homepage: http://sourceforge.net/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, intel/2018a, intel/2018b, iomkl/2018b

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

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: http://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

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/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, 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

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

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: http://www.bsc.es/computer-sciences/performance-tools

version toolchain
3.4.1 foss/2017a
3.7.1 intel/2019a

F

f90cache - faceswap - FALCON - FANN - fast5 - FASTA - FastaIndex - FastANI - FastME - fastp - fastPHASE - fastq-tools - FastQ_Screen - FastQC - FastQTL - fastqz - FastRFS - fastStructure - FastTree - FASTX-Toolkit - fbm - FCM - FDS - fdstools - FDTD_Solutions - feh - Ferret - FFC - FFLAS-FFPACK - FFmpeg - ffnet - FFTW - FGSL - FIAT - file - Filtlong - find_circ - findhap - findutils - fineRADstructure - fineSTRUCTURE - Firefox - FireWorks - fixesproto - FLANN - FLASH - Flask - FLEUR - flex - FlexiDot - FLINT - FLTK - FLUENT - Flye - FMILibrary - FMRIprep - fmt - FoldX - fontconfig - fontsproto - foss - fosscuda - FoX - FPM - fqtrim - fqzcomp - FragGeneScan - FRANz - FreeFem++ - freeglut - FreeImage - FreeSurfer - freetype - FreeXL - FriBidi - FSL - FSLeyes - FTGL - fullrmc - FUNWAVE-TVD - FUSE - 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

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 toolchain
1.8.8 intel/2017b

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

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: http://www.iodbc.org/

version toolchain
1.1 foss/2018b, intel/2018b

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 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

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-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

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

version versionsuffix toolchain
0.10.1 -Java-1.7.0_80 system
0.11.2 -Java-1.7.0_60 system
0.11.3 -Java-1.7.0_80 system
0.11.4 -Java-1.8.0_66 system
0.11.4 -Java-1.8.0_74 system
0.11.5 -Java-1.7.0_80 system
0.11.5 -Java-1.8.0_144 system
0.11.5 -Java-1.8.0_74 system
0.11.7 -Java-1.8.0_162 system
0.11.8 -Java-1.8 system

FastQTL

FastQTL is a QTL mapper

homepage: http://fastqtl.sourceforge.net/

version toolchain
2.184 foss/2018b

fastqz

fastqz is a compressor for FASTQ files. FASTQ is the output of DNA sequencing machines. It is one of the compressors described in the paper: Bonfield JK, Mahoney MV (2013) Compression of FASTQ and SAM Format Sequencing Data. (mirror) PLoS ONE 8(3): e59190. doi:10.1371/journal.pone.0059190

homepage: http://mattmahoney.net/dc/fastqz/

version toolchain
1.5 GCC/4.8.2

FastRFS

Fast Robinson Foulds Supertrees

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

version toolchain
1.0-20190613 gompi/2019a

fastStructure

fastStructure is an algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x.

homepage: https://rajanil.github.io/fastStructure/

version versionsuffix toolchain
1.0 -Python-2.7.11 foss/2016a
1.0 -Python-2.7.12 foss/2016b
1.0 -Python-2.7.13 foss/2017a

FastTree

FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.

homepage: http://www.microbesonline.org/fasttree/

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

FASTX-Toolkit

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

homepage: http://hannonlab.cshl.edu/fastx_toolkit/

version toolchain
0.0.14 GCCcore/7.3.0, foss/2016a, foss/2016b, intel/2018a

fbm

Exact methods for simulating fractional Brownian motion and fractional Gaussian noise in Python

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

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

FCM

FCM is a set of tools for managing and building source code.

homepage: http://www.metoffice.gov.uk/research/collaboration/fcm

version toolchain
2.3.1 system

FDS

Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires.

homepage: https://pages.nist.gov/fds-smv/

version versionsuffix toolchain
6.0.1 -no-OFED system
6.5.2   intel/2016b
6.5.3   intel/2017a
6.6.0   intel/2017b, intel/2018a
6.7.0   intel/2018a

fdstools

Forensic DNA Sequencing Tools Tools for characterisation and filtering of PCR stutter artefacts and other systemic noise in Next Generation Sequencing data of forensic STR markers.

homepage: https://git.lumc.nl/jerryhoogenboom/fdstools

version versionsuffix toolchain
20160322 -Python-2.7.11 foss/2016a

FDTD_Solutions

High performance FDTD-method Maxwell solver for the design, analysis and optimization of nanophotonic devices, processes and materials.

homepage: http://www.lumerical.com/tcad-products/fdtd/

version toolchain
8.6.2 system
8.11.337 system
8.16.982 system
8.20.1731 system

feh

feh is an X11 image viewer aimed mostly at console users. Unlike most other viewers, it does not have a fancy GUI, but simply displays images. It is controlled via commandline arguments and configurable key/mouse actions.

homepage: https://feh.finalrewind.org/

version toolchain
2.26 GCCcore/6.4.0

Ferret

Ferret is an interactive computer visualization and analysis environment designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data sets.

homepage: http://ferret.pmel.noaa.gov/

version toolchain
7.3 intel/2017b

FFC

The FEniCS Form Compiler (FFC) is a compiler for finite element variational forms.

homepage: https://bitbucket.org/fenics-project/ffc

version versionsuffix toolchain
2018.1.0 -Python-3.6.4 foss/2018a

FFLAS-FFPACK

Finite Field Linear Algebra Subroutines / Package

homepage: https://linbox-team.github.io/fflas-ffpack/

version toolchain
2.2.0 foss/2016a

FFmpeg

A complete, cross-platform solution to record, convert and stream audio and video.

homepage: https://www.ffmpeg.org/

version toolchain
0.10.16 gimkl/2.11.5, intel/2016a
2.8.6 intel/2016a
2.8.7 foss/2016a, intel/2016a
3.0.2 foss/2016a, intel/2016a
3.1.3 foss/2016b, intel/2016b
3.2.4 gimkl/2017a
3.3.1 foss/2016b
3.3.4 intel/2017a
3.4 GCCcore/6.4.0
3.4.1 foss/2017b, intel/2017b
3.4.2 foss/2018a, intel/2018a
3.4.5 foss/2018b
4.0 foss/2018a, intel/2018a
4.0.1 intel/2018a
4.1 foss/2018b, fosscuda/2018b, intel/2018b
4.1.3 GCCcore/8.2.0
4.2.1 GCCcore/8.3.0

ffnet

Feed-forward neural network solution for python

homepage: http://ffnet.sourceforge.net/

version versionsuffix toolchain
0.8.3 -Python-2.7.11 intel/2016a

FFTW

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.

homepage: http://www.fftw.org

version versionsuffix toolchain
2.1.5   intel/2016b, intel/2017a, intel/2018b
3.3.4   gmpich/2016a, gmvapich2/1.7.20, gmvapich2/2016a, gompi/2016.04, gompi/2016.06, gompi/2016.07, gompi/2016a, gompi/2016b, intel/2016a, intel/2016b
3.3.5   gompi/2016.07, gompi/2016.09, gompi/2016b, intel/2016b
3.3.6   gimpi/2017b, gimpic/2017b, gompi/2017a, gompi/2017b, gompic/2017b, intel/2016b, intel/2017a, intel/2017b, intelcuda/2017b
3.3.7   gimkl/2017a, gimpi/2018a, gmpich/2017.08, gompi/2018a, gompic/2018a, intel/2017b, intel/2018.00, intel/2018.01, intel/2018a, iomkl/2018a
3.3.7 -serial GCC/6.4.0-2.28
3.3.8   gompi/2018.08, gompi/2018b, gompi/2019a, gompi/2019b, gompic/2018b, gompic/2019a, gompic/2019b, intel/2018b, intel/2019a, iomkl/2018b

FGSL

FGSL: A Fortran interface to the GNU Scientific Library

homepage: https://www.lrz.de/services/software/mathematik/gsl/fortran/

version toolchain
1.1.0 intel/2016b

FIAT

The FInite element Automatic Tabulator (FIAT) supports generation of arbitrary order instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating arbitrary order instances of Jacobi-type quadrature rules on the same element shapes.

homepage: https://bitbucket.org/fenics-project/fiat

version versionsuffix toolchain
1.6.0 -Python-2.7.11 foss/2016a, intel/2016a
2018.1.0 -Python-3.6.4 foss/2018a

file

The file command is ‘a file type guesser’, that is, a command-line tool that tells you in words what kind of data a file contains.

homepage: http://www.darwinsys.com/file/

version toolchain
5.17 GCC/4.8.2
5.25 intel/2016a
5.28 foss/2016b
5.30 intel/2017a
5.33 GCCcore/6.4.0
5.35 GCCcore/7.3.0

Filtlong

Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter

homepage: https://github.com/rrwick/Filtlong

version toolchain
0.2.0 foss/2016b

find_circ

circRNA detection from RNA-seq reads

homepage: https://github.com/marvin-jens/find_circ

version versionsuffix toolchain
1.2-20170228 -Python-2.7.14 intel/2017b

findhap

Find haplotypes and impute genotypes using multiple chip sets and sequence data

homepage: http://aipl.arsusda.gov/software/findhap/

version toolchain
4 system

findutils

findutils: The GNU find, locate, updatedb, and xargs utilities

homepage: http://www.gnu.org/software/findutils/findutils.html

version toolchain
4.4.2 GCC/4.8.2

fineRADstructure

A package for population structure inference from RAD-seq data

homepage: http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html

version toolchain
20180709 intel/2018a

fineSTRUCTURE

fineSTRUCTURE is a fast and powerful algorithm for identifying population structure using dense sequencing data.

homepage: https://people.maths.bris.ac.uk/~madjl/finestructure/finestructure_info.html

version toolchain
2.1.3 intel/2017b

Firefox

Firefox is a free, open source Web browser for Windows, Linux and Mac OS X. It is based on the Mozilla code base and offers customization options and features such as its capability to block pop-up windows, tabbed browsing, privacy and security measures, smart searching, and RSS live bookmarks.

homepage: https://www.mozilla.org/en-US/firefox/new/

version toolchain
44.0.2 system

FireWorks

FireWorks helps run calculation workflows, with a centralized workflow server controlling many worker nodes.

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

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

fixesproto

X.org FixesProto protocol headers.

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version toolchain
5.0 foss/2016a, gimkl/2.11.5, intel/2016a

FLANN

FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces.

homepage: http://www.cs.ubc.ca/research/flann/

version versionsuffix toolchain
1.8.4 -Python-2.7.11 intel/2016a
1.8.4 -Python-2.7.14 intel/2017b

FLASH

FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data.

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

version toolchain
1.2.11 foss/2016a, foss/2018a, foss/2018b
2.2.00 foss/2018b

Flask

” Flask is a lightweight WSGI web application framework. It is designed to make getting started quick and easy, with the ability to scale up to complex applications.

homepage: https://www.palletsprojects.com/p/flask/

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

FLEUR

FLEUR is a feature-full, freely available FLAPW (full potential linearized augmented planewave) code, based on density-functional theory.

homepage: http://www.flapw.de/

version toolchain
0.26e intel/2016a

flex

Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.

homepage: http://flex.sourceforge.net/

version toolchain
2.5.35 system
2.5.38 GCC/4.8.2
2.5.39 GCC/4.9.2, GCC/4.9.2-binutils-2.25, GCC/4.9.3, GCC/4.9.3-binutils-2.25, GCC/5.1.0-binutils-2.25, GCCcore/4.9.2, GCCcore/4.9.3, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/8.2.0, GNU/4.9.3-2.25, foss/2016a, gimkl/2.11.5, intel/2016.02-GCC-4.9, intel/2016a, intel/2016b, system
2.6.0 GCC/4.9.2, GCCcore/4.9.3, GCCcore/4.9.4, GCCcore/5.3.0, GCCcore/5.4.0, GCCcore/6.1.0, GCCcore/6.2.0, foss/2016a, foss/2016b, gimkl/2.11.5, intel/2016a, intel/2016b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25, system
2.6.2 intel/2016b
2.6.3 GCCcore/5.4.0, GCCcore/6.3.0, GCCcore/7.1.0, gimkl/2017a, system
2.6.4 GCCcore/5.5.0, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/7.4.0, GCCcore/8.1.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.1.0, GCCcore/9.2.0, GCCcore/system, system

FlexiDot

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

homepage: https://github.com/molbio-dresden/flexidot

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

FLINT

FLINT (Fast Library for Number Theory) is a C library in support of computations in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides various low-level routines for fast arithmetic. FLINT is extensively documented and tested.

homepage: http://www.flintlib.org

version toolchain
2.5.2 GCC/7.3.0-2.30, iccifort/2018.3.222-GCC-7.3.0-2.30

FLTK

FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.

homepage: http://www.fltk.org

version toolchain
1.3.3 foss/2016a, foss/2016b, intel/2016a, intel/2016b
1.3.4 foss/2017b, foss/2018a, foss/2018b, fosscuda/2017b, fosscuda/2018a, fosscuda/2018b, intel/2017a, intel/2017b, intel/2018a, intel/2018b, intelcuda/2017b
1.3.5 GCC/8.2.0-2.31.1

FLUENT

ANSYS FLUENT software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants.

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

version toolchain
14.5 system
15.0.7 system
16.0 system
17.1 system
18.0 system
18.1 system

Flye

Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies.

homepage: https://github.com/fenderglass/Flye

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

FMILibrary

FMI library is intended as a foundation for applications interfacing FMUs (Functional Mockup Units) that follow FMI Standard. This version of the library supports FMI 1.0 and FMI2.0. See http://www.fmi-standard.org/

homepage: https://jmodelica.org/

version toolchain
2.0.3 intel/2018b

FMRIprep

FMRIprep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting.

homepage: https://fmriprep.readthedocs.io

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

fmt

fmt (formerly cppformat) is an open-source formatting library.

homepage: http://fmtlib.net/

version toolchain
3.0.1 foss/2016b, intel/2016b
3.0.2 GCCcore/6.4.0, intel/2017a
5.3.0 GCCcore/7.3.0, GCCcore/8.2.0

FoldX

FoldX is used to provide a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes.

homepage: http://foldx.crg.es/

version toolchain
2.5.2 system
3.0-beta5.1 system
3.0-beta6 system
3.0-beta6.1 system

fontconfig

Fontconfig is a library designed to provide system-wide font configuration, customization and application access.

homepage: https://www.freedesktop.org/wiki/Software/fontconfig/

version versionsuffix toolchain
2.11.94   foss/2016a, intel/2016a
2.11.95   foss/2016a, intel/2016a
2.12.1   GCCcore/5.4.0, GCCcore/6.3.0, foss/2016b, gimkl/2017a, intel/2016b
2.12.1 -libpng-1.6.29 GCCcore/6.3.0
2.12.4   GCCcore/6.4.0
2.12.6   GCCcore/6.4.0
2.13.0   GCCcore/6.4.0, GCCcore/7.3.0
2.13.1   GCCcore/8.2.0, GCCcore/8.3.0

fontsproto

X11 font extension wire protocol

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version toolchain
2.1.3 foss/2016a, gimkl/2.11.5, intel/2016a

foss

GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.

homepage: https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain

version toolchain
2016.04 system
2016.06 system
2016.07 system
2016.09 system
2016a system
2016b system
2017a system
2017b system
2018.08 system
2018a system
2018b system
2019a system
2019b system

fosscuda

GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.

homepage: (none)

version toolchain
2017b system
2018a system
2018b system
2019a system
2019b system

FoX

FoX is an XML library written in Fortran 95. It allows software developers to read, write and modify XML documents from Fortran applications without the complications of dealing with multi-language development.

homepage: http://homepages.see.leeds.ac.uk/~earawa/FoX/

version toolchain
4.1.2 intel/2017b, intel/2018a

FPM

Effing package management! Build packages for multiple platforms (deb, rpm, etc) with great ease and sanity.

homepage: https://github.com/jordansissel/fpm

version versionsuffix toolchain
1.3.3 -Ruby-2.1.6 system

fqtrim

fqtrim is a versatile stand-alone utility that can be used to trim adapters, poly-A tails, terminal unknown bases (Ns) and low quality 3’ regions in reads from high-throughput next-generation sequencing machines.

homepage: http://ccb.jhu.edu/software/fqtrim/

version toolchain
0.9.4 intel/2016b
0.9.5 intel/2017a

fqzcomp

Fqzcomp is a basic fastq compressor, designed primarily for high performance. Despite that it is comparable to bzip2 for compression levels.

homepage: http://sourceforge.net/projects/fqzcomp/

version toolchain
4.6 GCC/4.8.2

FragGeneScan

FragGeneScan is an application for finding (fragmented) genes in short reads.

homepage: http://omics.informatics.indiana.edu/FragGeneScan/

version toolchain
1.31 foss/2018b

FRANz

A fast and flexible parentage inference program for natural populations.

homepage: https://www.bioinf.uni-leipzig.de/Software/FRANz

version toolchain
2.0.0 foss/2018a

FreeFem++

FreeFem++ is a partial differential equation solver. It has its own language. freefem scripts can solve multiphysics non linear systems in 2D and 3D.

homepage: http://www.freefem.org/

version versionsuffix toolchain
3.58 -downloaded-deps foss/2017b
3.60 -downloaded-deps intel/2018a
3.61-1 -downloaded-deps intel/2018a

freeglut

freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library.

homepage: http://freeglut.sourceforge.net/

version versionsuffix toolchain
3.0.0   GCCcore/8.2.0, foss/2016a, foss/2016b, foss/2017b, foss/2018a, foss/2018b, intel/2016a, intel/2016b, intel/2017a, intel/2017b, intel/2018a
3.0.0 -Mesa-11.2.1 foss/2016a, intel/2016a

FreeImage

FreeImage is an Open Source library project for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today’s multimedia applications. FreeImage is easy to use, fast, multithreading safe.

homepage: http://freeimage.sourceforge.net

version toolchain
3.18.0 GCCcore/7.3.0

FreeSurfer

FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data.

homepage: https://surfer.nmr.mgh.harvard.edu/

version versionsuffix toolchain
5.3.0 -centos4_x86_64 system
5.3.0 -centos6_x86_64 system
6.0.0 -centos6_x86_64 system
6.0.1 -centos6_x86_64 system

freetype

FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well.

homepage: http://freetype.org

version versionsuffix toolchain
2.6.2   foss/2016a, gimkl/2.11.5, intel/2016a
2.6.3   foss/2016a, intel/2016a
2.6.5   GCCcore/4.9.3, GCCcore/5.4.0, foss/2016b, intel/2016b
2.7   foss/2016b, intel/2016b
2.7.1   GCCcore/5.4.0, GCCcore/6.3.0, gimkl/2017a, intel/2016b
2.7.1 -libpng-1.6.29 GCCcore/6.3.0
2.8   GCCcore/6.4.0
2.8.1   GCCcore/6.4.0
2.9   GCCcore/6.4.0
2.9.1   GCCcore/7.3.0, GCCcore/8.2.0
2.10.1   GCCcore/8.3.0

FreeXL

FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet.

homepage: https://www.gaia-gis.it/fossil/freexl/index

version toolchain
1.0.2 foss/2016b, intel/2016b
1.0.3 GCCcore/6.4.0
1.0.5 GCCcore/7.3.0, GCCcore/8.2.0

FriBidi

The Free Implementation of the Unicode Bidirectional Algorithm.

homepage: https://github.com/fribidi/fribidi

version toolchain
1.0.1 foss/2018a, intel/2018a
1.0.2 GCCcore/6.4.0
1.0.5 GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0

FSL

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.

homepage: http://www.fmrib.ox.ac.uk/fsl/

version versionsuffix toolchain
5.0.9   intel/2016a
5.0.9 -Mesa-11.2.1 intel/2016a
5.0.9 -centos6_64 system
5.0.10   foss/2017b, intel/2017a, intel/2017b
5.0.11   foss/2018b
5.0.11 -Python-3.6.6 foss/2018b
6.0.1 -Python-2.7.15 foss/2019a
6.0.1 -Python-3.7.2 foss/2019a

FSLeyes

FSLeyes is the FSL image viewer.

homepage: https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes

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

FTGL

FTGL is a free open source library to enable developers to use arbitrary fonts in their OpenGL (www.opengl.org) applications.

homepage: http://ftgl.sourceforge.net/docs/html/

version toolchain
2.1.3-rc5 GCCcore/8.2.0, foss/2017b, foss/2018a, fosscuda/2018b, intel/2017b

fullrmc

Reverse Monte Carlo (RMC) is probably best known for its applications in condensed matter physics and solid state chemistry. fullrmc which stands for FUndamental Library Language for Reverse Monte Carlo is different than traditional RMC but a stochastic modelling method to solve an inverse problem whereby an atomic/molecular model is adjusted until its atoms position havei the greatest consistency with a set of experimental data.

homepage: http://bachiraoun.github.io/fullrmc

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

FUNWAVE-TVD

FUNWAVE–TVD is the TVD version of the fully nonlinear Boussinesq wave model (FUNWAVE) initially developed by Kirby et al.

homepage: https://fengyanshi.github.io

version versionsuffix toolchain
3.1-20170525   intel/2017a
3.1-20170525 -no-storm intel/2017a

FUSE

The reference implementation of the Linux FUSE (Filesystem in Userspace) interface

homepage: https://github.com/libfuse/libfuse

version toolchain
3.2.6 intel/2018a
3.4.1 foss/2018a

future

python-future is the missing compatibility layer between Python 2 and Python 3.

homepage: http://python-future.org/

version versionsuffix toolchain
0.16.0 -Python-2.7.14 foss/2018a, intel/2017b, intel/2018a
0.16.0 -Python-2.7.15 foss/2018b, intel/2018b
0.16.0 -Python-3.6.3 intel/2017b
0.16.0 -Python-3.6.6 foss/2018b

fxtract

Extract sequences from a fastx (fasta or fastq) file given a subsequence.

homepage: https://github.com/ctSkennerton/fxtract

version toolchain
2.3 GCCcore/8.2.0

G

g2clib - g2lib - g2log - Gaia - GAMESS-US - gap - GapCloser - GapFiller - GAT - GATE - GATK - Gblocks - gbs2ploidy - gc - GC3Pie - GCC - GCCcore - gcccuda - GConf - Gctf - GD - GDAL - GDB - gdbgui - gdc-client - GDCHART - GDCM - GDGraph - gdist - Gdk-Pixbuf - Geant4 - gearshifft - GEM-library - GEMMA - gencore_variant_detection - GeneMark-ET - GenomeMapper - GenomeTester4 - GenomeThreader - GenotypeHarmonizer - gensim - geopy - GEOS - Gerris - GETORB - gettext - GffCompare - gffread - gflags - GFOLD - GHC - Ghostscript - giflib - gifsicle - GIMIC - gimkl - gimpi - gimpic - GIMPS - giolf - giolfc - git - git-lfs - GitPython - Givaro - Giza - GL2PS - Glade - glew - GLib - glibc - GLibmm - GLIMMER - GlimmerHMM - GLM - GlobalArrays - GlobusConnectPersonal - glog - GLPK - glproto - GMAP-GSNAP - GMP - gmpich - gmpolf - gmpy2 - gmsh - GMT - gmvapich2 - gmvolf - GNU - gnuplot - GnuTLS - Go - GObject-Introspection - golf - gomkl - gompi - gompic - google-java-format - googletest - GP2C - GPAW - GPAW-setups - gperf - gperftools - gpustat - Grace - grace - Gradle - graph-tool - Graphene - GraphicsMagick - Graphviz - graphviz - GRASS - Greenlet - Grep - grib_api - GRIT - GRNBoost - GroIMP - GROMACS - GroopM - GSL - gSOAP - GST-plugins-base - GStreamer - GTDB-Tk - gtest - GTK+ - GTOOL - GTS - guenomu - Guile - Gurobi - gzip

g2clib

Library contains GRIB2 encoder/decoder (‘C’ version).

homepage: http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/

version toolchain
1.6.0 intel/2017a, intel/2017b, intel/2018a, intel/2018b

g2lib

Library contains GRIB2 encoder/decoder and search/indexing routines.

homepage: http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/

version toolchain
1.4.0 intel/2017a, intel/2017b, intel/2018a
3.1.0 intel/2018b

g2log

g2log, efficient asynchronous logger using C++11

homepage: https://sites.google.com/site/kjellhedstrom2//g2log-efficient-background-io-processign-with-c11

version toolchain
1.0 foss/2016b

Gaia

Gaia is a C++ library with python bindings which implements similarity measures and classifications on the results of audio analysis, and generates classification models that Essentia can use to compute high-level description of music.

homepage: https://github.com/MTG/gaia

version versionsuffix toolchain
2.4.5 -Python-2.7.15 GCCcore/8.2.0

GAMESS-US

The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package.

homepage: http://www.msg.chem.iastate.edu/gamess/index.html

version versionsuffix toolchain
20141205-R1   intel/2016a
20170420-R1   intel/2016b
20170420-R1 -sockets intel/2016b
20180214-R1   foss/2016b
20180214-R1 -sockets foss/2016b

gap

GAP is a system for computational discrete algebra, with particular emphasis on Computational Group Theory.

homepage: https://www.gap-system.org

version toolchain
4.9.3 intel/2018b

GapCloser

GapCloser is designed to close the gaps emerging during the scaffolding process by SOAPdenovo or other assembler, using the abundant pair relationships of short reads.

homepage: https://sourceforge.net/projects/soapdenovo2/files/GapCloser/

version toolchain
1.12-r6 foss/2018a, intel/2017b

GapFiller

GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. It can be used for both DNA and RNA and it has been tested on Illumina data.

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

version toolchain
2.1.1 intel/2017a

GAT

The Genomic Association Tester (GAT) is a tool for computing the significance of overlap between multiple sets of genomic intervals. GAT estimates significance based on simulation.

homepage: https://gat.readthedocs.io/

version versionsuffix toolchain
1.2.2 -Python-2.7.11 foss/2016a

GATE

GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography

homepage: http://www.opengatecollaboration.org/

version versionsuffix toolchain
6.2 -Python-2.7.11 intel/2016a
7.1 -Python-2.7.11 intel/2016a
7.2 -Python-2.7.11 intel/2016a
8.0 -Python-2.7.14 foss/2017b, intel/2017b
8.0 -Python-2.7.14-Geant4-10.04 intel/2017b
8.1.p01 -Python-2.7.15 foss/2018b
8.2 -Python-2.7.14 foss/2017b, intel/2017b
8.2 -Python-2.7.15 foss/2018b

GATK

The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

homepage: https://www.broadinstitute.org/gatk/

version versionsuffix toolchain
1.0.5083   system
2.5-2 -Java-1.7.0_10 system
2.6-5 -Java-1.7.0_10 system
2.7-4   system
2.7-4 -Java-1.7.0_10 system
2.8-1 -Java-1.7.0_10 system
3.0-0 -Java-1.7.0_10 system
3.3-0 -Java-1.7.0_21 system
3.3-0 -Java-1.7.0_80 system
3.3-0 -Java-1.8.0_66 system
3.5 -Java-1.8.0_66 system
3.5 -Java-1.8.0_74 system
3.6 -Java-1.8.0_92 system
3.7 -Java-1.8.0_112 system
3.8-0 -Java-1.8.0_144 system
4.0.1.2 -Java-1.8 system
4.0.4.0 -Python-2.7.14 intel/2018a
4.0.4.0 -Python-3.6.4 intel/2018a
4.0.5.1 -Python-3.6.4 foss/2018a
4.0.7.0 -Python-2.7.14 intel/2018a
4.0.7.0 -Python-3.6.4 intel/2018a
4.0.8.1 -Python-2.7.15 foss/2018b
4.0.8.1 -Python-3.6.6 foss/2018b
4.0.10.0 -Python-3.6.6 foss/2018b
4.0.12.0 -Python-3.6.6 foss/2018b
4.1.0.0 -Python-3.6.6 foss/2018b
4.1.2.0 -Java-1.8 GCCcore/8.2.0
4.1.3.0 -Java-1.8 GCCcore/8.3.0

Gblocks

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

homepage: http://molevol.cmima.csic.es/castresana/Gblocks.html

version toolchain
0.91b system

gbs2ploidy

Inference of Ploidy from (Genotyping-by-Sequencing) GBS Data

homepage: https://cran.r-project.org/web/packages/gbs2ploidy

version versionsuffix toolchain
1.0 -R-3.4.3 intel/2017b

gc

The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new.

homepage: http://hboehm.info/gc/

version toolchain
7.4.4 GCC/4.9.3-2.25, foss/2016a
7.6.0 GCCcore/6.4.0
7.6.4 GCCcore/7.3.0
7.6.10 GCCcore/8.2.0

GC3Pie

GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution environments.

homepage: https://gc3pie.readthedocs.org

version toolchain
2.4.2 system
2.5.0 system
2.5.2 system

GCC

The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,…).

homepage: http://gcc.gnu.org/

version versionsuffix toolchain
4.8.1   system
4.8.1 -CLooG system
4.8.2   system
4.8.2 -CLooG system
4.8.2 -CLooG-multilib system
4.8.2 -multilib system
4.8.3   system
4.8.3 -CLooG-multilib system
4.8.4   system
4.8.4 -CLooG system
4.8.4 -CLooG-multilib system
4.8.5   system
4.9.0   system
4.9.0 -CLooG system
4.9.0 -CLooG-multilib system
4.9.1   system
4.9.1 -CLooG system
4.9.1 -CLooG-multilib system
4.9.2   system
4.9.2 -CLooG system
4.9.2 -CLooG-multilib system
4.9.2 -binutils-2.25 system
4.9.3   system
4.9.3 -2.25 system
4.9.3 -binutils-2.25 system
4.9.4 -2.25 system
5.1.0   system
5.1.0 -binutils-2.25 system
5.2.0   system
5.3.0   system
5.3.0 -2.26 system
5.4.0 -2.26 system
5.5.0 -2.26 system
6.1.0 -2.27 system
6.2.0 -2.27 system
6.3.0 -2.27 system
6.3.0 -2.28 system
6.4.0 -2.28 system
7.1.0 -2.28 system
7.2.0 -2.29 system
7.3.0 -2.30 system
7.4.0 -2.31.1 system
8.1.0 -2.30 system
8.2.0 -2.31.1 system
8.3.0   system
8.3.0 -2.32 system
9.1.0 -2.32 system
9.2.0 -2.32 system
system   system
system -2.29 system

GCCcore

The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,…).

homepage: http://gcc.gnu.org/

version toolchain
4.9.2 system
4.9.3 system
4.9.4 system
5.3.0 system
5.4.0 system
5.5.0 system
6.1.0 system
6.2.0 system
6.3.0 system
6.4.0 system
6.5.0 system
7.1.0 system
7.2.0 system
7.3.0 system
7.4.0 system
8.1.0 system
8.2.0 system
8.3.0 system
9.1.0 system
9.2.0 system
system system

gcccuda

GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.

homepage: (none)

version toolchain
2016.08 system
2017b system
2018a system
2018b system
2019a system
2019b system

GConf

GConf is a system for storing application preferences. It is intended for user preferences; not configuration of something like Apache, or arbitrary data storage.

homepage: https://projects.gnome.org/gconf/

version toolchain
3.2.6 GCCcore/8.2.0, foss/2016a, foss/2018b, intel/2016a, intel/2016b, intel/2017a, intel/2017b

Gctf

Gctf: real-time CTF determination and correction, Kai Zhang, 2016

homepage: https://www.mrc-lmb.cam.ac.uk/kzhang/

version toolchain
1.06 system

GD

GD.pm - Interface to Gd Graphics Library

homepage: https://github.com/lstein/Perl-GD

version versionsuffix toolchain
2.66 -Perl-5.24.0 foss/2016b
2.68 -Perl-5.26.1 GCCcore/6.4.0
2.69 -Perl-5.28.0 GCCcore/7.3.0

GDAL

GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.

homepage: https://www.gdal.org

version versionsuffix toolchain
2.0.2   foss/2016a, intel/2016a
2.1.0   foss/2016a, foss/2016b, intel/2016b
2.1.1   foss/2016a
2.1.1 -Python-2.7.12 intel/2016b
2.1.2 -Python-2.7.12 intel/2016b
2.1.3 -Python-2.7.12 foss/2016b, intel/2016b
2.1.3 -Python-2.7.13 intel/2017a
2.1.3 -Python-3.6.1 intel/2017a
2.2.0 -Python-2.7.13-HDF5-1.8.18 intel/2017a
2.2.0 -Python-2.7.13-HDF5-HDF intel/2017a
2.2.0 -Python-3.6.1 intel/2017a
2.2.2 -Python-2.7.14 intel/2017b
2.2.2 -Python-2.7.14-HDF5-1.8.19 intel/2017b
2.2.3 -Python-2.7.14 foss/2017b, foss/2018a, intel/2017b, intel/2018a
2.2.3 -Python-2.7.15 foss/2018b
2.2.3 -Python-3.6.3 foss/2017b
2.2.3 -Python-3.6.4 foss/2018a, intel/2018a, iomkl/2018a
2.2.3 -Python-3.6.6 foss/2018b, intel/2018b
3.0.0 -Python-2.7.15 foss/2019a
3.0.0 -Python-3.7.2 foss/2019a, intel/2019a

GDB

The GNU Project Debugger

homepage: http://www.gnu.org/software/gdb/gdb.html

version versionsuffix toolchain
7.8.2   GCC/4.9.2
7.9   GCC/4.9.2
7.10.1 -Python-2.7.11 foss/2016a, intel/2016a
7.11 -Python-2.7.11 foss/2016a, intel/2016a
7.11.1 -Python-2.7.12 foss/2016b, intel/2016b
8.0.1 -Python-2.7.14 foss/2017b
8.0.1 -Python-3.6.3 foss/2017b
8.1 -Python-2.7.14 foss/2018a
8.1.1 -Python-2.7.14 intel/2018a
8.3 -Python-3.7.2 GCCcore/8.2.0

gdbgui

Browser-based frontend to gdb (gnu debugger). Add breakpoints, view the stack, visualize data structures, and more in C, C++, Go, Rust, and Fortran. Run gdbgui from the terminal and a new tab will open in your browser.

homepage: https://gdbgui.com

version versionsuffix toolchain
0.13.1.2 -Python-3.7.2 GCCcore/8.2.0

gdc-client

The gdc-client provides several convenience functions over the GDC API which provides general download/upload via HTTPS.

homepage: https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool

version versionsuffix toolchain
1.0.1 -Python-2.7.12 intel/2016b
1.3.0 -Python-2.7.14 foss/2018a, intel/2017b
1.3.0 -Python-2.7.15 foss/2018b

GDCHART

Easy to use C API, high performance library to create charts and graphs in PNG, GIF and WBMP format.

homepage: http://users.fred.net/brv/chart

version toolchain
0.11.5dev GCCcore/8.2.0

GDCM

Grassroots DICOM: Cross-platform DICOM implementation

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

version toolchain
2.8.8 GCCcore/6.4.0

GDGraph

GDGraph is a Perl package to generate charts

homepage: https://metacpan.org/release/GDGraph

version versionsuffix toolchain
1.54 -Perl-5.26.1 intel/2018a
1.54 -Perl-5.28.0 foss/2018b

gdist

The gdist module is a Cython interface to a C++ library (http://code.google.com/p/geodesic/) for computing geodesic distance which is the length of shortest line between two vertices on a triangulated mesh in three dimensions, such that the line lies on the surface.

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

version versionsuffix toolchain
1.0.3 -Python-2.7.11 intel/2016a

Gdk-Pixbuf

The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3.

homepage: https://developer.gnome.org/gdk-pixbuf/stable/

version toolchain
2.32.3 intel/2016a
2.35.1 foss/2016a, intel/2016a
2.36.0 foss/2016b, intel/2016b
2.36.8 intel/2017a
2.36.10 intel/2017a
2.36.11 foss/2017b, foss/2018a, fosscuda/2018b, intel/2017b, intel/2018a
2.36.12 foss/2018b, fosscuda/2018b
2.38.1 GCCcore/8.2.0

Geant4

Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.

homepage: http://geant4.cern.ch/

version toolchain
9.5.p02 intel/2016a
9.6.p04 intel/2016a
10.01.p03 intel/2016a
10.02.p01 intel/2016a
10.03.p03 foss/2017b, intel/2017b
10.04 intel/2017b
10.5 foss/2017b, foss/2018b, intel/2017b, intel/2018b

gearshifft

Benchmark Suite for Heterogenuous FFT Implementations

homepage: https://github.com/mpicbg-scicomp/gearshifft

version toolchain
0.4.0 foss/2019a

GEM-library

Next-generation sequencing platforms (Illumina/Solexa, ABI/SOLiD, etc.) call for powerful and very optimized tools to index/analyze huge genomes. The GEM library strives to be a true “next-generation” tool for handling any kind of sequence data, offering state-of-the-art algorithms and data structures specifically tailored to this demanding task. At the moment, efficient indexing and searching algorithms based on the Burrows-Wheeler transform (BWT) have been implemented. The library core is written in C for maximum speed, with concise interfaces to higher-level programming languages like OCaml and Python. Many high-performance standalone programs (mapper, splice mapper, etc.) are provided along with the library; in general, new algorithms and tools can be easily implemented on the top of it.

homepage: http://algorithms.cnag.cat/wiki/The_GEM_library

version versionsuffix toolchain
20130406-045632 _pre-release-3_Linux-x86_64 system

GEMMA

Genome-wide Efficient Mixed Model Association

homepage: https://github.com/genetics-statistics/GEMMA

version toolchain
0.97 foss/2016b
0.98.1 foss/2018b

gencore_variant_detection

This is a bundled install of many software packages for doing variant detection analysis.

homepage: https://nyuad-cgsb.github.io/variant_detection/public/index.html

version toolchain
1.0 system

GeneMark-ET

Eukaryotic gene prediction suite with automatic training

homepage: http://exon.gatech.edu/GeneMark

version toolchain
4.38 GCCcore/8.2.0

GenomeMapper

GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. This version is used to align against a single reference. If you are unsure which one is the appropriate GenomeMapper, you might want to use this one.

homepage: https://1001genomes.org/software/genomemapper_singleref.html

version toolchain
0.4.4 foss/2016a

GenomeTester4

A toolkit for performing set operations - union, intersection and complement - on k-mer lists.

homepage: https://github.com/bioinfo-ut/GenomeTester4

version toolchain
4.0 intel/2018a

GenomeThreader

GenomeThreader is a software tool to compute gene structure predictions.

homepage: http://genomethreader.org

version versionsuffix toolchain
1.7.1 -Linux_x86_64-64bit system

GenotypeHarmonizer

The Genotype Harmonizer is an easy to use command-line tool that allows harmonization of genotype data stored using different file formats with different and potentially unknown strands.

homepage: https://github.com/molgenis/systemsgenetics/wiki/Genotype-Harmonizer

version versionsuffix toolchain
1.4.14 -Java-1.7.0_80 system

gensim

Gensim is a Python library for topic modelling, document indexing and similarity retrieval with large corpora.

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

version versionsuffix toolchain
0.13.2 -Python-2.7.11 foss/2016a

geopy

geopy is a Python 2 and 3 client for several popular geocoding web services.

homepage: https://github.com/geopy/geopy

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

GEOS

GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)

homepage: https://trac.osgeo.org/geos

version versionsuffix toolchain
3.5.0 -Python-2.7.11 intel/2016a
3.5.0 -Python-2.7.12 intel/2016b
3.6.1 -Python-2.7.12 foss/2016b, intel/2016b
3.6.1 -Python-2.7.13 intel/2017a
3.6.1 -Python-3.6.1 intel/2017a
3.6.2 -Python-2.7.14 foss/2017b, foss/2018a, intel/2017b, intel/2018a
3.6.2 -Python-2.7.15 foss/2018b
3.6.2 -Python-3.6.2 foss/2017b
3.6.2 -Python-3.6.3 foss/2017b, intel/2017b, intel/2018.01
3.6.2 -Python-3.6.4 foss/2018a, intel/2018a, iomkl/2018a
3.6.2 -Python-3.6.6 foss/2018b, intel/2018b
3.7.2 -Python-2.7.15 foss/2019a
3.7.2 -Python-3.7.2 foss/2019a, intel/2019a

Gerris

Gerris is a Free Software program for the solution of the partial differential equations describing fluid flow

homepage: http://gfs.sourceforge.net/wiki/index.php/Main_Page

version toolchain
20131206 foss/2017b

GETORB

GETORB software package contains programs to handle the orbital data records (ODRs)

homepage: http://www.deos.tudelft.nl/ers/precorbs/tools/getorb_pack.shtml

version toolchain
2.3.2 intel/2017a

gettext

GNU ‘gettext’ is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation

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

version versionsuffix toolchain
0.18.2   system
0.19.4   GCC/4.9.2, system
0.19.6   GNU/4.9.3-2.25, foss/2016a, gimkl/2.11.5, intel/2016a, system
0.19.7   foss/2016a, intel/2016a, system
0.19.8   GCCcore/4.9.3, GCCcore/5.4.0, foss/2016.04, foss/2016b, intel/2016b, system
0.19.8.1   GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, system
0.19.8.1 -libxml2-2.9.7 GCCcore/6.4.0
0.20.1   GCCcore/8.3.0

GffCompare

GffCompare provides classification and reference annotation mapping and matching statistics for RNA-Seq assemblies (transfrags) or other generic GFF/GTF files.

homepage: https://github.com/gpertea/gffcompare

version toolchain
0.10.1 foss/2016b
0.10.6 GCCcore/7.3.0

gffread

GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.

homepage: https://github.com/gpertea/gffread

version toolchain
0.9.12 foss/2016b
0.10.6 GCCcore/7.3.0

gflags

The gflags package contains a C++ library that implements commandline flags processing. It includes built-in support for standard types such as string and the ability to define flags in the source file in which they are used.

homepage: https://github.com/gflags/gflags

version toolchain
2.1.2 foss/2016a
2.2.1 GCCcore/6.4.0, intel/2017a, intel/2017b
2.2.2 GCCcore/8.2.0

GFOLD

Generalized fold change for ranking differentially expressed genes from RNA-seq data

homepage: http://www.tongji.edu.cn/~zhanglab/GFOLD/index.html

version toolchain
1.1.4 intel/2016a

GHC

The Glorious/Glasgow Haskell Compiler

homepage: http://haskell.org/ghc/

version toolchain
6.12.3 system

Ghostscript

Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that.

homepage: http://ghostscript.com

version versionsuffix toolchain
9.19   intel/2016a, intel/2016b
9.20   foss/2016b, intel/2016b
9.21   intel/2017a
9.22   GCCcore/6.4.0, foss/2017b, intel/2017b
9.22 -cairo-1.14.12 GCCcore/6.4.0
9.23   GCCcore/6.4.0, GCCcore/7.3.0
9.23 -cairo-1.14.12 GCCcore/6.4.0
9.27   GCCcore/8.2.0

giflib

giflib is a library for reading and writing gif images. It is API and ABI compatible with libungif which was in wide use while the LZW compression algorithm was patented.

homepage: http://libungif.sourceforge.net/

version toolchain
5.1.4 GCCcore/7.3.0, GCCcore/8.2.0

gifsicle

Gifsicle is a command-line tool for creating, editing, and getting information about GIF images and animations. Making a GIF animation with gifsicle is easy.

homepage: https://github.com/kohler/gifsicle

version toolchain
1.92 GCCcore/8.2.0

GIMIC

The GIMIC program calculates magnetically induced currents in molecules. You need to provide this program with a density matrix in atomic-orbital (AO) basis and three (effective) magnetically perturbed AO density matrices in the proper format. Currently ACES2, Turbomole, G09, QChem, FERMION++, and LSDalton can produce these matrices.

homepage: http://gimic.readthedocs.io

version versionsuffix toolchain
2018.04.20 -Python-2.7.14 intel/2018a

gimkl

GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI and MKL

homepage: (none)

version toolchain
2.11.5 system
2017a system
2018b system

gimpi

GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI.

homepage: (none)

version toolchain
2.11.5 system
2017a system
2017b system
2018a system
2018b system

gimpic

GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including IntelMPI for MPI support with CUDA features enabled.

homepage: (none)

version toolchain
2017b system

GIMPS

GIMPS: Great Internet Mersenne Prime Search; it can be useful for limited stress testing of nodes, in user space

homepage: http://www.mersenne.org/

version toolchain
p95v279 GCC/4.8.2
p95v279.linux64 system

giolf

GNU Compiler Collection (GCC) based compiler toolchain, including IntelMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.

homepage: (none)

version toolchain
2017b system
2018a system

giolfc

GCC based compiler toolchain __with CUDA support__, and including IntelMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.

homepage: (none)

version toolchain
2017b system

git

Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.

homepage: http://git-scm.com/

version versionsuffix toolchain
1.8.5.6   GCC/4.9.2
2.2.2   GCC/4.9.2
2.4.1   GCC/4.9.2
2.8.0   foss/2016a
2.12.2   foss/2016b
2.13.1   foss/2016b
2.14.1   GCCcore/6.4.0
2.16.1   foss/2018a
2.18.0   GCCcore/7.3.0
2.19.1   GCCcore/7.3.0
2.21.0   GCCcore/8.2.0
2.21.0 -nodocs GCCcore/8.2.0
2.23.0   GCCcore/8.3.0

git-lfs

Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com

homepage: https://git-lfs.github.com

version toolchain
1.1.1 system
2.7.1 system

GitPython

GitPython is a python library used to interact with Git repositories

homepage: https://github.com/gitpython-developers/GitPython

version versionsuffix toolchain
2.1.11 -Python-3.6.6 foss/2018b, intel/2018b

Givaro

C++ library for arithmetic and algebraic computations

homepage: http://givaro.forge.imag.fr/

version toolchain
4.0.1 foss/2016a

Giza

Giza is an open, lightweight scientific plotting library built on top of cairo that provides uniform output to multiple devices.

homepage: https://danieljprice.github.io/giza/

version toolchain
1.1.0 foss/2018b

GL2PS

GL2PS: an OpenGL to PostScript printing library

homepage: http://www.geuz.org/gl2ps/

version versionsuffix toolchain
1.3.9   foss/2016a, foss/2016b, intel/2016a, intel/2016b
1.3.9 -Mesa-11.2.1 foss/2016a, intel/2016a
1.4.0   foss/2017b, foss/2018a, foss/2018b, intel/2017a, intel/2017b, intel/2018a

Glade

Glade is a RAD tool to enable quick & easy development of user interfaces for the GTK+ toolkit and the GNOME desktop environment.

homepage: https://glade.gnome.org/

version versionsuffix toolchain
3.8.5 -Python-2.7.11 intel/2016a
3.8.5 -Python-2.7.14 intel/2017b

glew

The OpenGL Extension Wrangler Library The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. GLEW provides efficient run-time mechanisms for determining which OpenGL extensions are supported on the target platform. OpenGL core and extension functionality is exposed in a single header file. GLEW has been tested on a variety of operating systems, including Windows, Linux, Mac OS X, FreeBSD, Irix, and Solaris.

homepage: http://glew.sourceforge.net/

version toolchain
2.1.0 GCCcore/8.2.0, foss/2018b

GLib

GLib is one of the base libraries of the GTK+ project

homepage: https://www.gtk.org/

version toolchain
2.42.1 GCC/4.9.2
2.44.0 GCC/4.9.2
2.47.5 foss/2016a, gimkl/2.11.5, intel/2016a
2.48.0 foss/2016a, intel/2016a
2.49.5 foss/2016b, intel/2016b
2.52.0 foss/2017a, intel/2017a
2.53.5 GCCcore/6.3.0, GCCcore/6.4.0
2.54.2 GCCcore/6.4.0
2.54.3 GCCcore/6.4.0, GCCcore/7.3.0
2.60.1 GCCcore/8.2.0
2.62.0 GCCcore/8.3.0

glibc

The GNU C Library project provides the core libraries for the GNU system and GNU/Linux systems, as well as many other systems that use Linux as the kernel.

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

version toolchain
2.17 GCCcore/6.4.0
2.26 GCCcore/6.4.0

GLibmm

C++ bindings for Glib

homepage: http://www.gtk.org/

version toolchain
2.49.7 GCCcore/8.2.0

GLIMMER

Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.

homepage: http://www.cbcb.umd.edu/software/glimmer/

version toolchain
3.02b foss/2016b, foss/2018b

GlimmerHMM

GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model. Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models.

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

version toolchain
3.0.4 foss/2016b, foss/2018b

GLM

OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications.

homepage: https://github.com/g-truc/glm

version toolchain
0.9.7.6 intel/2016a
0.9.8.3 GCCcore/5.4.0
0.9.9.0 GCCcore/6.4.0

GlobalArrays

Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model

homepage: https://hpc.pnl.gov/globalarrays

version versionsuffix toolchain
5.7   intel/2018b
5.7 -peigs intel/2019a

GlobusConnectPersonal

Globus Connect Personal turns your laptop or other personal computer into a Globus endpoint with a just a few clicks. With Globus Connect Personal you can share and transfer files to/from a local machine—campus server, desktop computer or laptop—even if it’s behind a firewall and you don’t have administrator privileges.

homepage: https://www.globus.org/globus-connect-personal

version toolchain
2.3.6 system

glog

A C++ implementation of the Google logging module.

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

version toolchain
0.3.4 foss/2016a
0.3.5 GCCcore/6.4.0, intel/2017a, intel/2017b
0.4.0 GCCcore/8.2.0

GLPK

The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.

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

version toolchain
4.58 foss/2016a, intel/2016a
4.60 GCCcore/5.4.0, intel/2016b
4.61 intel/2017a
4.65 GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0

glproto

X protocol and ancillary headers

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version toolchain
1.4.17 foss/2016a, gimkl/2.11.5, intel/2016a

GMAP-GSNAP

GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program

homepage: http://research-pub.gene.com/gmap/

version toolchain
2016-05-01 foss/2016a
2016-11-07 foss/2016b
2018-05-11 intel/2018a
2018-07-04 intel/2018a
2019-03-15 foss/2018b

GMP

GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.

homepage: http://gmplib.org/

version toolchain
4.3.2 system
5.1.3 GCC/4.8.2
6.0.0 GCC/4.9.2
6.0.0a GCC/4.8.4, GCC/4.9.2, GNU/4.9.3-2.25
6.1.0 GCC/4.9.3-2.25, foss/2016a, gimkl/2.11.5, intel/2016.02-GCC-4.9, intel/2016a, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25
6.1.1 GCC/5.4.0-2.26, GCCcore/5.4.0, GCCcore/6.3.0, foss/2016.04, foss/2016a, foss/2016b, intel/2016b
6.1.2 GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, foss/2016b

gmpich

gcc and GFortran based compiler toolchain, including MPICH for MPI support.

homepage: (none)

version toolchain
2016a system
2017.08 system

gmpolf

gcc and GFortran based compiler toolchain, MPICH for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.

homepage: (none)

version toolchain
2016a system
2017.10 system

gmpy2

GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x

homepage: https://github.com/aleaxit/gmpy

version versionsuffix toolchain
2.0.8 -Python-2.7.13 intel/2017a
2.0.8 -Python-2.7.14 foss/2017b, intel/2017b
2.0.8 -Python-3.6.3 foss/2017b, intel/2017b
2.1.0b1 -Python-2.7.14 foss/2017b, intel/2017b
2.1.0b1 -Python-3.6.3 foss/2017b, intel/2017b

gmsh

Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor.

homepage: http://geuz.org/gmsh

version versionsuffix toolchain
3.0.6 -Python-2.7.14 foss/2017b
3.0.6 -Python-3.6.6 foss/2018b
4.2.2 -Python-3.6.6 foss/2018b

GMT

GMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another 40 more specialized and discipline-specific tools.

homepage: https://gmt.soest.hawaii.edu/

version toolchain
4.5.17 foss/2018a
5.4.1 intel/2017a
5.4.3 foss/2018a, intel/2017b
5.4.5 foss/2019a

gmvapich2

GNU Compiler Collection (GCC) based compiler toolchain, including MVAPICH2 for MPI support.

homepage: (none)

version toolchain
1.7.20 system
2016a system

gmvolf

GNU Compiler Collection (GCC) based compiler toolchain, including MVAPICH2 for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.

homepage: (none)

version toolchain
1.7.20 system
2016a system

GNU

Compiler-only toolchain with GCC and binutils.

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

version toolchain
4.9.2-2.25 system
4.9.3-2.25 system
5.1.0-2.25 system

gnuplot

Portable interactive, function plotting utility

homepage: http://gnuplot.sourceforge.net/

version toolchain
5.0.3 foss/2016a, intel/2016a
5.0.5 foss/2016b, intel/2016b
5.0.6 intel/2017a
5.2.2 foss/2017b, foss/2018a, intel/2017b, intel/2018a
5.2.5 foss/2018b
5.2.6 GCCcore/8.2.0, foss/2018b, fosscuda/2018b

GnuTLS

GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them. It provides a simple C language application programming interface (API) to access the secure communications protocols as well as APIs to parse and write X.509, PKCS #12, OpenPGP and other required structures. It is aimed to be portable and efficient with focus on security and interoperability.

homepage: http://www.gnutls.org/

version toolchain
3.3.21 intel/2016a
3.4.7 GNU/4.9.3-2.25
3.4.11 foss/2016a

Go

Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.

homepage: http://www.golang.org

version toolchain
1.2.1 GCC/4.8.2
1.4.2 GCC/4.8.4
1.5 GCC/4.8.4
1.8.1 system
1.11.5 system
1.12 system
1.12.1 GCCcore/7.3.0
1.13.1 system

GObject-Introspection

GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library.

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

version versionsuffix toolchain
1.47.1   foss/2016a, intel/2016a
1.48.0   foss/2016a, intel/2016a
1.49.1   foss/2016b, intel/2016b
1.52.0   intel/2017a
1.53.5 -Python-2.7.13 intel/2017a
1.53.5 -Python-2.7.14 foss/2017b, intel/2017b
1.53.5 -Python-3.6.1 intel/2017a
1.54.1 -Python-2.7.14 foss/2018a, intel/2018a
1.54.1 -Python-2.7.15 foss/2018b, fosscuda/2018b
1.54.1 -Python-3.6.6 fosscuda/2018b
1.60.1 -Python-3.7.2 GCCcore/8.2.0

golf

GNU Compiler Collection (GCC) based compiler toolchain, including OpenBLAS (BLAS and LAPACK support) and FFTW.

homepage: (none)

version toolchain
2018a system

gomkl

GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL

homepage: (none)

version toolchain
2018b system
2019a system

gompi

GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.

homepage: (none)

version versionsuffix toolchain
2016.04   system
2016.06   system
2016.07   system
2016.09   system
2016a   system
2016b   system
2017a   system
2017b   system
2018.08   system
2018a   system
2018b   system
2019a   system
2019b   system
system -2.29 system

gompic

GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled.

homepage: (none)

version toolchain
2017b system
2018a system
2018b system
2019a system
2019b system

google-java-format

Reformats Java source code to comply with Google Java Style.

homepage: https://github.com/google/google-java-format

version versionsuffix toolchain
1.7 -Java-1.8 system

googletest

Google’s C++ test framework

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

version toolchain
1.8.0 GCCcore/6.3.0, GCCcore/6.4.0, foss/2016b, intel/2016b

GP2C

The gp2c compiler is a package for translating GP routines into the C programming language, so that they can be compiled and used with the PARI system or the GP calculator.

homepage: http://pari.math.u-bordeaux.fr/pub/pari/manuals/gp2c/gp2c.html

version toolchain
0.0.9pl5 foss/2016a

GPAW

GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or atom-centered basis-functions.

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

version versionsuffix toolchain
1.4.0 -Python-3.6.6 foss/2018b, intel/2018b
19.8.1 -ASE-3.18.0-Python-3.6.6 foss/2018b, intel/2018b
19.8.1 -Python-3.7.2 foss/2019a, intel/2019a

GPAW-setups

PAW setup for the GPAW Density Functional Theory package. Users can install setups manually using ‘gpaw install-data’ or use setups from this package. The versions of GPAW and GPAW-setups can be intermixed.

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

version toolchain
0.8.7929 system
0.9.9672 system
0.9.11271 system
0.9.20000 system

gperf

GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.

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

version toolchain
3.0.4 GCCcore/4.9.3, GCCcore/5.4.0, foss/2016a, gimkl/2.11.5, intel/2016a, intel/2016b, intel/2017a
3.1 GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0

gperftools

gperftools are for use by developers so that they can create more robust applications. Especially of use to those developing multi-threaded applications in C++ with templates. Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler.

homepage: http://github.com/gperftools/gperftools

version toolchain
2.5 foss/2016a, intel/2016b
2.6.3 GCCcore/6.4.0

gpustat

dstat-like utilization monitor for NVIDIA GPUs

homepage: https://github.com/wookayin/gpustat

version versionsuffix toolchain
0.5.0 -Python-2.7.15 fosscuda/2018b

Grace

Grace is a WYSIWYG tool to make two-dimensional plots of numerical data.

homepage: http://plasma-gate.weizmann.ac.il/Grace/

version versionsuffix toolchain
5.1.25 -5build1 foss/2017b, foss/2018a, intel/2017b

grace

Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.

homepage: http://freecode.com/projects/grace

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

Gradle

Complete Gradle install. From mobile apps to microservices, from small startups to big enterprises, Gradle helps teams build, automate and deliver better software, faster.

homepage: https://gradle.org

version toolchain
4.5.1 system

graph-tool

Graph-tool is an efficient Python module for manipulation and statistical analysis of graphs (a.k.a. networks). Contrary to most other python modules with similar functionality, the core data structures and algorithms are implemented in C++, making extensive use of template metaprogramming, based heavily on the Boost Graph Library. This confers it a level of performance that is comparable (both in memory usage and computation time) to that of a pure C/C++ library.

homepage: https://graph-tool.skewed.de/

version versionsuffix toolchain
2.26 -Python-3.6.3 foss/2017b
2.27 -Python-3.6.6 foss/2018b

Graphene

Graphene is a a thin layer of types for graphic libraries

homepage: http://ebassi.github.io/graphene/

version toolchain
1.6.0 intel/2017a

GraphicsMagick

GraphicsMagick is the swiss army knife of image processing.

homepage: http://www.graphicsmagick.org/

version toolchain
1.3.23 foss/2016a, intel/2016a
1.3.25 intel/2016b, intel/2017a
1.3.28 foss/2018a
1.3.31 foss/2018b

Graphviz

Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains.

homepage: http://www.graphviz.org/

version toolchain
2.38.0 foss/2016b, intel/2016b
2.40.1 intel/2018a

graphviz

Simple Python interface for Graphviz

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

version versionsuffix toolchain
0.5.1 -Python-2.7.12 foss/2016b, intel/2016b
0.5.1 -Python-3.5.2 intel/2016b
0.8.2 -Python-3.6.4 intel/2018a

GRASS

The Geographic Resources Analysis Support System - used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization

homepage: http://grass.osgeo.org

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

Greenlet

The greenlet package is a spin-off of Stackless, a version of CPython that supports micro-threads called “tasklets”. Tasklets run pseudo-concurrently (typically in a single or a few OS-level threads) and are synchronized with data exchanges on “channels”. A “greenlet”, on the other hand, is a still more primitive notion of micro-thread with no implicit scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs.

homepage: https://github.com/python-greenlet/greenlet

version versionsuffix toolchain
0.4.9 -Python-2.7.11 intel/2016a
0.4.9 -Python-3.5.1 intel/2016a
0.4.11 -Python-2.7.12 intel/2016b
0.4.12 -Python-2.7.14 intel/2017b

Grep

The grep command searches one or more input files for lines containing a match to a specified pattern. By default, grep prints the matching lines.

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

version toolchain
2.21 GCC/4.9.2

grib_api

The ECMWF GRIB API is an application program interface accessible from C, FORTRAN and Python programs developed for encoding and decoding WMO FM-92 GRIB edition 1 and edition 2 messages. A useful set of command line tools is also provided to give quick access to GRIB messages.

homepage: https://software.ecmwf.int/wiki/display/GRIB/Home

version toolchain
1.16.0 intel/2016a
1.21.0 foss/2017a
1.24.0 foss/2017b, intel/2017a, intel/2017b

GRIT

GRIT - A tool for the integrative analysis of RNA-seq type assays

homepage: https://github.com/nboley/grit

version versionsuffix toolchain
2.0.5 -Python-2.7.12 intel/2016b

GRNBoost

XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, flexible and portable.

homepage: https://github.com/dmlc/xgboost

version versionsuffix toolchain
20171009 -Java-1.8.0_152 intel/2017b

GroIMP

GroIMP (Growth Grammar-related Interactive Modelling Platform) is a 3D-modelling platform.

homepage: http://www.grogra.de/software/groimp

version toolchain
1.5 system

GROMACS

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

homepage: http://www.gromacs.org

version versionsuffix toolchain