List of supported software

EasyBuild 3.2.1 supports 1267 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

A

a2ps - ABAQUS - ABINIT - ABySS - ack - ACML - ACTC - AdapterRemoval - ADF - ADMIXTURE - Advisor - AFNI - ALADIN - Allinea - ALLPATHS-LG - ALPS - Amber - AMOS - Anaconda2 - Anaconda3 - AnalyzeFMRI - angsd - animation - annovar - ANSYS - ANSYS_CFD - ant - ANTLR - ANTs - APBS - APR - APR-util - ARB - argtable - aria2 - Armadillo - arpack-ng - ART - ASE - ASHS - Aspera-Connect - astropy - ATK - Atkmm - ATLAS - atomate - atools - ATSAS - attr - Autoconf - AutoDock - AutoDock_Vina - AutoGrid - Automake - Autotools - awscli

a2ps

a2ps-4.14: Formats an ascii file for printing on a postscript printer

homepage: http://www-inf.enst.fr/~demaille/a2ps/

version toolchain
4.14 goolf/1.4.10, ictce/5.3.0

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 dummy
6.13.5 -linux-x86_64 dummy
6.14.1 -linux-x86_64 dummy

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 dummy
7.0.5 -x86_64_linux_gnu4.5 dummy
7.2.1 -x86_64_linux_gnu4.5 dummy
7.4.3 -ETSF_IO-1.0.4 goolf/1.4.10
7.6.2   foss/2015a
7.10.4   intel/2015a
7.10.4 -incl-deps intel/2015a
7.10.5   intel/2016.02-GCC-4.9
7.10.5 -libxc intel/2016.02-GCC-4.9
7.11.6   intel/2015a
8.0.8   intel/2016a
8.0.8b   intel/2016b

ABySS

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

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

version versionsuffix toolchain
1.3.4 -Python-2.7.3 goolf/1.4.10, ictce/5.3.0
1.3.6 -Python-2.7.5 goolf/1.4.10
1.3.7 -Python-2.7.9 intel/2015a
1.5.2   goolf/1.4.10
1.9.0   foss/2016a

ack

ack is a tool like grep, optimized for programmers

homepage: http://beyondgrep.com/

version toolchain
2.14 dummy

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 dummy
4.4.0 -gfortran-64bit-int64 dummy
4.4.0 -ifort-64bit dummy
4.4.0 -ifort-64bit-int64 dummy
5.2.0 -gfortran-64bit dummy
5.2.0 -gfortran-64bit-int64 dummy
5.2.0 -ifort-64bit dummy
5.2.0 -ifort-64bit-int64 dummy
5.3.0 -ifort-64bit dummy
5.3.1 -ifort-64bit dummy

ACTC

ACTC converts independent triangles into triangle strips or fans.

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

version toolchain
1.1 intel/2016b

AdapterRemoval

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

homepage: https://github.com/MikkelSchubert/%(namelower)s

version toolchain
2.2.0 foss/2016b

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 dummy
2014.02 dummy
2014.11.r48287 intel/2016a
2016.101 dummy

ADMIXTURE

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

homepage: https://www.genetics.ucla.edu/software/admixture

version toolchain
1.3.0 dummy

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 dummy
2017_update1 dummy

AFNI

Free software for analysis and display of FMRI data

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

version versionsuffix toolchain
20150717   intel/2015a
20160329 -Python-2.7.11 intel/2016a
linux_openmp_64 -20141023 goolf/1.5.14, intel/2015a

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 goolf/1.4.10, ictce/5.3.0, intel/2015b, intel/2016a

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 dummy
4.1-32834-Redhat-6.0-x86_64 dummy
6.1.1-Ubuntu-14.04-x86_64 dummy

ALLPATHS-LG

ALLPATHS-LG, the new short read genome assembler.

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

version toolchain
46968 goolf/1.4.10
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

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

AMOS

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

homepage: http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS

version toolchain
3.1.0 goolf/1.4.10, ictce/5.3.0

Anaconda2

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

homepage: https://www.continuum.io/anaconda-overview

version toolchain
4.0.0 dummy
4.2.0 dummy

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.continuum.io/anaconda-overview

version toolchain
4.0.0 dummy
4.2.0 dummy

AnalyzeFMRI

Functions for I/O, visualisation and analysis of functional Magnetic Resonance Imaging (fMRI) datasets stored in the ANALYZE or NIFTI format.

homepage: http://cran.r-project.org/web/packages/AnalyzeFMRI

version versionsuffix toolchain
1.1-15 -R-2.15.2 ictce/5.3.0

angsd

Program for analysing NGS data.

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

version toolchain
0.910 foss/2016a

animation

animation: A Gallery of Animations in Statistics and Utilities to Create Animations

homepage: http://cran.r-project.org/web/packages/%(name)s

version versionsuffix toolchain
2.4 -R-3.2.1 intel/2015b

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 dummy

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 dummy
17.0 dummy

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 dummy
1.8.4 -Java-1.7.0_21 dummy
1.9.0 -Java-1.7.0_15 dummy
1.9.0 -Java-1.7.0_21 dummy
1.9.3 -Java-1.7.0_60 dummy
1.9.3 -Java-1.7.0_79 dummy
1.9.6 -Java-1.7.0_75 dummy
1.9.6 -Java-1.7.0_79 dummy
1.9.6 -Java-1.7.0_80 dummy
1.9.6 -Java-1.8.0_66 dummy
1.9.6 -Java-1.8.0_72 dummy
1.9.6 -Java-1.8.0_77 dummy
1.9.7 -Java-1.8.0_92 dummy
1.10.0 -Java-1.8.0_112 dummy
1.10.1 -Java-1.8.0_121 dummy

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   ictce/5.4.0, intel/2014b
2.7.7 -Python-2.7.10 intel/2015a, intel/2015b
2.7.7 -Python-2.7.11 foss/2016a

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 toolchain
2.1.0rc3 goolf/1.5.14

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 dummy

APR

Apache Portable Runtime (APR) libraries.

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

version toolchain
1.5.0 goolf/1.4.10
1.5.2 foss/2015a

APR-util

Apache Portable Runtime (APR) util libraries.

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

version toolchain
1.5.3 goolf/1.4.10
1.5.4 foss/2015a

ARB

The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria.

homepage: http://www.arb-home.de/

version toolchain
5.5 goolf/1.4.10

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 foss/2015b, foss/2016b, goolf/1.4.10

aria2

aria2-1.15.1: Multi-threaded, multi-protocol, flexible download accelerator

homepage: http://aria2.sourceforge.net/

version toolchain
1.15.1 goolf/1.4.10, ictce/5.3.0

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: http://arma.sourceforge.net/

version versionsuffix toolchain
2.4.4 -Python-2.7.3 goolf/1.4.10, ictce/5.3.0
4.300.8 -Python-2.7.5 ictce/5.5.0
6.400.3 -Python-2.7.11 intel/2015b
7.600.2 -Python-2.7.12 foss/2016b
7.800.0 -Python-2.7.12 intel/2016b

arpack-ng

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

homepage: http://forge.scilab.org/index.php/p/arpack-ng/

version versionsuffix toolchain
3.1.3   ictce/5.3.0, ictce/5.5.0
3.1.3 -mt ictce/5.3.0, ictce/5.5.0
3.1.5   ictce/7.1.2
3.1.5 -mt ictce/7.1.2
3.2.0   intel/2015a
3.2.0 -mt intel/2015a
3.3.0   foss/2016a, intel/2015b, intel/2016a
3.4.0   foss/2016b, foss/2017a, intel/2016b, intel/2017a

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 intel/2016b

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
3.6.0.2515 -Python-2.7.3 goolf/1.4.10, ictce/5.3.0
3.9.1.4567 -Python-2.7.10 intel/2015b
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-2.7.13 intel/2017a

ASHS

Automatic Segmentation of Hippocampal Subfields (ASHS)

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

version toolchain
rev103_20140612 dummy

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 dummy

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
1.0.6 -Python-2.7.3 goolf/1.4.10

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
2.16.0 intel/2015a, intel/2015b
2.18.0 intel/2016a
2.20.0 foss/2016a, intel/2016a
2.22.0 foss/2016b, intel/2016b

Atkmm

Atkmm is the official C++ interface for the ATK accessibility toolkit library.

homepage: https://developer.gnome.org/ATK/stable/

version toolchain
2.22.7 intel/2015a, intel/2015b

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

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 dummy
2.5.1-1 .sl5.x86_64 dummy
2.7.1-1 .el7.x86_64 dummy

attr

Commands for Manipulating Filesystem Extended Attributes

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

version toolchain
2.4.47 GCC/4.6.3

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
2.69 GCC/4.7.2, GCC/4.8.2, GCC/4.8.4, GCC/4.9.2, GCC/4.9.3-2.25, GCC/5.4.0-2.26, GCCcore/4.9.3, GCCcore/5.4.0, GCCcore/6.3.0, GNU/4.9.2-2.25, GNU/4.9.3-2.25, GNU/5.1.0-2.25, dummy, foss/2015a, foss/2015b, foss/2016.04, foss/2016a, foss/2016b, gimkl/2.11.5, goolf/1.4.10, ictce/5.3.0, ictce/5.5.0, intel/2015a, intel/2015b, intel/2016.02-GCC-4.9, intel/2016a, intel/2016b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25

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 dummy

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
1.13.4 goolf/1.4.10, ictce/5.3.0, ictce/5.5.0
1.14 GCC/4.8.2, ictce/5.3.0, ictce/5.5.0, intel/2016a
1.14.1 GCC/4.8.2
1.15 GCC/4.7.2, GCC/4.8.4, GCC/4.9.2, GCC/4.9.3-2.25, GCC/5.4.0-2.26, GCCcore/4.9.3, GCCcore/5.4.0, GCCcore/6.3.0, GNU/4.9.2-2.25, GNU/4.9.3-2.25, GNU/5.1.0-2.25, dummy, foss/2015a, foss/2015b, foss/2016.04, foss/2016a, foss/2016b, gimkl/2.11.5, ictce/5.3.0, ictce/5.5.0, intel/2015a, intel/2015b, intel/2016.02-GCC-4.9, intel/2016a, intel/2016b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25

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/4.7.2, GCC/4.8.4, GCC/4.9.2, GCC/4.9.3-2.25, GCC/5.4.0-2.26, GCCcore/4.9.3, GCCcore/5.4.0, GCCcore/6.3.0, GNU/4.9.2-2.25, GNU/4.9.3-2.25, GNU/5.1.0-2.25, dummy, foss/2015a, foss/2015b, foss/2016.04, foss/2016a, foss/2016b, gimkl/2.11.5, ictce/5.3.0, ictce/5.5.0, intel/2015a, intel/2015b, intel/2016.02-GCC-4.9, intel/2016a, intel/2016b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25

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

bam-readcount - bam2fastq - BamTools - BamUtil - basemap - Bash - BayesAss - BayeScan - BayeScEnv - BayesTraits - BayPass - Bazel - bbcp - bbFTP - bbftpPRO - BBMap - bc - BCFtools - beagle-lib - Beast - BEDOPS - BEDTools - BEEF - behave - BerkeleyGW - BFAST - BH - bibtexparser - Biggus - binutils - biodeps - BioKanga - BioPerl - Biopython - BiSearch - Bismark - Bison - BitSeq - BLACS - blasr - BLASR - blasr_libcpp - BLAST - BLAST+ - BLAT - Blender - Blitz++ - Blosc - BOINC - bokeh - BoltzTraP - Bonnie++ - Boost - Bowtie - Bowtie2 - BreakDancer - BSMAP - bsoft - buildenv - Bullet - BWA - bwakit - bx-python - BXH_XCEDE_TOOLS - byacc - bzip2

bam-readcount

Count DNA sequence reads in BAM files

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

version toolchain
0.7.4 foss/2015b

bam2fastq

The BAM format is an efficient method for storing and sharing data from modern, highly parallel sequencers. While primarily used for storing alignment information, BAMs can (and frequently do) store unaligned reads as well.

homepage: http://www.hudsonalpha.org/gsl/information/software/bam2fastq

version toolchain
1.1.0 goolf/1.4.10, ictce/5.3.0

BamTools

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

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

version toolchain
2.2.3 goolf/1.4.10, ictce/5.3.0
2.4.0 foss/2015b, foss/2016b, goolf/1.7.20
2.4.1 intel/2017a

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 foss/2015b, intel/2016b

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-2.7.10 intel/2015b

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
4.2 goolf/1.4.10, ictce/5.3.0
4.3 GCC/4.9.2

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, goolf/1.4.10

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, goolf/1.4.10

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   dummy
2.0 -Beta-Linux64 dummy

BayPass

BayPass is a population genomics software which is primarily aimed at identifying genetic markers subjected to selection and/or associated to population-specific covariates (e.g., environmental variables, quantitative or categorical phenotypic characteristics). The underlying models explicitly account for (and may estimate) the covariance structure among the population allele frequencies that originates from the shared history of the populations under study

homepage: http://www1.montpellier.inra.fr/CBGP/software/baypass/index.html

version toolchain
2.1 foss/2015a, goolf/1.7.20

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
0.3.0 CrayGNU/2016.03
0.4.4 dummy

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 dummy

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
3.2.0 goolf/1.4.10
3.2.1 intel/2016a

bbftpPRO

bbftpPRO is a data transfer program - as opposed to ordinary file transfer programs, capable of transferring arbitrary data over LAN/WANs at parallel speed. bbftpPRO has been started at the Particle Physics Dept. of Weizmann Institute of Science as an enhancement of bbftp, developed at IN2P3, ref: http://doc.in2p3.fr/bbftp/

homepage: http://bbftppro.myftp.org/

version toolchain
9.3.1 goolf/1.4.10, ictce/5.3.0

BBMap

BBMap short read aligner, and other bioinformatic tools.

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

version versionsuffix toolchain
35.82 -Java-1.8.0_66 foss/2015b
35.82 -Java-1.8.0_74 foss/2015b
36.62 -Java-1.8.0_112 intel/2016b

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

BCFtools

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF

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

version toolchain
1.1 goolf/1.4.10
1.2 foss/2015a, intel/2015a
1.3 foss/2016a, intel/2016a
1.3.1 goolf/1.7.20

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: http://code.google.com/p/beagle-lib/

version toolchain
2.1.2 foss/2016a, goolf/1.7.20
20120124 goolf/1.4.10, ictce/5.3.0
20141202 intel/2015a

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 dummy
2.1.3 dummy
2.4.0 foss/2016a

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 dummy

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
2.17.0 goolf/1.4.10
2.18.1 goolf/1.4.10
2.19.1 goolf/1.4.10
2.22.0 intel/2014b
2.23.0 goolf/1.4.10, intel/2015a
2.25.0 foss/2015a, foss/2015b, foss/2016a, goolf/1.7.20
2.26.0 foss/2015a, foss/2015b, foss/2016a, goolf/1.7.20, intel/2016b

BEEF

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

homepage: http://suncat.stanford.edu/facility/software/functional

version toolchain
0.1.1 intel/2015a
0.1.1-r16 intel/2015a

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

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

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 goolf/1.4.10, goolf/1.7.20, ictce/5.3.0

BH

BH: Boost C++ Header Files for R

homepage: http://cran.r-project.org/web/packages/%(name)s

version versionsuffix toolchain
1.60.0-1 -R-3.2.3 foss/2015b

bibtexparser

Bibtex parser in Python 2.7 and 3.x

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

version versionsuffix toolchain
0.5 -Python-2.7.9 foss/2015a, intel/2015a
0.6.0 -Python-2.7.9 foss/2015a, intel/2015a

Biggus

Virtual large arrays and lazy evaluation.

homepage: https://github.com/SciTools/biggus

version versionsuffix toolchain
0.5.0 -Python-2.7.3 goolf/1.4.10
0.11.0 -Python-2.7.3 goolf/1.4.10

binutils

binutils: GNU binary utilities

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

version toolchain
2.22 goolf/1.4.10, goolf/1.5.14
2.24 foss/2014b, intel/2014b
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, dummy
2.25.1 dummy
2.26 GCCcore/5.3.0, GCCcore/5.4.0, dummy
2.27 GCCcore/6.1.0, GCCcore/6.2.0, GCCcore/6.3.0, dummy
2.28 GCCcore/6.3.0, GCCcore/7.1.0, dummy

biodeps

The purpose of this collection is to provide common dependencies in a bundle, so that software/modules can be mixed and matched easily for composite pipelines in Life Sciences

homepage: http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2013-01.html

version versionsuffix toolchain
1.6   goolf/1.4.10, ictce/5.3.0
1.6 -extended goolf/1.4.10, ictce/5.3.0

BioKanga

BioKanga is an integrated toolkit of high performance bioinformatics subprocesses targeting the challenges of next generation sequencing analytics. Kanga is an acronym standing for ‘K-mer Adaptive Next Generation Aligner’.

homepage: https://github.com/csiro-crop-informatics/biokanga

version toolchain
3.4.5 foss/2015b
4.3.4 foss/2015b
4.3.5 foss/2015b
4.3.6 foss/2015b

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
1.6.1 -Perl-5.16.3 goolf/1.4.10, ictce/5.3.0
1.6.923 -Perl-5.18.2 ictce/5.5.0
1.6.923 -Perl-5.20.3 intel/2015b
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

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
1.61 -Python-2.7.3 goolf/1.4.10, ictce/5.3.0
1.65 -Python-2.7.11 foss/2016a
1.68 -Python-2.7.12 foss/2016b, intel/2016b
1.68 -Python-3.5.2 intel/2016b

BiSearch

BiSearch is a primer-design algorithm for DNA sequences.

homepage: http://bisearch.enzim.hu/

version toolchain
20051222 goolf/1.4.10, ictce/5.3.0

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
0.10.1 goolf/1.4.10

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
2.5 GCC/4.6.3, goolf/1.4.10, ictce/5.3.0, ictce/5.4.0, ictce/5.5.0, intel/2014b
2.6.5 ictce/5.3.0
2.7 GCC/4.7.2, GCC/4.7.3, GCC/4.8.1, GCC/4.8.4, dummy, goolf/1.4.10, goolf/1.5.14, ictce/5.3.0, ictce/5.4.0, ictce/5.5.0, ictce/6.1.5, intel/2014b, intel/2015a
2.7.1 ictce/5.4.0, ictce/5.5.0
3.0.1 ictce/5.5.0
3.0.2 CrayGNU/2015.06, CrayGNU/2015.11, GCC/4.8.2, foss/2014b, foss/2015a, ictce/7.1.2, intel/2014b, intel/2015a
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/6.1.0, GCCcore/6.2.0, GCCcore/6.3.0, GCCcore/7.1.0, GNU/4.9.3-2.25, dummy, foss/2015a, foss/2015b, foss/2016a, foss/2016b, gimkl/2.11.5, intel/2015a, intel/2015b, intel/2016.02-GCC-4.9, intel/2016a, intel/2016b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25

BitSeq

BitSeq (Bayesian Inference of Transcripts from Sequencing Data) is an application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions. An advantage of this approach is the ability to account for both technical uncertainty and intrinsic biological variance in order to avoid false DE calls. The technical contribution to the uncertainty comes both from finite read-depth and the possibly ambiguous mapping of reads to multiple transcripts.

homepage: https://code.google.com/p/bitseq/

version toolchain
0.7.0 goolf/1.4.10

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

BLASR (Basic Local Alignment with Successive Refinement) rapidly maps reads to genomes by finding the highest scoring local alignment or set of local alignments between the read and the genome. Optimized for PacBio’s extraordinarily long reads and taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy.

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

version toolchain
smrtanalysis-2.1 goolf/1.4.10

BLASR

BLASR (Basic Local Alignment with Successive Refinement) rapidly maps reads to genomes by finding the highest scoring local alignment or set of local alignments between the read and the genome. Optimized for PacBio’s extraordinarily long reads and taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy.

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

version toolchain
2.1 goolf/1.4.10
2.2 intel/2016b
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 dummy

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
2.2.27   goolf/1.4.10
2.2.28   goolf/1.4.10, ictce/5.3.0
2.2.28 -Python-2.7.3 goolf/1.4.10, ictce/5.3.0
2.2.30   goolf/1.4.10
2.2.30 -Python-2.7.9 foss/2015a, intel/2015a
2.2.31 -Python-2.7.10 foss/2015b, intel/2015a, intel/2015b
2.3.0 -Python-2.7.11 foss/2016a

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 versionsuffix toolchain
3.5   goolf/1.4.10, ictce/5.5.0, intel/2016b, intel/2017a
3.5 -libpng-1.6.9 ictce/5.5.0

Blender

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

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

version versionsuffix toolchain
2.77a -Python-3.5.2 intel/2016b

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 foss/2016a, goolf/1.5.16

Blosc

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

homepage: http://www.blosc.org/

version toolchain
1.11.1 intel/2016b

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
7.0.65 -client goolf/1.4.10
7.2.42 -client GCC/4.8.2, ictce/5.5.0

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

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

Bonnie++

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

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

version toolchain
1.03e goolf/1.4.10, ictce/5.3.0
1.97 foss/2016a

Boost

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

homepage: http://www.boost.org/

version versionsuffix toolchain
1.47.0   goolf/1.4.10
1.49.0 -Python-2.7.3 goolf/1.4.10, ictce/5.3.0
1.49.0 -Python-2.7.5 goolf/1.4.10
1.51.0   goolf/1.4.10, ictce/5.2.0, ictce/5.3.0
1.51.0 -Python-2.7.3 goolf/1.4.10, ictce/5.3.0
1.52.0   foss/2015a
1.53.0   goolf/1.4.10, goolf/1.7.20, ictce/5.2.0, ictce/5.3.0, ictce/6.2.5
1.53.0 -Python-2.7.3 ictce/5.3.0
1.53.0 -Python-2.7.5 ictce/5.3.0, ictce/5.5.0
1.53.0 -serial GCC/4.7.3
1.54.0 -Python-2.7.10 intel/2015b
1.55.0   dummy, goolf/1.7.20
1.55.0 -Python-2.7.11 foss/2016a
1.55.0 -Python-2.7.6 ictce/5.5.0
1.55.0 -Python-2.7.8 foss/2014b, ictce/7.1.2, intel/2014b, intel/2015a
1.55.0 -Python-2.7.9 foss/2015a
1.57.0   goolf/1.4.10
1.57.0 -Python-2.7.10 foss/2015b, gimkl/2.11.5
1.57.0 -Python-2.7.9 foss/2015a, intel/2015a
1.58.0   goolf/1.7.20
1.58.0 -Python-2.7.10 foss/2015a, foss/2015b, goolf/1.7.20, intel/2015a, intel/2015b
1.58.0 -Python-2.7.11 foss/2016a, intel/2016a
1.58.0 -Python-2.7.9 foss/2015.05, foss/2015a, intel/2015a
1.58.0 -serial GCC/4.9.2
1.59.0   intel/2015b
1.59.0 -Python-2.7.10 intel/2015a, intel/2015b
1.59.0 -Python-2.7.11 foss/2016a, intel/2015b, intel/2016a
1.60.0   foss/2015a, foss/2015b, foss/2016a, intel/2016a
1.60.0 -Python-2.7.11 CrayGNU/2016.03, 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
1.62.0 -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-3.5.2 foss/2016b
1.64.0   intel/2017a

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
1.0.0 goolf/1.4.10
1.1.1 goolf/1.4.10
1.1.2 foss/2015b, foss/2016a, intel/2015a, intel/2015b, intel/2016b, intel/2017a

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
2.0.2 goolf/1.4.10, ictce/5.3.0
2.0.5 goolf/1.4.10
2.0.6 goolf/1.4.10
2.1.0 goolf/1.4.10, ictce/5.5.0
2.2.0 goolf/1.4.10
2.2.2 goolf/1.4.10
2.2.4 goolf/1.4.10
2.2.5 goolf/1.7.20, intel/2015a
2.2.6 foss/2015b, intel/2015b
2.2.7 foss/2015b
2.2.8 foss/2015b, foss/2016a
2.2.9 foss/2016a, goolf/1.7.20, intel/2016b

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

BSMAP

BSMAP is a short reads mapping software for bisulfite sequencing reads.

homepage: https://code.google.com/p/bsmap/

version toolchain
2.74 goolf/1.4.10

bsoft

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

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

version toolchain
1.8.8 goolf/1.5.14

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 intel/2015a, intel/2016b

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

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
0.6.2 goolf/1.4.10, ictce/5.3.0
0.7.4 goolf/1.4.10, ictce/5.3.0
0.7.5a goolf/1.4.10
0.7.13 foss/2015b, foss/2016a, goolf/1.4.10, intel/2016a
0.7.15 foss/2016a, intel/2016b

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 dummy

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-2.7.13 intel/2017a

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 dummy

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
20120526 goolf/1.4.10, ictce/5.3.0
20150711 foss/2015b, intel/2015b
20160324 intel/2016a
20160606 foss/2016b, intel/2016b

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: http://www.bzip.org/

version toolchain
1.0.6 CrayGNU/2015.06, CrayGNU/2015.11, CrayGNU/2016.03, 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, GNU/4.9.3-2.25, dummy, foss/2014b, foss/2015.05, foss/2015a, foss/2015b, foss/2016.04, foss/2016a, foss/2016b, gimkl/2.11.5, gompi/1.5.16, goolf/1.4.10, goolf/1.5.14, goolf/1.5.16, goolf/1.7.20, ictce/5.2.0, ictce/5.3.0, ictce/5.4.0, ictce/5.5.0, ictce/6.2.5, ictce/7.1.2, intel/2014.06, intel/2014b, intel/2015a, intel/2015b, intel/2016.02-GCC-4.9, intel/2016a, intel/2016b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25

C

Caffe - cairo - cairomm - Cantera - canu - CAP3 - Cargo - CastXML - CBLAS - ccache - CCfits - cclib - CD-HIT - CDO - CEM - CFITSIO - cflow - CGAL - cgdb - Chapel - CHARMM - CHASE - Check - CheMPS2 - Chimera - ChIP-Seq - Circos - Circuitscape - Clang - CLHEP - CLooG - Clustal-Omega - ClustalW2 - Cluster-Buster - ClusterShell - CMake - Commet - configparser - configurable-http-proxy - ConnectomeWorkbench - CONTRAfold - CONTRAlign - Cookiecutter - Coot - Coreutils - Corkscrew - CosmoloPy - CP2K - CPLEX - cppcheck - CppUnit - cramtools - CrayCCE - CrayGNU - CrayIntel - CrayPGI - CRF++ - CrossTalkZ - CRPropa - CryptoMiniSat - csvkit - ctffind - Cube - Cuby - CUDA - cuDNN - Cufflinks - cURL - custodian - cutadapt - CVS - CVXOPT - Cython

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
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
1.12.14   goolf/1.4.10
1.12.18   goolf/1.7.20, intel/2014b, intel/2015a
1.14.2   goolf/1.7.20, intel/2015a, intel/2015b
1.14.4   intel/2015b
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

cairomm

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

homepage: http://cairographics.org

version toolchain
1.10.0 intel/2015a, intel/2015b

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

canu

Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II or Oxford Nanopore MinION). Canu is a hierarchical assembly pipeline which runs in four steps: Detect overlaps in high-noise sequences using MHAP Generate corrected sequence consensus Trim corrected sequences Assemble trimmed corrected sequences

homepage: https://github.com/marbl/canu

version toolchain
1.4 foss/2016b

CAP3

CAP3 assembly program

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

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

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

CBLAS

C interface to the BLAS

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

version toolchain
20110120 foss/2016b

ccache

ccache-3.1.9: Cache for C/C++ compilers

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

version toolchain
3.1.9 goolf/1.4.10, ictce/5.3.0
3.2.5 dummy
3.3.1 dummy
3.3.3 dummy

CCfits

CCfits is an object oriented interface to the cfitsio library. It is designed to make the capabilities of cfitsio available to programmers working in C++.

homepage: http://heasarc.gsfc.nasa.gov/fitsio/CCfits/

version toolchain
2.4 goolf/1.4.10, ictce/5.3.0

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
4.5.4 -2011-03-07 ictce/5.3.0
4.6.1 -2012-08-27 foss/2015b, goolf/1.4.10, ictce/5.5.0
4.6.4 -2015-0603 GNU/4.9.3-2.25, foss/2015b
4.6.6   foss/2016b

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
1.6.0 goolf/1.4.10
1.6.2 ictce/5.5.0
1.7.1 foss/2015a
1.7.2 intel/2016b

CEM

CEM: Transcriptome Assembly and Isoform Expression Level Estimation from Biased RNA-Seq Reads. CEM is an algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.

homepage: http://alumni.cs.ucr.edu/~liw/cem.html

version toolchain
0.9.1 goolf/1.4.10

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: http://heasarc.gsfc.nasa.gov/fitsio/

version toolchain
3.34 goolf/1.4.10, ictce/5.3.0, ictce/5.5.0
3.37 intel/2015a
3.38 foss/2016a, intel/2016a
3.41 intel/2016b
3.300 ictce/5.5.0
3.350 ictce/5.5.0

cflow

cflow-1.4: Code-path flow analyzer for C

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

version toolchain
1.4 goolf/1.4.10, ictce/5.3.0

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
4.0 -Python-2.7.3 goolf/1.4.10, ictce/5.3.0
4.6 -GLib-2.44.1-Python-2.7.10 intel/2015a
4.6 -Python-2.7.10 foss/2015a, intel/2015a
4.6 -Python-2.7.9 foss/2015a, intel/2015a
4.6.3 -Python-2.7.10 intel/2015b
4.7 -Python-2.7.10 intel/2015b
4.7 -Python-2.7.11 intel/2015b
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

cgdb

cgdb-0.6.5: Curses-based interface to the GNU Debugger GDB

homepage: http://cgdb.sourceforge.net/

version toolchain
0.6.5 goolf/1.4.10, ictce/5.3.0

Chapel

Chapel is an emerging parallel programming language whose design and development is being led by Cray Inc. Chapel is designed to improve the productivity of high-end computer users while also serving as a portable parallel programming model that can be used on commodity clusters or desktop multicore systems. Chapel strives to vastly improve the programmability of large-scale parallel computers while matching or beating the performance and portability of current programming models like MPI.

homepage: http://chapel.cray.com

version toolchain
1.6.0 goolf/1.4.10
1.7.0 goolf/1.4.10
1.8.0 goolf/1.4.10, goolf/1.6.10
1.9.0 goolf/1.4.10, goolf/1.5.14, goolf/1.6.10
1.10.0 goolf/1.4.10, goolf/1.6.10

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 versionsuffix toolchain
37b2   foss/2016a, ictce/5.5.0, intel/2015a, intel/2015b, intel/2016a
37b2 -mt ictce/5.5.0

CHASE

Case-control HAplotype Sharing analyses. Haplotype sharing analyses for genome-wide association studies.

homepage: http://people.duke.edu/~asallen/Software.html

version toolchain
20130626 dummy

Check

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

homepage: http://check.sourceforge.net

version toolchain
0.9.12 goolf/1.4.10

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

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 dummy

ChIP-Seq

The ChIP-Seq software provides methods for the analysis of ChIP-seq data and other types of mass genome annotation data. The most common analysis tasks include positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-depleted regions.

homepage: http://chip-seq.sourceforge.net/

version toolchain
1.5-1 goolf/1.4.10, goolf/1.7.20

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
0.64 -Perl-5.18.2 ictce/5.5.0
0.69-2 -Perl-5.18.2 ictce/5.5.0

Circuitscape

Circuitscape is a free, open-source program which borrows algorithms from electronic circuit theory to predict patterns of movement, gene flow, and genetic differentiation among plant and animal populations in heterogeneous landscapes. Circuit theory complements least-cost path approaches because it considers effects of all possible pathways across a landscape simultaneously.

homepage: http://www.circuitscape.org/

version versionsuffix toolchain
4.0.5 -Python-2.7.8 intel/2014b

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 toolchain
3.2 GCC/4.7.3
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

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 goolf/1.4.10, ictce/5.3.0, intel/2015a, intel/2016a
2.1.3.1 ictce/5.5.0, intel/2015a, intel/2016a
2.2.0.5 intel/2015a
2.2.0.8 intel/2016a
2.3.1.1 intel/2016a

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/2015b, foss/2016b, goolf/1.4.10

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/2015b, foss/2016b, goolf/1.4.10, ictce/5.3.0

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 dummy

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
2.8.4 GCC/4.7.2, GCC/4.7.3, goolf/1.4.10, ictce/5.2.0, ictce/5.3.0, intel/2015a
2.8.10.2 goolf/1.5.14, ictce/5.2.0, ictce/5.3.0
2.8.11 GCC/4.8.1, goolf/1.4.10, ictce/5.3.0
2.8.12 GCC/4.8.1, GCC/4.8.2, foss/2014b, goolf/1.4.10, goolf/1.7.20, ictce/5.3.0, ictce/5.4.0, ictce/5.5.0, ictce/6.2.5, ictce/7.1.2, intel/2014b
3.0.0 GCC/4.8.3, foss/2014b, foss/2015a, intel/2014.06, intel/2014b, intel/2015a
3.0.2 goolf/1.5.14
3.1.0 GCC/4.9.2, intel/2014b
3.1.3 GCC/4.9.2, dummy, foss/2015a, intel/2015a
3.2.1 GCC/4.9.2, GNU/4.9.3-2.25, intel/2015a
3.2.2 CrayGNU/2015.06, CrayGNU/2015.11, CrayIntel/2015.11, intel/2015a
3.2.3 foss/2015a, goolf/1.4.10, intel/2015a, intel/2015b
3.3.1 dummy, intel/2015a
3.3.2 GNU/4.9.3-2.25, gimkl/2.11.5, intel/2015b
3.4.0 intel/2015b
3.4.1 GCC/4.9.2, GCCcore/4.9.3, foss/2015a, foss/2015b, foss/2016a, intel/2015b, 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, goolf/1.7.20, ictce/7.3.5, intel/2016a
3.5.0 CrayGNU/2015.11, CrayGNU/2016.03
3.5.1 intel/2016a
3.5.2 GCC/4.9.3-2.25, dummy, foss/2016a, foss/2016b, goolf/1.7.20, intel/2016a, intel/2016b
3.6.1 GCC/5.4.0-2.26, GCCcore/4.9.3, foss/2016b, intel/2016b
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

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

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

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

ConnectomeWorkbench

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

homepage: http://www.humanconnectome.org/software/connectome-workbench.html

version toolchain
1.2.2 dummy

CONTRAfold

CONditional TRAining for RNA Secondary Structure Prediction

homepage: http://contra.stanford.edu/contrafold/

version toolchain
2.02 goolf/1.4.10

CONTRAlign

CONditional TRAining for Protein Sequence Alignment

homepage: http://contra.stanford.edu/contralign/

version versionsuffix toolchain
2.01 -proteins goolf/1.4.10
2.01 -rna goolf/1.4.10

Cookiecutter

Command-line utility that creates projects from cookiecutters (project templates). E.g. Python package projects, jQuery plugin projects.

homepage: https://github.com/audreyr/cookiecutter

version versionsuffix toolchain
1.4.0 -Python-2.7.11 goolf/1.7.20

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 dummy

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
8.22 goolf/1.4.10, ictce/5.3.0
8.23 GCC/4.9.2
8.27 GCCcore/5.4.0

Corkscrew

Corkscrew-2.0: Tool for tunneling SSH through HTTP proxies

homepage: http://www.agroman.net/corkscrew/

version toolchain
2.0 goolf/1.4.10, ictce/5.3.0

CosmoloPy

A cosmology package for Python. CosmoloPy is built on and designed for use with NumPy and SciPy.

homepage: https://github.com/roban/CosmoloPy

version versionsuffix toolchain
0.1.104 -Python-2.7.3 goolf/1.4.10

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
2.4.0   goolf/1.4.10, ictce/5.5.0
2.4.0 -ipi goolf/1.4.10
2.5.1   intel/2014b
2.6.0   CrayGNU/2015.06, CrayGNU/2015.11, intel/2015a
2.6.1   foss/2015b, intel/2015b
3.0   CrayGNU/2015.11, intel/2016a, intel/2016b
3.0 -cuda-7.0 CrayGNU/2015.11
3.0 -psmp intel/2016b
4.1   intel/2016b
4.1 -psmp foss/2016b
20111205   goolf/1.4.10, ictce/5.3.0, ictce/5.5.0
20111205 -libsmm goolf/1.4.10
20111205 -psmp goolf/1.4.10
20130228   intel/2015a
20131211   ictce/5.5.0, intel/2014b
20150904 -PLUMED-2.1.3 intel/2015a

CPLEX

IBM ILOG CPLEX Optimizer’s mathematical programming technology enables analytical decision support for improving efficiency, reducing costs, and increasing profitability.

homepage: http://www-01.ibm.com/software/commerce/optimization/cplex-optimizer/

version toolchain
12.4 dummy
12.6.3 foss/2015b

cppcheck

Cppcheck is a static analysis tool for C/C++ code

homepage: http://cppcheck.sourceforge.net/

version toolchain
1.75 intel/2015b

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 foss/2016a, intel/2015b

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 dummy
3.0 -Java-1.7.0_80 dummy

CrayCCE

Toolchain using Cray compiler wrapper, using PrgEnv-cray module (PE release: November 2015).

homepage: http://docs.cray.com/books/S-9407-1511

version toolchain
2015.06 dummy
2015.11 dummy

CrayGNU

Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: June 2016).

homepage: http://docs.cray.com/books/S-9408-1606/

version toolchain
2015.06 dummy
2015.11 dummy
2016.03 dummy
2016.04 dummy
2016.06 dummy

CrayIntel

Toolchain using Cray compiler wrapper, using PrgEnv-intel module (PE release: June 2016).

homepage: http://docs.cray.com/books/S-9407-1606

version toolchain
2015.06 dummy
2015.11 dummy
2016.06 dummy

CrayPGI

Toolchain using Cray compiler wrapper, using PrgEnv-pgi module.

homepage: http://www.pgroup.com/

version toolchain
2016.04 dummy

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
0.57 goolf/1.4.10, ictce/5.3.0
0.58 intel/2015b

CrossTalkZ

CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment between pairs of gene or protein groups in large biological networks.

homepage: http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/

version toolchain
1.4 foss/2016a

CRPropa

CRPropa is a publicly available code to study the propagation of ultra high energy nuclei up to iron on their voyage through an extra galactic environment.

homepage: https://crpropa.desy.de

version toolchain
2.0.3 ictce/5.5.0

CryptoMiniSat

CryptoMiniSat is an advanced SAT solver

homepage: https://github.com/msoos/cryptominisat

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

csvkit

csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats.

homepage: https://github.com/wireservice/csvkit

version versionsuffix toolchain
0.9.1 -Python-2.7.10 foss/2015b

ctffind

CTFFIND and CTFTILT are two programs for finding CTFs of electron micrographs.

homepage: http://grigoriefflab.janelia.org/ctf

version toolchain
4.0.8 intel/2014b
4.0.17 intel/2015b
140609 foss/2014b, intel/2014b

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
4.2 goolf/1.5.14
4.2.3 goolf/1.5.14
4.3 foss/2015a
4.3.2 foss/2015a
4.3.4 foss/2016a

Cuby

Cuby is a computational chemistry framework written in ruby. For users, it provides an unified access to various computational methods available in difefrent software packages. For developers, Cuby is much more - it is a complex framework that provides object-oriented access to the data enetering the calculations and to their results, making it easy to create new computational protocols by combining existing blocks of the framework.

homepage: http://cuby.molecular.cz/cuby4/

version toolchain
4 intel/2014b

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 versionsuffix toolchain
5.0.35 -1 GCC/4.6.4, dummy
5.5.22   GCC/4.7.2, GCC/4.8.2, dummy
6.0.37   dummy
6.5.14   dummy
7.0.28   dummy
7.5.18   GCC/4.9.4-2.25, dummy, iccifort/2015.3.187-GNU-4.9.3-2.25, iccifort/2016.3.210-GCC-4.9.3-2.25
8.0.44   GCC/5.4.0-2.26, dummy, iccifort/2016.3.210-GCC-5.4.0-2.26
8.0.61   dummy
8.0.61_375.26   GCC/5.4.0-2.26

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   dummy
5.0 -CUDA-7.5.18 dummy
5.0-rc   dummy
5.1 -CUDA-8.0.44 dummy
6.0 -CUDA-8.0.61 dummy

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: http://curl.haxx.se

version toolchain
7.27.0 goolf/1.4.10, ictce/5.3.0
7.28.1 ictce/5.3.0
7.29.0 goolf/1.4.10
7.33.0 GCC/4.8.2, ictce/5.3.0
7.34.0 GCC/4.8.2, ictce/5.4.0, ictce/5.5.0
7.37.1 foss/2014b, foss/2015a, intel/2014b, intel/2015a
7.40.0 GCC/4.9.2, foss/2015a, intel/2015a
7.41.0 intel/2015a
7.43.0 foss/2015b, goolf/1.7.20, intel/2015a, intel/2015b
7.44.0 foss/2015a, goolf/1.7.20, intel/2015a
7.45.0 foss/2015b, intel/2015b
7.46.0 foss/2015a, 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 foss/2016a, foss/2016b, intel/2016a, intel/2016b
7.52.1 intel/2016b
7.53.1 GCCcore/6.3.0
7.54.0 GCCcore/6.3.0

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
1.3 -Python-2.7.3 goolf/1.4.10
1.3 -Python-2.7.5 goolf/1.4.10
1.4.1 -Python-2.7.5 goolf/1.4.10
1.4.1 -Python-2.7.8 foss/2014b
1.5 -Python-2.7.10 goolf/1.4.10
1.5 -Python-2.7.8 foss/2014b, intel/2014b
1.6 -Python-2.7.8 foss/2014b
1.7 -Python-2.7.8 foss/2014b
1.7.1 -Python-2.7.8 foss/2014b
1.8.1 -Python-2.7.9 intel/2015a
1.9.1 -Python-2.7.10 foss/2015b
1.9.1 -Python-2.7.11 foss/2016a
1.9.1 -Python-2.7.12 foss/2016b

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

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://abel.ee.ucla.edu/cvxopt/

version versionsuffix toolchain
1.1.5 -Python-2.7.3 goolf/1.4.10, ictce/5.3.0

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
0.16 -Python-2.7.3 goolf/1.4.10, ictce/5.3.0
0.19.1 -Python-2.7.3 goolf/1.4.10, ictce/5.3.0
0.19.2 -Python-2.7.6 ictce/5.5.0
0.22 -Python-2.7.3 goolf/1.4.10
0.23.4 -Python-2.7.10 gimkl/2.11.5
0.24.1 -Python-2.7.11 foss/2016a

D

dadi - damageproto - dask - DB - DB_File - DBD-mysql - DBD-Pg - DBD-SQLite - DBG2OLC - DBus - dbus-glib - DCA++ - deap - DendroPy - DFT-D3 - DFTB+ - DIAL - DIALIGN-TX - DIAMOND - DicomBrowser - Diffutils - DIRAC - disambiguate - DISCOVARdenovo - distributed - DL_POLY_Classic - DMTCP - Docutils - DOLFIN - Doris - Doxygen - drFAST - DSRC

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

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

dask

Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.

homepage: http://github.com/dask/dask/

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-2.7.12 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 intel/2016b

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
2.7.7 ictce/5.5.0
4.7.25 goolf/1.4.10
4.8.30 goolf/1.4.10, ictce/5.5.0, intel/2015b, intel/2016a
5.3.21 goolf/1.4.10
6.0.20 goolf/1.4.10
6.2.23 foss/2016a

DB_File

Perl5 access to Berkeley DB version 1.x.

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

version versionsuffix toolchain
1.831 -Perl-5.18.2 ictce/5.5.0
1.831 -Perl-5.20.0 ictce/5.5.0
1.831 -Perl-5.20.3 intel/2015b
1.835 -Perl-5.20.3 intel/2016a
1.835 -Perl-5.22.1 foss/2016a

DBD-mysql

Perl binding for MySQL

homepage: http://search.cpan.org/~capttofu/DBD-mysql-%(version)s/

version versionsuffix toolchain
4.028 -Perl-5.20.0 intel/2014b
4.032 -Perl-5.20.3 intel/2015b
4.032 -Perl-5.22.2 intel/2016a
4.033 -Perl-5.24.0 intel/2016b

DBD-Pg

Perl binding for PostgreSQL

homepage: http://search.cpan.org/~turnstep/DBD-Pg-3.4.1/

version versionsuffix toolchain
3.4.1 -Perl-5.20.0 intel/2014b

DBD-SQLite

Perl binding for SQLite

homepage: http://search.cpan.org/~ishigaki/DBD-SQLite-1.42/

version versionsuffix toolchain
1.42 -Perl-5.20.0 intel/2014b

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

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/doc/dbus-glib

version toolchain
1.10.8 foss/2016a, intel/2016a
1.10.12 intel/2016b

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

DCA++

The DCA++ software project is a C++ implementation of the dynamical cluster approximation (DCA) and its DCA+ extension. It aims to solve lattice models of strongly correlated electron systems. This module bundles all the dependencies for the CPU+GPU version.

homepage: http://www.itp.phys.ethz.ch/research/comp/computation.html

version versionsuffix toolchain
1.0 -cpu CrayGNU/2015.11
1.0 -cuda CrayGNU/2015.11

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-2.7.10 intel/2015b
0.9.2 -Python-2.7.12 intel/2016b

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
3.12.0 -Python-2.7.3 goolf/1.4.10

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
3.1.1 intel/2015a

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 toolchain
1.3.1 intel/2017a

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

DIALIGN-TX

greedy and progressive approaches for segment-based multiple sequence alignment

homepage: http://dialign-tx.gobics.de/

version toolchain
1.0.2 goolf/1.4.10

DIAMOND

Accelerated BLAST compatible local sequence aligner

homepage: https://github.com/bbuchfink/diamond

version toolchain
0.8.35 goolf/1.7.20

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 dummy

Diffutils

Diffutils: GNU diff utilities - find the differences between files

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

version toolchain
3.2 goolf/1.4.10, ictce/5.3.0
3.3 GCC/4.8.2

DIRAC

The DIRAC program computes molecular properties using relativistic quantum chemical methods.

homepage: http://diracprogram.org/

version versionsuffix toolchain
14.1 -Python-2.7.10 intel/2015b

disambiguate

Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem

homepage: https://github.com/AstraZeneca-NGS/disambiguate

version versionsuffix toolchain
1.0.0 -Python-2.7.11 goolf/1.7.20

DISCOVARdenovo

DISCOVAR de novo can generate de novo assemblies for both large and small genomes. It currently does not call variants.

homepage: http://www.broadinstitute.org/software/discovar/blog/

version toolchain
52488 foss/2015a

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

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-2.1.4 foss/2015b
1.9 -PLUMED-2.2.0 foss/2015b
1.9 -PLUMED-2.2.3 intel/2016b
1.9 -no-gui ictce/5.3.0

DMTCP

DMTCP (Distributed MultiThreaded Checkpointing) transparently checkpoints a single-host or distributed computation in user-space – with no modifications to user code or to the O/S.

homepage: http://dmtcp.sourceforge.net/index.html

version toolchain
2.4.5 dummy
2.5.0 foss/2016a

Docutils

Docutils is an open-source text processing system for processing plaintext documentation into useful formats, such as HTML, LaTeX, man-pages, open-document or XML. It includes reStructuredText, the easy to read, easy to use, what-you-see-is-what-you-get plaintext markup language.

homepage: http://docutils.sourceforge.net/

version versionsuffix toolchain
0.9.1 -Python-2.7.3 goolf/1.4.10, ictce/5.3.0

DOLFIN

DOLFIN is the C++/Python interface of FEniCS, providing a consistent PSE (Problem Solving Environment) for ordinary and partial differential equations.

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

version versionsuffix toolchain
1.0.0 -Python-2.7.3 goolf/1.4.10
1.6.0 -Python-2.7.11 intel/2015b

Doris

Delft object-oriented radar interferometric software

homepage: http://doris.tudelft.nl/

version toolchain
4.02 intel/2017a

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
1.8.1.1 goolf/1.4.10, ictce/5.3.0, ictce/5.4.0
1.8.2 ictce/5.3.0
1.8.3.1 goolf/1.4.10, goolf/1.5.14, ictce/5.3.0, ictce/5.4.0, ictce/5.5.0, ictce/6.1.5
1.8.5 ictce/5.5.0, intel/2014b
1.8.6 ictce/5.4.0, ictce/5.5.0
1.8.7 foss/2014b, foss/2015a, intel/2014b, intel/2015a
1.8.8 ictce/7.1.2, intel/2014b
1.8.9.1 GCC/4.9.2
1.8.10 GNU/4.9.3-2.25, foss/2015b, intel/2015b, intel/2016.02-GCC-4.9
1.8.11 GCC/4.9.2, foss/2015a, 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

drFAST

drFAST is designed to map di-base reads (SOLiD color space reads) to reference genome assemblies; in a fast and memory-efficient manner.

homepage: http://drfast.sourceforge.net/

version toolchain
1.0.0.0 goolf/1.4.10, ictce/6.2.5

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 dummy

E

ea-utils - EasyBuild - ECore - ed - ED2 - EggLib - Eigen - EIGENSOFT - ELinks - Elk - ELPA - ELPH - Emacs - EMAN2 - EMBOSS - enchant - entrypoints - EPD - ErlangOTP - ESMF - ESPResSo - ETE - ETSF_IO - eudev - evmix - Exonerate - expat - 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

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: http://hpcugent.github.com/easybuild/

version toolchain
1.0.0 dummy
1.0.1 dummy
1.0.2 dummy
1.1.0 dummy
1.2.0 dummy
1.3.0 dummy
1.4.0 dummy
1.5.0 dummy
1.6.0 dummy
1.7.0 dummy
1.8.0 dummy
1.8.1 dummy
1.8.2 dummy
1.9.0 dummy
1.10.0 dummy
1.11.0 dummy
1.11.1 dummy
1.12.0 dummy
1.12.1 dummy
1.13.0 dummy
1.14.0 dummy
1.15.0 dummy
1.15.1 dummy
1.15.2 dummy
1.16.0 dummy
1.16.1 dummy
1.16.2 dummy
2.0.0 dummy
2.1.0 dummy
2.1.1 dummy
2.2.0 dummy
2.3.0 dummy
2.4.0 dummy
2.5.0 dummy
2.6.0 dummy
2.7.0 dummy
2.8.0 dummy
2.8.1 dummy
2.8.2 dummy
2.9.0 dummy
3.0.0 dummy
3.0.1 dummy
3.0.2 dummy
3.1.0 dummy
3.1.1 dummy
3.1.2 dummy
3.2.0 dummy

ECore

The e-Core technology simulates the natural processes of sedimentary rock formation; i.e. sedimentation, compaction and diagenesis.

homepage: http://www.numericalrocks.com/index.php?option=com_content&task=blogcategory&id=25&Itemid=25

version versionsuffix toolchain
1.5.2   ictce/5.5.0
1.5.2 -clusterapps ictce/5.5.0

ed

GNU ed is a line-oriented text editor.

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

version toolchain
1.9 goolf/1.4.10, ictce/5.3.0

ED2

The Ecosystem Demography Biosphere Model (ED2) is an integrated terrestrial biosphere model incorporating hydrology, land-surface biophysics, vegetation dynamics, and soil carbon and nitrogen biogeochemistry

homepage: https://github.com/EDmodel/ED2

version versionsuffix toolchain
20170201   intel/2017a
20170201 -serial intel/2017a

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

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
2.0.17 goolf/1.4.10
3.1.1 goolf/1.4.10, ictce/5.3.0
3.1.4 goolf/1.4.10, ictce/5.3.0, ictce/5.5.0
3.2.0 ictce/5.5.0
3.2.2 goolf/1.5.14, ictce/7.1.2, intel/2014b
3.2.3 foss/2015a, foss/2016a, foss/2016b, intel/2015a
3.2.5 dummy
3.2.6 dummy, goolf/1.7.20
3.2.7 foss/2016a, intel/2015b, intel/2016a
3.2.8 dummy, foss/2016a, intel/2016a
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

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, goolf/1.7.20
6.1.4 foss/2016b

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

ELPA

Eigenvalue SoLvers for Petaflop-Applications .

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

version toolchain
2013.11 ictce/5.3.0, ictce/5.5.0
2016.05.004 intel/2016b, intel/2017a

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 goolf/1.4.10, ictce/6.2.5

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

EMAN2

EMAN2 is the successor to EMAN1. It is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes.

homepage: http://blake.bcm.edu/emanwiki/EMAN2

version versionsuffix toolchain
2.11 -Python-2.7.9 foss/2015a, intel/2015a

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 toolchain
6.5.7 goolf/1.4.10, ictce/5.3.0
6.6.0 foss/2016b

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 dummy

ErlangOTP

Erlang is a programming language used to build massively scalable soft real-time systems with requirements on high availability. Some of its uses are in telecoms, banking, e-commerce, computer telephony and instant messaging. Erlang’s runtime system has built-in support for concurrency, distribution and fault tolerance.

homepage: http://www.erlang.org/

version versionsuffix toolchain
R16B02   GCC/4.7.2
R16B02 -no-Java GCC/4.7.2, goolf/1.4.10

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 toolchain
5.3.0 goolf/1.4.10
6.1.1 goolf/1.4.10
6.3.0rp1 intel/2017a
7.0.0 foss/2016a

ESPResSo

ESPResSo is a highly versatile software package for performing and analyzing scientific Molecular Dynamics many-particle simulations of coarse-grained atomistic or bead-spring models as they are used in soft-matter research in physics, chemistry and molecular biology.

homepage: http://espressomd.org/

version versionsuffix toolchain
3.1.1 -parallel goolf/1.4.10, ictce/5.3.0
3.1.1 -serial goolf/1.4.10, ictce/5.3.0

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 goolf/1.4.10, intel/2015b

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
3.0 intel/2014b, intel/2015a
3.1.2 intel/2015b
3.1.5 foss/2016a, gimkl/2.11.5, intel/2015b, intel/2016a
3.2 GCCcore/4.9.3

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
2.1 -R-3.1.1 intel/2014b
2.3 -R-3.1.1 intel/2014b
2.6 -R-3.3.1 intel/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: http://www.ebi.ac.uk/~guy/exonerate/

version toolchain
2.2.0 foss/2015b, goolf/1.4.10, ictce/5.3.0
2.4.0 foss/2015b, foss/2016a, foss/2016b

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: http://expat.sourceforge.net/

version toolchain
2.1.0 GCC/4.9.2, foss/2014b, foss/2015a, foss/2015b, foss/2016a, goolf/1.4.10, goolf/1.7.20, ictce/5.3.0, ictce/5.4.0, ictce/5.5.0, intel/2014b, intel/2015a, intel/2015b, intel/2016a
2.1.1 foss/2016a, intel/2016a
2.2.0 GCCcore/4.9.3, GCCcore/6.3.0, foss/2016a, foss/2016b, intel/2016b

eXpress

eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. Example applications include transcript-level RNA-Seq quantification, allele-specific/haplotype expression analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data.

homepage: http://bio.math.berkeley.edu/eXpress/index.html

version toolchain
1.5.1 goolf/1.4.10

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
3.0.1 foss/2015a

F

f90cache - FASTA - fastahack - fastPHASE - FastQC - fastQValidator - fastqz - FastTree - FASTX-Toolkit - FCM - FDS - fdstools - FDTD_Solutions - Ferret - FFC - FFindex - FFLAS-FFPACK - FFmpeg - ffnet - FFTW - FGSL - FIAT - file - findhap - findutils - Firefox - FireWorks - fixesproto - FLAC - FLANN - FLASH - FLEUR - flex - FLTK - FLUENT - fmri - fmt - FoldX - fontconfig - fontsproto - foss - FPM - fqtrim - fqzcomp - FragGeneScan - FRC_align - frealign - freeglut - FreeSurfer - freetype - FreeXL - FSA - FSL

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 dummy

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 goolf/1.4.10, ictce/5.3.0

fastahack

Utilities for indexing and sequence extraction from FASTA files

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

version toolchain
20110215 goolf/1.4.10

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 dummy

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 dummy
0.11.2 -Java-1.7.0_60 dummy
0.11.3 -Java-1.7.0_80 dummy
0.11.4 -Java-1.8.0_66 dummy
0.11.4 -Java-1.8.0_74 dummy
0.11.5 -Java-1.7.0_80 dummy
0.11.5 -Java-1.8.0_74 dummy

fastQValidator

Validate FastQ Files

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

version versionsuffix toolchain
0.1.1a-20151214 -aadc6f9 goolf/1.7.20

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

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
2.1.7 goolf/1.4.10, ictce/5.5.0

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
0.0.13.2 goolf/1.4.10, ictce/5.3.0
0.0.14 foss/2015b, foss/2016a, foss/2016b, goolf/1.4.10, intel/2015a

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 dummy

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://code.google.com/p/fds-smv/

version versionsuffix toolchain
6.0.1 -no-OFED dummy
6.3.0   intel/2015b
6.5.2   intel/2016b
r17534   intel/2015a
r18915   goolf/1.4.10, ictce/5.5.0, intel/2015a
r22681   intel/2015a

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 dummy
8.11.337 dummy

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
6.72 goolf/1.4.10

FFC

FEniCS Form Compiler (FFC) works as a compiler for multilinear forms by generating code (C++) for the evaluation of a multilinear form given in mathematical notation.

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

version versionsuffix toolchain
1.0.0 -Python-2.7.3 goolf/1.4.10, ictce/5.3.0
1.6.0 -Python-2.7.11 intel/2015b

FFindex

simple index/database for huge amounts of small files

homepage: http://www.splashground.de/~andy/programs/FFindex/

version toolchain
0.9.9 goolf/1.4.10

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
2.4 intel/2014.06, intel/2014b, intel/2015a
2.8 intel/2015b
2.8.4 foss/2015a
2.8.5 foss/2015a
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

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   GCC/4.6.3, ictce/5.3.0, ictce/5.5.0
3.3.1   ictce/5.3.0
3.3.3   gompi/1.4.10, gompi/1.6.10, ictce/5.2.0, ictce/5.3.0, ictce/5.5.0, intel/2015a
3.3.3 -single ictce/5.2.0, ictce/5.3.0
3.3.4   gmpich/2016a, gmvapich2/1.7.20, gmvapich2/2016a, gompi/1.5.14, gompi/1.5.16, gompi/1.7.20, gompi/2014b, gompi/2015.05, gompi/2015a, gompi/2015b, gompi/2016.04, gompi/2016.06, gompi/2016.07, gompi/2016a, gompi/2016b, gompic/2016.08, ictce/5.5.0, ictce/7.1.2, intel/2014b, intel/2015a, intel/2016a
3.3.4 -PFFT-20150905 intel/2015b
3.3.5   gompi/2016.07, gompi/2016.09, gompi/2016b, gompic/2016.10, intel/2016b
3.3.6   gompi/2017a, gompic/2017.01, intel/2016b, intel/2017a

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
1.0.0 -Python-2.7.3 goolf/1.4.10, ictce/5.3.0
1.1 -Python-2.7.3 ictce/5.2.0, ictce/5.3.0
1.1 -Python-2.7.8 intel/2014b
1.5.0 -Python-2.7.9 intel/2015a
1.6.0 -Python-2.7.11 foss/2016a, intel/2015b, intel/2016a

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

findhap

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

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

version toolchain
4 dummy

findutils

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

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

version toolchain
4.2.33 goolf/1.4.10, ictce/5.3.0
4.4.2 GCC/4.8.2

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 dummy

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, goolf/1.4.10, ictce/5.3.0, intel/2015a, intel/2015b, intel/2016a

FLAC

Programs and libraries for working with Free Lossless Audio Codec (FLAC) files.

homepage: https://xiph.org/flac/

version toolchain
1.3.1 foss/2015a

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

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/2015b, foss/2016a

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 dummy, goolf/1.4.10, ictce/5.3.0, ictce/5.4.0, ictce/5.5.0
2.5.37 goolf/1.4.10, goolf/1.5.14, ictce/5.3.0, ictce/5.4.0, ictce/5.5.0, ictce/6.1.5, ictce/7.1.2, intel/2014b, intel/2015a
2.5.38 GCC/4.8.2, ictce/6.1.5
2.5.39 CrayGNU/2015.06, CrayGNU/2015.11, 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, GNU/4.9.3-2.25, dummy, foss/2014b, foss/2015.05, foss/2015a, foss/2015b, foss/2016a, gimkl/2.11.5, ictce/7.1.2, intel/2014b, intel/2015a, intel/2015b, intel/2016.02-GCC-4.9, intel/2016a, intel/2016b
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, dummy, foss/2015a, foss/2016a, foss/2016b, gimkl/2.11.5, intel/2015b, intel/2016a, intel/2016b, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25
2.6.2 intel/2016b
2.6.3 GCCcore/5.4.0, GCCcore/6.3.0, GCCcore/7.1.0, dummy

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
1.3.2 foss/2014b, goolf/1.4.10, ictce/5.3.0, intel/2014b
1.3.3 foss/2016a, foss/2016b, intel/2016a, intel/2016b

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 dummy
15.0.7 dummy
16.0 dummy
17.1 dummy
18.0 dummy

fmri

The package contains R-functions to perform an fmri analysis as described in K. Tabelow, J. Polzehl, H.U. Voss, and V. Spokoiny, Analysing fMRI experiments with structure adaptive smoothing procedures, NeuroImage, 33:55-62 (2006) and J. Polzehl, H.U. Voss, K. Tabelow, Structural adaptive segmentation for statistical parametric mapping, NeuroImage, 52:515-523 (2010).

homepage: http://cran.r-project.org/web/packages/fmri

version versionsuffix toolchain
1.4-8 -R-2.15.2 ictce/5.3.0
1.5-0 -R-2.15.3 ictce/5.3.0

fmt

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

homepage: http://fmtlib.net/

version toolchain
3.0.1 foss/2016b, intel/2016b

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 dummy
3.0-beta5.1 dummy
3.0-beta6 dummy
3.0-beta6.1 dummy

fontconfig

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

homepage: http://www.freedesktop.org/software/fontconfig

version versionsuffix toolchain
2.10.91   goolf/1.4.10
2.11.1   foss/2014b, goolf/1.7.20, ictce/5.5.0, intel/2014b, intel/2015a
2.11.93   intel/2015a
2.11.94   foss/2016a, goolf/1.7.20, intel/2015a, intel/2015b, intel/2016a
2.11.94 -libpng-1.6.19 intel/2015b
2.11.95   foss/2016a, intel/2016a
2.12.1   GCCcore/6.3.0, foss/2015a, foss/2016b, intel/2016b
2.12.1 -libpng-1.6.29 GCCcore/6.3.0

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/2015a, intel/2015b, intel/2016a

foss

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

homepage: (none)

version toolchain
2014b dummy
2015.05 dummy
2015a dummy
2015b dummy
2016.04 dummy
2016.06 dummy
2016.07 dummy
2016.09 dummy
2016a dummy
2016b dummy
2017a dummy

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 dummy

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
1.19 intel/2014b

FRC_align

Computes FRC from SAM/BAM file and not from afg files.

homepage: https://github.com/vezzi/FRC_align

version toolchain
20130521 goolf/1.4.10

frealign

Frealign is a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles.

homepage: http://grigoriefflab.janelia.org/frealign

version versionsuffix toolchain
9.09 -avx-mp intel/2015a

freeglut

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

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

version versionsuffix toolchain
2.8.1   goolf/1.4.10, ictce/5.3.0, intel/2015a, intel/2015b
3.0.0   foss/2016a, foss/2016b, intel/2016a, intel/2016b
3.0.0 -Mesa-11.2.1 foss/2016a, intel/2016a

FreeSurfer

FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging.

homepage: http://freesurfer.net/

version versionsuffix toolchain
5.3.0 -centos4_x86_64 dummy
5.3.0 -centos6_x86_64 dummy

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
2.4.10   goolf/1.4.10, ictce/5.3.0
2.4.11   goolf/1.4.10, ictce/5.3.0
2.5.0.1   goolf/1.4.10, ictce/5.3.0, ictce/5.5.0
2.5.2   ictce/5.5.0
2.5.3   foss/2014b, goolf/1.7.20, intel/2014b
2.5.5   foss/2015a, goolf/1.7.20, intel/2015a, intel/2015b
2.6   foss/2015a, goolf/1.7.20, intel/2015a
2.6.1   intel/2015b
2.6.1 -libpng-1.6.19 intel/2015b
2.6.2   CrayGNU/2015.11, foss/2015a, foss/2015b, foss/2016a, gimkl/2.11.5, goolf/1.7.20, intel/2015b, intel/2016a
2.6.3   foss/2016a, intel/2016a
2.6.5   GCCcore/4.9.3, foss/2016b, intel/2016b
2.7   foss/2016b, intel/2016b
2.7.1   GCCcore/5.4.0, GCCcore/6.3.0, intel/2016b
2.7.1 -libpng-1.6.29 GCCcore/6.3.0

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
1.0.0g goolf/1.5.14
1.0.1 intel/2015a
1.0.2 foss/2015a, foss/2016b, intel/2016b

FSA

FSA:Fast Statistical Alignment, is a probabilistic multiple sequence alignment algorithm which uses a distance-based approach to aligning homologous protein, RNA or DNA sequences.

homepage: http://fsa.sourceforge.net/

version toolchain
1.15.8 goolf/1.4.10, ictce/5.3.0

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
4.1.9   goolf/1.4.10, ictce/5.3.0
5.0.4   goolf/1.4.10, ictce/5.3.0
5.0.8   intel/2015a
5.0.9   intel/2015b, intel/2016a
5.0.9 -Mesa-11.2.1 intel/2016a
5.0.9 -centos6_64 dummy

G

g2clib - g2lib - g2log - GAMESS-US - GapFiller - GATE - GATK - gawk - gc - GC3Pie - GCC - GCCcore - gcccuda - GConf - GD - GDAL - GDB - gdc-client - gdist - Gdk-Pixbuf - Geant4 - GEM-library - GEMSTAT - gencore_variant_detection - GenotypeHarmonizer - gensim - GeoIP - GeoIP-C - GEOS - getdp - GETORB - gettext - gflags - GFOLD - GHC - Ghostscript - gimkl - gimpi - GIMPS - git - git-lfs - Givaro - GL2PS - Glade - GLib - GLibmm - GLIMMER - GLM - GlobalArrays - glog - GLPK - glproto - GMAP-GSNAP - GMP - gmpich - gmpolf - gmsh - GMT - gmvapich2 - gmvolf - GNU - gnuplot - GnuTLS - Go - GObject-Introspection - gompi - gompic - googletest - goolf - goolfc - GP2C - GPAW - gperf - gperftools - gputools - grabix - grace - graph-tool - GraphicsMagick - Graphviz - graphviz - GraphViz - GraphViz2 - Greenlet - grep - Grep - grib_api - GRIT - GroIMP - GROMACS - GROMOS++ - gromosXX - gsl - GSL - GSSAPI - GST-plugins-base - GStreamer - gtest - GTI - GTK+ - gtkglext - Gtkmm - GTOOL - GTS - Guile - Gurobi - gzip

g2clib

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

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

version toolchain
1.2.3 goolf/1.4.10, ictce/5.3.0
1.4.0 ictce/5.3.0
1.6.0 intel/2017a

g2lib

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

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

version toolchain
1.2.4 goolf/1.4.10, ictce/5.3.0
1.4.0 ictce/5.3.0, intel/2017a

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/2014b, intel/2015b

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 toolchain
20130501-R1 intel/2015a
20141205-R1 intel/2015a, intel/2016a

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

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   goolf/1.4.10, intel/2015a
6.2 -Python-2.7.11 intel/2016a
7.0   intel/2015a
7.1 -Python-2.7.11 intel/2016a
7.2 -Python-2.7.11 intel/2016a

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: http://www.broadinstitute.org/gatk/

version versionsuffix toolchain
1.0.5083   dummy
2.5-2 -Java-1.7.0_10 dummy
2.6-5 -Java-1.7.0_10 dummy
2.7-4   dummy
2.7-4 -Java-1.7.0_10 dummy
2.8-1 -Java-1.7.0_10 dummy
3.0-0 -Java-1.7.0_10 dummy
3.3-0 -Java-1.7.0_21 dummy
3.3-0 -Java-1.7.0_80 dummy
3.3-0 -Java-1.8.0_66 dummy
3.5 -Java-1.8.0_66 dummy
3.5 -Java-1.8.0_74 dummy
3.6 -Java-1.8.0_92 dummy
3.7 -Java-1.8.0_112 dummy

gawk

gawk: GNU awk

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

version toolchain
4.0.2 goolf/1.4.10, ictce/5.3.0

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

GC3Pie

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

homepage: https://gc3pie.readthedocs.org

version toolchain
2.2.3 dummy
2.3 dummy
2.4.0 dummy
2.4.1 dummy
2.4.2 dummy

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
4.1.2   dummy
4.2.4   dummy
4.3.6   dummy
4.4.7   dummy
4.5.2   dummy
4.5.3   dummy
4.5.3 -CLooG-PPL dummy
4.6.0   dummy
4.6.3   dummy
4.6.3 -CLooG-PPL dummy
4.6.4   dummy
4.7.0   dummy
4.7.0 -CLooG-PPL dummy
4.7.1   dummy
4.7.1 -CLooG-PPL dummy
4.7.2   dummy
4.7.3   dummy
4.7.3 -CLooG-PPL dummy
4.7.4   dummy
4.7.4 -CLooG-PPL dummy
4.8.1   dummy
4.8.1 -CLooG dummy
4.8.2   dummy
4.8.2 -CLooG dummy
4.8.2 -CLooG-multilib dummy
4.8.2 -multilib dummy
4.8.3   dummy
4.8.3 -CLooG-multilib dummy
4.8.4   dummy
4.8.4 -CLooG dummy
4.8.4 -CLooG-multilib dummy
4.8.5   dummy
4.9.0   dummy
4.9.0 -CLooG dummy
4.9.0 -CLooG-multilib dummy
4.9.1   dummy
4.9.1 -CLooG dummy
4.9.1 -CLooG-multilib dummy
4.9.2   dummy
4.9.2 -CLooG dummy
4.9.2 -CLooG-multilib dummy
4.9.2 -binutils-2.25 dummy
4.9.3   dummy
4.9.3 -2.25 dummy
4.9.3 -binutils-2.25 dummy
4.9.4 -2.25 dummy
5.1.0   dummy
5.1.0 -binutils-2.25 dummy
5.2.0   dummy
5.3.0   dummy
5.3.0 -2.26 dummy
5.4.0 -2.26 dummy
6.1.0 -2.27 dummy
6.2.0 -2.27 dummy
6.3.0 -2.27 dummy
6.3.0 -2.28 dummy
7.1.0 -2.28 dummy
system   dummy

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 dummy
4.9.3 dummy
4.9.4 dummy
5.3.0 dummy
5.4.0 dummy
6.1.0 dummy
6.2.0 dummy
6.3.0 dummy
7.1.0 dummy

gcccuda

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

homepage: (none)

version toolchain
2016.08 dummy
2016.10 dummy
2017.01 dummy

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 foss/2016a, intel/2016a, intel/2016b

GD

GD.pm - Interface to Gd Graphics Library

homepage: http://search.cpan.org/~lds/GD/

version versionsuffix toolchain
2.52 -Perl-5.18.2 ictce/5.5.0

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: http://www.gdal.org/

version versionsuffix toolchain
1.9.2   goolf/1.4.10, goolf/1.5.16, ictce/5.3.0
1.10.1 -Python-2.7.10 intel/2015b
2.0.0   intel/2015a
2.0.1   foss/2015a, foss/2015b
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

GDB

The GNU Project Debugger

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

version versionsuffix toolchain
7.5.1   goolf/1.4.10
7.8   intel/2014b
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

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

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
2.31.4 intel/2015a, intel/2015b
2.32.3 intel/2016a
2.35.1 foss/2016a, intel/2016a
2.36.0 foss/2016b, intel/2016b

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.p01 goolf/1.4.10, ictce/5.3.0, intel/2015a
9.5.p02 intel/2016a
9.6.p04 intel/2015a, intel/2016a
10.01.p01 intel/2015a
10.01.p03 intel/2016a
10.02.p01 intel/2016a

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 dummy

GEMSTAT

thermodynamics-based model to predict gene expression driven by any DNA sequence, as a function of transcription factor concentrations and their DNA-binding specificities.

homepage: http://veda.cs.uiuc.edu/Seq2Expr/

version toolchain
1.0 goolf/1.4.10

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 dummy

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 dummy

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
0.11.1-1 -Python-2.7.10 intel/2015a
0.13.2 -Python-2.7.11 foss/2016a

GeoIP

MaxMind GeoIP Legacy Database - Python API

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

version versionsuffix toolchain
1.3.2 -Python-2.7.10 intel/2015a, intel/2015b

GeoIP-C

GeoIP Legacy C Library

homepage: https://github.com/maxmind/geoip-api-c

version toolchain
1.6.7 intel/2015a, intel/2015b

GEOS

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

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

version versionsuffix toolchain
3.3.5   goolf/1.4.10, ictce/5.3.0
3.5.0 -Python-2.7.10 intel/2015b
3.5.0 -Python-2.7.11 foss/2015a, 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

getdp

GetDP is an open source finite element solver using mixed elements to discretize de Rham-type complexes in one, two and three dimensions.

homepage: http://geuz.org/getdp

version versionsuffix toolchain
2.5.0 -Python-2.7.9 intel/2015a

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

version toolchain
0.18.2 dummy, foss/2015b, goolf/1.4.10, goolf/1.5.14, ictce/5.2.0, ictce/5.3.0
0.19.2 goolf/1.5.14, goolf/1.7.20, intel/2014.06, intel/2014b, intel/2015a, intel/2015b
0.19.4 GCC/4.9.2, dummy, foss/2015a, intel/2015a
0.19.6 GNU/4.9.3-2.25, dummy, foss/2016a, gimkl/2.11.5, intel/2015b, intel/2016a
0.19.7 dummy, foss/2015b, foss/2016a, intel/2016a
0.19.8 GCCcore/4.9.3, dummy, foss/2016.04, foss/2016b, intel/2016b
0.19.8.1 GCCcore/6.3.0, dummy

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

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 goolf/1.7.20, intel/2016a

GHC

GHC is the Glasgow Haskell Compiler.

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

version toolchain
6.12.3 dummy
7.4.2 goolf/1.4.10
7.6.2 goolf/1.4.10
7.8.3 goolf/1.4.10

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 toolchain
9.10 goolf/1.4.10
9.14 intel/2014b
9.16 goolf/1.7.20, intel/2015a
9.19 intel/2016a, intel/2016b
9.20 foss/2016b, intel/2016b
9.21 intel/2017a

gimkl

GNU Compiler Collection (GCC) based compiler toolchain, next to Intel MPI and Intel MKL (BLAS, (Sca)LAPACK, FFTW).

homepage: (none)

version toolchain
2.11.5 dummy

gimpi

GNU Compiler Collection (GCC) based compiler toolchain, next to Intel MPI.

homepage: (none)

version toolchain
2.11.5 dummy

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 dummy

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 toolchain
1.7.12 goolf/1.4.10, ictce/5.3.0
1.8.2 goolf/1.4.10
1.8.3.1 goolf/1.4.10
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

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 or GitHub Enterprise.

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

version toolchain
1.1.1 dummy

Givaro

C++ library for arithmetic and algebraic computations

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

version toolchain
4.0.1 foss/2016a

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

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

GLib

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

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

version versionsuffix toolchain
2.34.3   foss/2015b, goolf/1.4.10, goolf/1.5.14, ictce/5.2.0, ictce/5.3.0
2.40.0   goolf/1.5.14, goolf/1.7.20, intel/2014.06, intel/2014b, intel/2015a
2.41.2   intel/2014b, intel/2015a, intel/2015b
2.42.1   GCC/4.9.2, foss/2015a
2.44.0   GCC/4.9.2, foss/2015a, intel/2015a
2.44.1   goolf/1.7.20, intel/2015a
2.44.1 -Python-2.7.10 intel/2015a
2.46.0   intel/2015b
2.46.0 -Python-2.7.11 intel/2015b
2.46.2   foss/2015b
2.47.1   intel/2015b
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   intel/2017a

GLibmm

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

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

version toolchain
2.41.2 intel/2015a, intel/2015b

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 goolf/1.4.10, ictce/5.3.0

GLM

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

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

version toolchain
0.9.7.2 intel/2015b

GlobalArrays

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

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

version versionsuffix toolchain
5.3 -openib intel/2015a
5.4b -openib foss/2015a

glog

A C++ implementation of the Google logging module.

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

version toolchain
0.3.4 foss/2016a

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
4.48 ictce/5.2.0, ictce/5.3.0
4.53 goolf/1.4.10, ictce/6.2.5
4.55 foss/2015a, intel/2015a
4.58 foss/2016a, intel/2016a
4.60 intel/2016b

glproto

X protocol and ancillary headers

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

version toolchain
1.4.16 goolf/1.4.10, ictce/5.3.0, ictce/5.5.0
1.4.17 foss/2016a, gimkl/2.11.5, intel/2015a, intel/2015b, 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
2013-11-27 goolf/1.4.10, ictce/5.3.0, ictce/5.5.0
2014-01-21 goolf/1.4.10
2014-06-10 goolf/1.4.10
2015-12-31.v2 foss/2015b
2016-05-01 foss/2016a
2016-11-07 foss/2016b

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 dummy
5.0.5 goolf/1.4.10, ictce/5.3.0, intel/2015a
5.1.1 goolf/1.4.10, ictce/5.2.0, ictce/5.3.0, ictce/6.2.5
5.1.3 GCC/4.8.2, foss/2015a, goolf/1.4.10, ictce/5.3.0, ictce/5.5.0, intel/2015a
6.0.0 GCC/4.9.2
6.0.0a GCC/4.7.2, GCC/4.8.4, GCC/4.9.2, GNU/4.9.3-2.25, foss/2015a, foss/2015b, intel/2015b
6.1.0 CrayGNU/2015.11, CrayGNU/2016.03, GCC/4.9.3-2.25, foss/2015a, foss/2016a, gimkl/2.11.5, goolf/1.7.20, intel/2015b, 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/6.3.0, foss/2016.04, foss/2016a, foss/2016b, intel/2016b
6.1.2 GCCcore/6.3.0, foss/2016b

gmpich

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

homepage: (none)

version toolchain
2016a dummy

gmpolf

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

homepage: (none)

version toolchain
2016a dummy

gmsh

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

homepage: http://geuz.org/gmsh

version toolchain
2.9.1 intel/2015a

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: http://gmt.soest.hawaii.edu/

version toolchain
5.1.0 goolf/1.4.10
5.1.2 intel/2015a

gmvapich2

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

homepage: (none)

version toolchain
1.7.20 dummy
2016a dummy

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 dummy
2016a dummy

GNU

Compiler-only toolchain with GCC and binutils.

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

version toolchain
4.9.2-2.25 dummy
4.9.3-2.25 dummy
5.1.0-2.25 dummy

gnuplot

Portable interactive, function plotting utility

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

version toolchain
4.6.0 goolf/1.4.10, ictce/5.3.0
4.6.6 intel/2014b
5.0.0 intel/2014b, intel/2015a
5.0.1 intel/2015b
5.0.3 foss/2016a, intel/2016a
5.0.5 foss/2016b, intel/2016b

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
3.1.8 goolf/1.4.10
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 dummy

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 toolchain
1.42.0 intel/2014b
1.44.0 intel/2015a
1.47.1 foss/2016a, intel/2015b, intel/2016a
1.48.0 foss/2016a, intel/2016a
1.49.1 foss/2016b, intel/2016b

gompi

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

homepage: (none)

version toolchain
1.4.10 dummy
1.5.14 dummy
1.5.16 dummy
1.6.10 dummy
1.7.20 dummy
2014b dummy
2015.05 dummy
2015a dummy
2015b dummy
2016.04 dummy
2016.06 dummy
2016.07 dummy
2016.09 dummy
2016a dummy
2016b dummy
2017a dummy

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
2016.08 dummy
2016.10 dummy
2017.01 dummy

googletest

Google’s C++ test framework

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

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

goolf

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

homepage: (none)

version toolchain
1.4.10 dummy
1.5.14 dummy
1.5.16 dummy
1.6.10 dummy
1.7.20 dummy

goolfc

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
2016.08 dummy
2016.10 dummy
2017.01 dummy

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
0.9.0.8965 -Python-2.7.3 goolf/1.4.10, ictce/5.3.0

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

version toolchain
3.0.4 GCCcore/4.9.3, foss/2016a, gimkl/2.11.5, goolf/1.4.10, ictce/5.3.0, intel/2014b, intel/2015a, intel/2015b, intel/2016a, intel/2016b

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
2.1 goolf/1.4.10, ictce/5.3.0
2.4 foss/2015a
2.5 foss/2016a, intel/2016b

gputools

This package provides R interfaces to a handful of common functions implemented using the Nvidia CUDA toolkit. Some of the functions require at least GPU Compute Capability 1.3.

homepage: https://github.com/nullsatz/gputools/wiki

version versionsuffix toolchain
0.28 -e5cb024-R-3.0.2 ictce/5.3.0

grabix

a wee tool for random access into BGZF files

homepage: https://github.com/arq5x/grabix

version toolchain
0.1.6 goolf/1.7.20

grace

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

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

version toolchain
5.1.23 intel/2014b, intel/2015a
5.1.25 foss/2016a, intel/2016a

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
2.2.42 -Python-2.7.10 foss/2015a
2.2.42 -Python-2.7.9 foss/2015a

GraphicsMagick

GraphicsMagick is the swiss army knife of image processing.

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

version toolchain
1.3.21 intel/2015b
1.3.23 foss/2016a, intel/2016a
1.3.25 intel/2016b

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 versionsuffix toolchain
2.38.0   foss/2016b, intel/2014b, intel/2016b
2.38.0 -Python-2.7.10 intel/2015a

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

GraphViz

This module provides a Perl interface to the amazing Graphviz, an open source graph visualization tool from AT&T.

homepage: https://metacpan.org/pod/GraphViz

version versionsuffix toolchain
2.18 -Perl-5.20.0 intel/2014b

GraphViz2

This module provides a Perl interface to the amazing Graphviz, an open source graph visualization tool from AT&T.

homepage: https://metacpan.org/pod/GraphViz2

version versionsuffix toolchain
2.33 -Perl-5.20.0 intel/2014b

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
0.4.0 -Python-2.7.3 goolf/1.4.10, ictce/5.3.0
0.4.2 -Python-2.7.10 intel/2015b
0.4.2 -Python-2.7.5 ictce/5.5.0
0.4.2 -Python-2.7.6 ictce/5.5.0
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

grep

grep: GNU grep

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

version toolchain
2.15 goolf/1.4.10, ictce/5.3.0

Grep

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

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

version toolchain
2.21 GCC/4.9.2

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
1.9.18 goolf/1.4.10, ictce/5.3.0
1.10.0 goolf/1.4.10, ictce/5.3.0
1.14.4 intel/2015b
1.16.0 intel/2016a
1.21.0 foss/2017a

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

GroIMP

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

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

version toolchain
1.5 dummy

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
3.3.3   goolf/1.5.14
4.6.1 -hybrid goolf/1.4.10, ictce/5.3.0
4.6.1 -mt goolf/1.4.10, ictce/5.3.0
4.6.5   intel/2015a
4.6.5 -double goolf/1.4.10
4.6.5 -hybrid goolf/1.4.10, ictce/5.5.0
4.6.5 -mt goolf/1.4.10, ictce/5.5.0
4.6.7 -mpi CrayGNU/2015.06, CrayGNU/2015.11, CrayIntel/2015.11
5.0.2 -mt ictce/7.1.2
5.0.4 -hybrid intel/2015a
5.0.4 -mt intel/2015a
5.0.5 -hybrid intel/2015a
5.0.7 -hybrid intel/2015a
5.1.1 -hybrid intel/2015b
5.1.2 -cuda-7.0.28-hybrid CrayGNU/2016.03
5.1.2 -hybrid foss/2015b, foss/2016a, intel/2016a
5.1.2 -hybrid-dp intel/2016a
5.1.2 -mt foss/2016a, goolf/1.7.20
5.1.4 -hybrid foss/2016b
5.1.4 -mt foss/2016b
2016 -hybrid foss/2016b
2016 -mt foss/2016b
2016.1 -PLUMED foss/2017a
2016.2   foss/2017a
2016.3   foss/2017a, intel/2017a

GROMOS++

GROMOS™ is an acronym of the GROningen MOlecular Simulation computer program package, which has been developed since 1978 for the dynamic modelling of (bio)molecules, until 1990 at the University of Groningen, The Netherlands, and since then at the ETH, the Swiss Federal Institute of Technology, in Zürich, Switzerland.

homepage: http://www.gromos.net/

version versionsuffix toolchain
1.0.2211 -openmp goolf/1.5.14
1.0.2211 -serial goolf/1.5.14

gromosXX

GROMOS™ is an acronym of the GROningen MOlecular Simulation computer program package, which has been developed since 1978 for the dynamic modelling of (bio)molecules, until 1990 at the University of Groningen, The Netherlands, and since then at the ETH, the Swiss Federal Institute of Technology, in Zürich, Switzerland.

homepage: http://www.gromos.net/

version versionsuffix toolchain
1.0.1737 -mpi goolf/1.5.14
1.0.1737 -openmp goolf/1.5.14
1.0.1737 -serial goolf/1.5.14

gsl

An R wrapper for the special functions and quasi random number generators of the Gnu Scientific Library (GSL).

homepage: http://cran.r-project.org/web/packages/gsl

version versionsuffix toolchain
1.9-10 -R-3.1.1 intel/2014b

GSL

The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.

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

version toolchain
1.15 goolf/1.4.10, goolf/1.5.14, ictce/5.3.0, intel/2014b, intel/2015a
1.16 foss/2015a, foss/2015b, foss/2016a, goolf/1.4.10, goolf/1.5.14, goolf/1.7.20, ictce/5.3.0, ictce/5.4.0, ictce/5.5.0, ictce/6.2.5, intel/2014b, intel/2015a, intel/2015b, intel/2016a
2.1 CrayGNU/2015.11, foss/2015b, foss/2016a, foss/2016b, intel/2015b, intel/2016a, intel/2016b
2.2.1 intel/2016a, intel/2016b
2.3 foss/2016b, foss/2017a, intel/2016b, intel/2017a

GSSAPI

Perl extension providing access to the GSSAPIv2 library.

homepage: http://search.cpan.org/~agrolms/GSSAPI-0.28/

version versionsuffix toolchain
0.28 -Perl-5.20.0 intel/2014b

GST-plugins-base

GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.

homepage: http://gstreamer.freedesktop.org/

version toolchain
0.10.36 foss/2016a, intel/2016a, intel/2016b
1.6.4 foss/2016a
1.8.3 foss/2016a

GStreamer

GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.

homepage: http://gstreamer.freedesktop.org/

version toolchain
0.10.36 foss/2016a, intel/2016a, intel/2016b
1.6.4 foss/2016a
1.8.3 foss/2016a

gtest

Google’s framework for writing C++ tests on a variety of platforms

homepage: https://code.google.com/p/googletest/

version toolchain
1.6.0 intel/2014b
1.7.0 CrayGNU/2015.11

GTI

A Generic Tools Infrastructure for Event-Based Tools in Parallel Systems.

homepage: http://www.tu-dresden.de/zih/must/

version toolchain
1.2.0 goolf/1.5.14

GTK+

The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.

homepage: https://developer.gnome.org/gtk+/stable/

version toolchain
2.24.28 intel/2015a, intel/2015b, intel/2016a
2.24.30 foss/2016a, intel/2016a
2.24.31 foss/2016b, intel/2016b

gtkglext

GtkGLExt is an OpenGL extension to GTK+.

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

version toolchain
1.2.0 intel/2015b

Gtkmm

The Gtkmm package provides a C++ interface to GTK+ 2.

homepage: https://developer.gnome.org/gtk+/stable/

version toolchain
2.24.4 intel/2015a, intel/2015b

GTOOL

GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE.

homepage: http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html

version toolchain
0.7.5 dummy

GTS

GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles.

homepage: http://gts.sourceforge.net/

version versionsuffix toolchain
0.7.6   foss/2016a, foss/2016b, intel/2014b, intel/2016a, intel/2016b
0.7.6 -GLib-2.44.1 intel/2015a

Guile

Guile is a programming language, designed to help programmers create flexible applications that can be extended by users or other programmers with plug-ins, modules, or scripts.

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

version toolchain
1.8.8 GNU/4.9.3-2.25, foss/2015b, foss/2016a, foss/2016b, foss/2017a, goolf/1.4.10, ictce/5.3.0, intel/2015a, intel/2015b, intel/2016a, intel/2016b
2.0.11 GCC/4.9.3-2.25, foss/2016a

Gurobi

The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms.

homepage: http://www.gurobi.com

version toolchain
6.5.1 dummy
6.5.2 dummy
7.0.1 dummy

gzip

gzip (GNU zip) is a popular data compression program as a replacement for compress

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

version toolchain
1.5 goolf/1.4.10, ictce/5.3.0
1.6 goolf/1.5.14, goolf/1.6.10, ictce/5.3.0, ictce/5.5.0, ictce/6.2.5, intel/2015b

H

h4toh5 - H5hut - h5py - h5utils - Hadoop - hanythingondemand - HAPGEN2 - HarfBuzz - Harminv - HBase - HDF - HDF5 - HEALPix - help2man - HH-suite - hisat - HISAT2 - HMMER - Hoard - horton - HPCBIOS_Bioinfo - HPCBIOS_Debuggers - HPCBIOS_LifeSciences - HPCBIOS_Math - HPCBIOS_Profilers - HPCG - HPL - htop - HTSeq - HTSlib - hub - hunspell - hwloc - hyperspy - Hypre

h4toh5

The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects.

homepage: http://www.hdfgroup.org/h4toh5/

version versionsuffix toolchain
2.2.2 -linux-x86_64-static dummy

H5hut

HDF5 Utility Toolkit: High-Performance I/O Library for Particle-based Simulations

homepage: https://amas.psi.ch/H5hut/

version toolchain
1.99.13 intel/2016b

h5py

HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.

homepage: http://www.h5py.org/

version versionsuffix toolchain
2.0.1 -Python-2.7.3 goolf/1.4.10, ictce/5.3.0
2.1.3 -Python-2.7.3 goolf/1.4.10, ictce/5.3.0
2.2.1 -Python-2.7.3 goolf/1.4.10
2.2.1 -Python-2.7.5 ictce/5.5.0
2.4.0 -Python-2.7.9-serial intel/2015a
2.5.0 -Python-2.7.10-HDF5-1.8.15-patch1 intel/2015b
2.5.0 -Python-2.7.10-HDF5-1.8.15-patch1-serial intel/2015b
2.5.0 -Python-2.7.11-HDF5-1.8.16 foss/2016a, intel/2015b, intel/2016a
2.5.0 -Python-2.7.11-HDF5-1.8.16-serial foss/2016a, intel/2016a
2.5.0 -Python-2.7.11-parallel CrayGNU/2015.11
2.5.0 -Python-2.7.11-serial CrayGNU/2015.11
2.5.0 -Python-2.7.9 intel/2015a
2.5.0 -Python-3.5.1-HDF5-1.8.16 foss/2016a
2.6.0 -Python-2.7.11 intel/2016a
2.6.0 -Python-2.7.12-HDF5-1.10.0-patch1 foss/2016b, intel/2016b
2.6.0 -Python-2.7.12-HDF5-1.8.17 foss/2016b, intel/2016b
2.6.0 -Python-2.7.12-HDF5-1.8.18 foss/2016b, intel/2016b
2.6.0 -Python-3.5.2-HDF5-1.10.0-patch1 foss/2016b, intel/2016b
2.6.0 -Python-3.5.2-HDF5-1.8.17 intel/2016b
2.6.0 -Python-3.5.2-HDF5-1.8.18 foss/2016b, intel/2016b
2.7.0 -Python-2.7.12 intel/2016b
2.7.0 -Python-2.7.13 intel/2017a
2.7.0 -Python-3.6.1 intel/2017a

h5utils

h5utils is a set of utilities for visualization and conversion of scientific data in the free, portable HDF5 format. Besides providing a simple tool for batch visualization as PNG images, h5utils also includes programs to convert HDF5 datasets into the formats required by other free visualization software (e.g. plain text, Vis5d, and VTK).

homepage: http://ab-initio.mit.edu/wiki/index.php/H5utils

version toolchain
1.12.1 goolf/1.4.10, ictce/5.3.0

Hadoop

Hadoop MapReduce by Cloudera

homepage: http://archive.cloudera.com/cdh5/cdh/5/

version versionsuffix toolchain
2.4.0 -seagate-722af1-native dummy
2.5.0-cdh5.3.1 -native dummy
2.6.0-cdh5.4.5 -native dummy
2.6.0-cdh5.7.0 -native dummy
2.6.0-cdh5.8.0 -native dummy

hanythingondemand

HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. It uses the Torque resource manager to do node allocation.

homepage: https://github.com/hpcugent/hanythingondemand

version versionsuffix toolchain
2.2.1 -Python-2.7.9 intel/2015a
2.2.2 -Python-2.7.9 intel/2015a
2.2.3 -Python-2.7.9 intel/2015a
2.2.4 -Python-2.7.9 intel/2015a
3.0.0 -Python-2.7.10 intel/2015b
3.0.0 -cli dummy
3.0.1 -Python-2.7.10 intel/2015b
3.0.1 -cli dummy
3.0.2 -Python-2.7.10 intel/2015b
3.0.2 -cli dummy
3.0.3 -Python-2.7.10 intel/2015b
3.0.3 -cli dummy
3.0.4 -Python-2.7.10 intel/2015b
3.0.4 -cli dummy
3.1.0 -Python-2.7.11 intel/2016a
3.1.0 -cli dummy
3.1.1 -Python-2.7.11 intel/2016a
3.1.1 -cli dummy
3.1.2 -Python-2.7.11 intel/2016a
3.1.2 -cli dummy
3.1.3 -Python-2.7.12 intel/2016b
3.1.3 -cli dummy
3.1.4 -Python-2.7.12 intel/2016b
3.1.4 -cli dummy
3.2.0 -Python-2.7.12 intel/2016b
3.2.0 -cli dummy
3.2.2 -Python-2.7.12 intel/2016b
3.2.2 -cli dummy

HAPGEN2

‘HAPGEN2’ simulates case control datasets at SNP markers.

homepage: https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html

version toolchain
2.2.0 dummy

HarfBuzz

HarfBuzz is an OpenType text shaping engine.

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

version toolchain
0.9.35 intel/2014b
0.9.41 intel/2015a, intel/2015b
1.0.1 intel/2015a
1.1.0 intel/2015b
1.1.3 foss/2016a, intel/2016a
1.2.7 foss/2016a, intel/2016a
1.3.1 foss/2016b, intel/2016b

Harminv

Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.

homepage: http://ab-initio.mit.edu/wiki/index.php/Harminv

version toolchain
1.3.1 goolf/1.4.10, ictce/5.3.0
1.4 foss/2016a, intel/2015a

HBase

Apache HBase. is the Hadoop database, a distributed, scalable, big data store.

homepage: http://hbase.apache.org/

version toolchain
1.0.2 dummy

HDF

HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.

homepage: http://www.hdfgroup.org/products/hdf4/

version toolchain
4.2.7-patch1 goolf/1.4.10, ictce/5.3.0
4.2.8 ictce/5.3.0
4.2.11 foss/2015a, intel/2016a
4.2.12 intel/2017a

HDF5

HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.

homepage: http://www.hdfgroup.org/HDF5/

version versionsuffix toolchain
1.8.7   goolf/1.4.10, ictce/5.3.0
1.8.9   goolf/1.4.10, goolf/1.5.16, ictce/5.2.0, ictce/5.3.0, ictce/5.4.0, intel/2014b
1.8.10   goolf/1.4.10, ictce/5.3.0
1.8.10 -gpfs ictce/5.3.0, ictce/5.4.0, ictce/5.5.0, ictce/6.1.5, intel/2014b
1.8.10 -gpfs-zlib-1.2.5 ictce/5.3.0
1.8.10 -serial GCC/4.8.1, ictce/5.3.0
1.8.10-patch1   goolf/1.4.10, goolf/1.5.14, ictce/5.3.0
1.8.11   goolf/1.4.10
1.8.11 -serial GCC/4.8.1, ictce/5.3.0
1.8.12   ictce/5.4.0, ictce/5.5.0, intel/2016b
1.8.12 -zlib-1.2.7 goolf/1.4.10
1.8.12 -zlib-1.2.8 ictce/5.5.0
1.8.13   foss/2014b, foss/2015a, intel/2014b, intel/2015a, intel/2015b
1.8.14   foss/2015a, ictce/7.1.2, intel/2015a
1.8.14 -serial ictce/7.1.2, intel/2015a
1.8.15   foss/2015a, intel/2015a, intel/2015b
1.8.15-patch1   foss/2015a, foss/2015b, intel/2015a, intel/2015b
1.8.16   foss/2015a, foss/2016a, intel/2015b, intel/2016.02-GCC-4.9, intel/2016a, iomkl/2016.07, iomkl/2016.09-GCC-4.9.3-2.25
1.8.16 -serial foss/2016a, gimkl/2.11.5, intel/2015b, intel/2016a
1.8.17   foss/2016a, foss/2016b, intel/2016a, intel/2016b
1.8.17 -serial foss/2016a, intel/2016b
1.8.18   foss/2016b, foss/2017a, intel/2016b, intel/2017.01, intel/2017a
1.8.18 -serial intel/2017a
1.10.0-patch1   foss/2016b, goolfc/2016.10, intel/2016b, intel/2017.01, intel/2017a
1.10.1   intel/2017a

HEALPix

Hierarchical Equal Area isoLatitude Pixelation of a sphere.

homepage: http://healpix.sourceforge.net/

version toolchain
2.20a ictce/5.5.0

help2man

help2man produces simple manual pages from the ‘–help’ and ‘–version’ output of other commands.

homepage: https://www.gnu.org/software/help2man/

version toolchain
1.47.4 GCCcore/5.4.0, GCCcore/6.3.0, GCCcore/7.1.0, dummy, intel/2016b

HH-suite

HH-suite is an open-source software package for sensitive protein sequence searching. It contains programs that can search for similar protein sequences in protein sequence databases.

homepage: http://en.wikipedia.org/wiki/HH-suite

version toolchain
2.0.16 goolf/1.4.10

hisat

HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads. In addition to one global FM index that represents a whole genome, HISAT uses a large set of small FM indexes that collectively cover the whole genome (each index represents a genomic region of ~64,000 bp and ~48,000 indexes are needed to cover the human genome). These small indexes (called local indexes) combined with several alignment strategies enable effective alignment of RNA-seq reads, in particular, reads spanning multiple exons. The memory footprint of HISAT is relatively low (~4.3GB for the human genome). We have developed HISAT based on the Bowtie2 implementation to handle most of the operations on the FM index.

homepage: http://ccb.jhu.edu/software/hisat/index.shtml

version toolchain
0.1.5-beta goolf/1.7.20

HISAT2

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome).

homepage: https://ccb.jhu.edu/software/hisat2/index.shtml

version toolchain
2.0.3-beta intel/2016a
2.0.4 foss/2016b
2.0.5 intel/2017a

HMMER

HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.

homepage: http://hmmer.org/

version toolchain
3.0 goolf/1.4.10, ictce/5.3.0
3.1b1 goolf/1.4.10, ictce/5.3.0, ictce/6.2.5
3.1b2 foss/2016a, intel/2015a, intel/2017a

Hoard

Hoard is a fast, scalable, and memory-efficient memory allocator that can speed up your applications.

homepage: http://www.hoard.org/

version toolchain
3.10 intel/2015a

horton

HORTON is a Helpful Open-source Research TOol for N-fermion systems, written primarily in the Python programming language. (HORTON is named after the helpful pachyderm, not the Canadian caffeine supply store.) The ultimate goal of HORTON is to provide a platform for testing new ideas on the quantum many-body problem at a reasonable computational cost. Although HORTON is primarily designed to be a quantum-chemistry program, it can perform computations involving model Hamiltonians, and could be extended for computations in nuclear physics.

homepage: http://theochem.github.io/horton

version versionsuffix toolchain
1.0.2 -Python-2.7.3 goolf/1.4.10
1.1.0 -Python-2.7.3 goolf/1.4.10
1.2.0 -Python-2.7.3 goolf/1.4.10
1.2.1 -Python-2.7.3 goolf/1.4.10
2.0.0 -Python-2.7.10-HDF5-1.8.15-patch1-serial intel/2015b

HPCBIOS_Bioinfo

Bioinformatics & Computational Biology productivity environment includes a set of HPC tools, which are needed for scientific computing and visualization in the respective domain.

homepage: http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html

version toolchain
20130829 goolf/1.4.10, ictce/5.3.0

HPCBIOS_Debuggers

Common Set of Debuggers includes a set of debuggers that can assist HPC users for managing parallel codes.

homepage: http://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-05.html

version toolchain
20130829 goolf/1.4.10

HPCBIOS_LifeSciences

Life Sciences productivity environment includes a set of HPC tools, which are needed for scientific computing and visualization in the respective domain.

homepage: http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html

version toolchain
20130829 goolf/1.4.10, ictce/5.3.0

HPCBIOS_Math

Common Set of Open Source Math Libraries includes a set of HPC tools which are needed for scientific computing in multiple occasions; As of August 2013, ictce/5.3.0 loads all of: * icc/2013.4.183 * ifort/2013.4.183 * impi/4.1.0.030 * imkl/11.0.4.183

homepage: http://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-01.html

version toolchain
20130829 goolf/1.4.10, ictce/5.3.0

HPCBIOS_Profilers

Common Set of Profilers

homepage: http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html

version toolchain
20130829 goolf/1.4.10

HPCG

The HPCG Benchmark project is an effort to create a more relevant metric for ranking HPC systems than the High Performance LINPACK (HPL) benchmark, that is currently used by the TOP500 benchmark.

homepage: https://software.sandia.gov/hpcg

version toolchain
2.1 goolf/1.4.10, ictce/5.5.0

HPL

HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.

homepage: http://www.netlib.org/benchmark/hpl/

version toolchain
2.0 foss/2014b, goolf/1.4.10, goolf/1.5.16, ictce/5.3.0, ictce/6.1.5
2.1 CrayCCE/2015.06, CrayCCE/2015.11, CrayGNU/2015.06, CrayGNU/2015.11, CrayGNU/2016.03, CrayGNU/2016.04, CrayGNU/2016.06, CrayIntel/2015.06, CrayIntel/2015.11, CrayIntel/2016.06, foss/2015.05, foss/2015a, foss/2015b, foss/2016.04, foss/2016.06, foss/2016a, foss/2016b, gimkl/2.11.5, gmpolf/2016a, gmvolf/1.7.20, gmvolf/2016a, goolf/1.7.20, ictce/7.1.2, ictce/7.3.5, intel/2014.06, intel/2014.10, intel/2014.11, intel/2014b, intel/2015.02, intel/2015.08, intel/2015a, intel/2015b, intel/2016.00, intel/2016.01, intel/2016.02-GCC-4.9, intel/2016.02-GCC-5.3, intel/2016.03-GCC-4.9, intel/2016.03-GCC-5.3, intel/2016.03-GCC-5.4, intel/2016a, intel/2016b, iomkl/2015.01, iomkl/2015.02, iomkl/2015.03, iomkl/2016.07, pomkl/2016.03, pomkl/2016.04, pomkl/2016.09
2.2 foss/2016.07, foss/2016.09, foss/2017a, goolfc/2016.08, goolfc/2016.10, intel/2017.00, intel/2017.01, intel/2017.02, intel/2017a, intelcuda/2016.10, iomkl/2016.09-GCC-4.9.3-2.25, iomkl/2016.09-GCC-5.4.0-2.26, iomkl/2017.01, iomkl/2017a, pomkl/2016.09

htop

An interactive process viewer for Unix

homepage: http://hisham.hm/htop/

version toolchain
2.0.0 dummy

HTSeq

A framework to process and analyze data from high-throughput sequencing (HTS) assays

homepage: http://www-huber.embl.de/users/anders/HTSeq/

version versionsuffix toolchain
0.5.4p5 -Python-2.7.3 goolf/1.4.10, ictce/5.3.0
0.5.4p5 -Python-2.7.6 goolf/1.4.10, ictce/5.5.0
0.6.1p1 -Python-2.7.10 foss/2015b
0.6.1p1 -Python-2.7.11 foss/2016a
0.6.1p1 -Python-2.7.12 foss/2016b, intel/2016b
0.6.1p1 -Python-2.7.8 intel/2014b

HTSlib

PacBio fork of C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix

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

version versionsuffix toolchain
1.1   goolf/1.4.10
1.2.1   foss/2015a, foss/2016b, goolf/1.7.20, intel/2015a, intel/2015b
1.3   foss/2016a, intel/2016a
1.3.1   foss/2016a, foss/2016b, goolf/1.7.20, intel/2016b
1.3.2   intel/2016b
1.4   foss/2016b, intel/2016b
20160107 -PacBio intel/2017a

hub

hub is a command-line wrapper for git that makes you better at GitHub.

homepage: https://hub.github.com/

version versionsuffix toolchain
2.2.2 -linux-amd64 dummy

hunspell

Hunspell is a spell checker and morphological analyzer library and program designed for languages with rich morphology and complex word compounding or character encoding.

homepage: http://hunspell.github.io/

version toolchain
1.6.1 intel/2017a

hwloc

The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.

homepage: http://www.open-mpi.org/projects/hwloc/

version toolchain
1.5.1 GCC/4.6.3, ictce/5.3.0
1.6 ictce/5.3.0
1.6.2 GCC/4.6.4, GCC/4.7.2, ictce/5.3.0
1.7.2 GCC/4.8.2, ictce/5.3.0, ictce/5.5.0
1.8.1 GCC/4.8.2, GCC/4.8.3, iccifort/2013_sp1.2.144
1.9 GCC/4.8.3, iccifort/2013_sp1.4.211
1.10.0 GCC/4.9.2, iccifort/2015.1.133-GCC-4.9.2, iccifort/2015.2.164-GCC-4.9.2
1.10.1 GCC/4.8.4, GNU/4.9.2-2.25
1.11.0 GNU/4.9.3-2.25
1.11.1 GCC/4.9.3, iccifort/2015.3.187-GNU-4.9.3-2.25
1.11.2 GCC/4.9.3-2.25, GNU/4.9.3-2.25
1.11.3 GCC/5.2.0, GCC/5.3.0-2.26, GCC/5.4.0-2.26, GCC/6.1.0-2.27, PGI/16.3-GCC-4.9.3-2.25, PGI/16.4-GCC-5.3.0-2.26, gcccuda/2016.08, iccifort/2016.3.210-GCC-4.9.3-2.25, iccifort/2016.3.210-GCC-5.4.0-2.26, intel/2016a, intel/2016b
1.11.4 GCC/6.2.0-2.27, PGI/16.7-GCC-5.4.0-2.26, gcccuda/2016.10, iccifort/2017.1.132-GCC-5.4.0-2.26
1.11.5 GCC/5.4.0-2.26, GCC/6.3.0-2.27, iccifort/2017.1.132-GCC-6.3.0-2.27
1.11.6 GCC/6.3.0-2.28

hyperspy

HyperSpy is an open source Python library which provides tools to facilitate the interactive data analysis of multi-dimensional datasets that can be described as multi-dimensional arrays of a given signal (e.g. a 2D array of spectra a.k.a spectrum image)

homepage: http://hyperspy.org/

version versionsuffix toolchain
1.1.1 -Python-3.5.2 intel/2016b

Hypre

Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.

homepage: https://computation.llnl.gov/casc/linear_solvers/sls_hypre.html

version versionsuffix toolchain
2.8.0b   goolf/1.4.10, ictce/5.3.0
2.9.0b   intel/2014b
2.10.0b   intel/2015a
2.10.1   intel/2015b
2.10.1 -babel intel/2015b
2.11.1   foss/2016a, intel/2016a

I

i-cisTarget - i-PI - I-TASSER - icc - iccifort - iccifortcuda - icmake - ictce - IDBA-UD - ifort - igraph - IGV - IGVTools - iimpi - iimpic - IMa2 - IMa2p - ImageJ - ImageMagick - imake - IMB - imbalanced-learn - imkl - IMOD - impi - IMPUTE2 - Infernal - inputproto - Inspector - Instant - intel - intelcuda - InterProScan - intltool - io_lib - iomkl - iompi - IOR - IOzone - Iperf - ipp - IPy - ipyrad - IPython - IronPython - ISIS - ISL - IsoInfer - ispc - itac

i-cisTarget

An integrative genomics method for the prediction of regulatory features and cis-regulatory modules in Human, Mouse, and Fly

homepage: https://gbiomed.kuleuven.be/apps/lcb/i-cisTarget

version versionsuffix toolchain
20160602 -Python-2.7.11 intel/2016a

i-PI

A Python wrapper for (ab initio) (path integrals) molecular dynamics

homepage: https://github.com/i-pi/i-pi

version versionsuffix toolchain
1.0-20160213 -Python-2.7.11 intel/2016a

I-TASSER

I-TASSER is a set of pre-compiled binaries and scripts for protein structure and function modelling and comparison.

homepage: http://zhanglab.ccmb.med.umich.edu/I-TASSER/

version toolchain
4.0 dummy
4.2 dummy

icc

C and C++ compiler from Intel

homepage: http://software.intel.com/en-us/intel-compilers/

version versionsuffix toolchain
11.1.073   dummy
11.1.073 -32bit dummy
11.1.075   dummy
2011.3.174   dummy
2011.6.233   dummy
2011.10.319   dummy
2011.13.367   dummy
2013.1.117   dummy
2013.2.146   dummy
2013.3.163   dummy
2013.4.183   dummy
2013.5.192   dummy
2013.5.192 -GCC-4.8.3 dummy
2013_sp1.0.080   dummy
2013_sp1.1.106   dummy
2013_sp1.2.144   dummy
2013_sp1.3.174   dummy
2013_sp1.4.211   dummy
2015.0.090   dummy
2015.0.090 -GCC-4.9.2 dummy
2015.1.133   dummy
2015.1.133 -GCC-4.9.2 dummy
2015.2.164 -GCC-4.9.2 dummy
2015.3.187   dummy
2015.3.187 -GNU-4.9.3-2.25 dummy
2015.5.223 -GCC-4.9.3-2.25 dummy
2016.0.109   dummy
2016.0.109 -GCC-4.9.3-2.25 dummy
2016.1.150 -GCC-4.9.3-2.25 dummy
2016.2.181 -GCC-4.9.3-2.25 dummy
2016.2.181 -GCC-5.3.0-2.26 dummy
2016.3.210 -GCC-4.9.3-2.25 dummy
2016.3.210 -GCC-5.3.0-2.26 dummy
2016.3.210 -GCC-5.4.0-2.26 dummy
2017.0.098 -GCC-5.4.0-2.26 dummy
2017.1.132 -GCC-5.4.0-2.26 dummy
2017.1.132 -GCC-6.3.0-2.27 dummy
2017.2.174 -GCC-6.3.0-2.27 dummy

iccifort

Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL

homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/

version versionsuffix toolchain
2013.2.146   dummy
2013.3.163   dummy
2013.4.183   dummy
2013.5.192   dummy
2013.5.192 -GCC-4.8.3 dummy
2013_sp1.1.106   dummy
2013_sp1.2.144   dummy
2013_sp1.4.211   dummy
2015.0.090   dummy
2015.0.090 -GCC-4.9.2 dummy
2015.1.133   dummy
2015.1.133 -GCC-4.9.2 dummy
2015.2.164 -GCC-4.9.2 dummy
2015.3.187   dummy
2015.3.187 -GNU-4.9.3-2.25 dummy
2015.5.223 -GCC-4.9.3-2.25 dummy
2016.0.109   dummy
2016.0.109 -GCC-4.9.3-2.25 dummy
2016.1.150 -GCC-4.9.3-2.25 dummy
2016.2.181 -GCC-4.9.3-2.25 dummy
2016.2.181 -GCC-5.3.0-2.26 dummy
2016.3.210 -GCC-4.9.3-2.25 dummy
2016.3.210 -GCC-5.3.0-2.26 dummy
2016.3.210 -GCC-5.4.0-2.26 dummy
2017.0.098 -GCC-5.4.0-2.26 dummy
2017.1.132 -GCC-5.4.0-2.26 dummy
2017.1.132 -GCC-6.3.0-2.27 dummy
2017.2.174 -GCC-6.3.0-2.27 dummy

iccifortcuda

Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit

homepage: (none)

version toolchain
2016.10 dummy

icmake

Icmake is a hybrid between a ‘make’ utility and a ‘shell script’ language. Originally, it was written to provide a useful tool for automatic program maintenance and system administrative tasks on old MS-DOS platforms.

homepage: http://icmake.sourceforge.net/

version toolchain
7.23.02 foss/2016a

ictce

Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.

homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/

version toolchain
5.2.0 dummy
5.3.0 dummy
5.4.0 dummy
5.5.0 dummy
6.1.5 dummy
6.2.5 dummy
7.1.2 dummy
7.3.5 dummy

IDBA-UD

IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions.

homepage: http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/

version toolchain
1.1.1 goolf/1.4.10

ifort

Fortran compiler from Intel

homepage: http://software.intel.com/en-us/intel-compilers/

version versionsuffix toolchain
11.1.073   dummy
11.1.073 -32bit dummy
11.1.075   dummy
2011.3.174   dummy
2011.6.233   dummy
2011.10.319   dummy
2011.13.367   dummy
2013.1.117   dummy
2013.2.146   dummy
2013.3.163   dummy
2013.4.183   dummy
2013.5.192   dummy
2013.5.192 -GCC-4.8.3 dummy
2013_sp1.0.080   dummy
2013_sp1.1.106   dummy
2013_sp1.2.144   dummy
2013_sp1.3.174   dummy
2013_sp1.4.211   dummy
2015.0.090   dummy
2015.0.090 -GCC-4.9.2 dummy
2015.1.133   dummy
2015.1.133 -GCC-4.9.2 dummy
2015.2.164 -GCC-4.9.2 dummy
2015.3.187   dummy
2015.3.187 -GNU-4.9.3-2.25 dummy
2015.5.223 -GCC-4.9.3-2.25 dummy
2016.0.109   dummy
2016.0.109 -GCC-4.9.3-2.25 dummy
2016.1.150 -GCC-4.9.3-2.25 dummy
2016.2.181 -GCC-4.9.3-2.25 dummy
2016.2.181 -GCC-5.3.0-2.26 dummy
2016.3.210 -GCC-4.9.3-2.25 dummy
2016.3.210 -GCC-5.3.0-2.26 dummy
2016.3.210 -GCC-5.4.0-2.26 dummy
2017.0.098 -GCC-5.4.0-2.26 dummy
2017.1.132 -GCC-5.4.0-2.26 dummy
2017.1.132 -GCC-6.3.0-2.27 dummy
2017.2.174 -GCC-6.3.0-2.27 dummy

igraph

igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++.

homepage: http://igraph.org

version toolchain
0.7.1 intel/2016b

IGV

The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

homepage: http://www.broadinstitute.org/software/igv/

version versionsuffix toolchain
2.3.68 -Java-1.7.0_80 dummy
2.3.80 -Java-1.7.0_80 dummy

IGVTools

This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files. See also http://www.broadinstitute.org/software/igv/igvtools_commandline.

homepage: http://www.broadinstitute.org/software/igv/

version versionsuffix toolchain
2.3.68 -Java-1.7.0_80 dummy
2.3.72 -Java-1.7.0_80 dummy
2.3.75 -Java-1.7.0_80 dummy

iimpi

Intel C/C++ and Fortran compilers, alongside Intel MPI.

homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/

version versionsuffix toolchain
5.2.0   dummy
5.3.0   dummy
5.4.0   dummy
5.5.0   dummy
5.5.0 -GCC-4.8.3 dummy
5.5.3 -GCC-4.8.3 dummy
6.1.5   dummy
6.2.5   dummy
7.1.2   dummy
7.1.2 -GCC-4.9.2 dummy
7.2.3 -GCC-4.9.2 dummy
7.2.5 -GCC-4.9.2 dummy
7.3.5   dummy
7.3.5 -GNU-4.9.3-2.25 dummy
7.5.5 -GCC-4.9.3-2.25 dummy
8.1.5 -GCC-4.9.3-2.25 dummy
2016.00 -GCC-4.9.3-2.25 dummy
2016.01 -GCC-4.9.3-2.25 dummy
2016.02 -GCC-4.9.3-2.25 dummy
2016.02 -GCC-5.3.0-2.26 dummy
2016.03 -GCC-4.9.3-2.25 dummy
2016.03 -GCC-5.3.0-2.26 dummy
2016.03 -GCC-5.4.0-2.26 dummy
2016b   dummy
2017.00 -GCC-5.4.0-2.26 dummy
2017.01 -GCC-5.4.0-2.26 dummy
2017.02 -GCC-6.3.0-2.27 dummy
2017a   dummy

iimpic

Intel C/C++ and Fortran compilers, alongside Intel MPI.

homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/

version toolchain
2016.10 dummy

IMa2

IMa2 is a progam for population genetic analysis that can handle two or more populations.

homepage: https://bio.cst.temple.edu/~hey/software/software.htm#IMa2

version toolchain
8.27.12 foss/2016a, goolf/1.4.10, ictce/5.5.0

IMa2p

IMa2p is a parallel implementation of IMa2, using OpenMPI-C++ - a Bayesian MCMC based method for inferring population demography under the IM (Isolation with Migration) model. http://dx.doi.org/10.1111/1755-0998.12437

homepage: https://github.com/arunsethuraman/ima2p

version toolchain
20151123 foss/2016a
20160804 intel/2016b

ImageJ

Image Processing and Analysis in Java

homepage: https://imagej.nih.gov/ij

version toolchain
1.51i dummy
1.51k dummy

ImageMagick

ImageMagick is a software suite to create, edit, compose, or convert bitmap images

homepage: http://www.imagemagick.org/

version toolchain
6.9.3-3 goolf/1.4.10
6.9.4-8 intel/2016a
7.0.1-6 intel/2016a
7.0.1-9 intel/2016a
7.0.2-9 intel/2016a
7.0.3-1 intel/2016b
7.0.5-4 intel/2017a

imake

imake is a Makefile-generator that is intended to make it easier to develop software portably for multiple systems.

homepage: http://www.x.org/

version toolchain
1.0.5 goolf/1.4.10, ictce/5.3.0
1.0.7 intel/2016a

IMB

The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and global communication operations for a range of message sizes

homepage: https://software.intel.com/en-us/articles/intel-mpi-benchmarks

version toolchain
4.0.1 goolf/1.6.10, intel/2015a
4.1 foss/2016a, foss/2017a, intel/2017.02, intel/2017a

imbalanced-learn

imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in datasets showing strong between-class imbalance.

homepage: https://github.com/scikit-learn-contrib/imbalanced-learn

version versionsuffix toolchain
0.2.1 -Python-3.5.2 intel/2016b

imkl

Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.

homepage: http://software.intel.com/en-us/intel-mkl/

version versionsuffix toolchain
10.2.6.038   dummy
10.2.6.038 -32bit dummy
10.3.6.233   dummy
10.3.10.319   dummy
10.3.12.361   dummy
11.0.1.117   dummy
11.0.2.146   dummy, iimpi/5.2.0
11.0.3.163   dummy, iimpi/5.3.0
11.0.4.183   dummy, iimpi/5.4.0
11.0.5.192   dummy, iimpi/5.5.0, iimpi/5.5.0-GCC-4.8.3
11.1.0.080   dummy
11.1.1.106   dummy, iimpi/6.1.5
11.1.2.144   dummy, iimpi/5.5.3-GCC-4.8.3, iimpi/6.2.5, iompi/2015.01
11.1.2.144 -2013.5.192-GCC-4.8.3 dummy
11.1.2.144 -GCC-4.8.3 dummy
11.1.2.144 -OpenMPI-1.6.5 dummy
11.1.3.174   dummy
11.2.0.090   iimpi/7.1.2, iimpi/7.1.2-GCC-4.9.2
11.2.1.133   iimpi/7.2.3-GCC-4.9.2
11.2.2.164   iimpi/7.2.5-GCC-4.9.2, iompi/2015.02
11.2.3.187   gimpi/2.11.5, iimpi/7.3.5, iimpi/7.3.5-GNU-4.9.3-2.25, iompi/2015.03
11.3.0.109   iimpi/2016.00-GCC-4.9.3-2.25
11.3.1.150   iimpi/2016.01-GCC-4.9.3-2.25, iimpi/7.5.5-GCC-4.9.3-2.25, iimpi/8.1.5-GCC-4.9.3-2.25
11.3.2.181   iimpi/2016.02-GCC-4.9.3-2.25, iimpi/2016.02-GCC-5.3.0-2.26, pompi/2016.03
11.3.3.210   iimpi/2016.03-GCC-4.9.3-2.25, iimpi/2016.03-GCC-5.3.0-2.26, iimpi/2016.03-GCC-5.4.0-2.26, iimpi/2016b, iimpic/2016.10, iompi/2016.07, iompi/2016.09-GCC-4.9.3-2.25, iompi/2016.09-GCC-5.4.0-2.26, pompi/2016.04, pompi/2016.09
2017.0.098   iimpi/2017.00-GCC-5.4.0-2.26
2017.1.132   iimpi/2017.01-GCC-5.4.0-2.26, iimpi/2017a, iompi/2017.01, iompi/2017a
2017.2.174   iimpi/2017.02-GCC-6.3.0-2.27

IMOD

IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim Kremer, Quanren Xiong, and John Heumann at the University of Colorado.

homepage: http://bio3d.colorado.edu/imod/

version versionsuffix toolchain
4.7.15 _RHEL6-64_CUDA6.0 dummy

impi

The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.

homepage: http://software.intel.com/en-us/intel-mpi-library/

version versionsuffix toolchain
3.2.2.006   dummy
4.0.0.028   dummy
4.0.0.028 -32bit dummy
4.0.2.003   dummy
4.1.0.027   dummy
4.1.0.030   dummy, iccifort/2013.2.146, iccifort/2013.3.163, iccifort/2013.4.183
4.1.1.036   dummy, iccifort/2013.5.192, iccifort/2013.5.192-GCC-4.8.3
4.1.2.040   dummy
4.1.3.045   dummy, iccifort/2013_sp1.1.106
4.1.3.049   GCC/4.8.3, dummy, iccifort/2013.5.192-GCC-4.8.3, iccifort/2013_sp1.2.144
5.0.1.035   iccifort/2015.0.090, iccifort/2015.0.090-GCC-4.9.2
5.0.2.044   iccifort/2015.1.133-GCC-4.9.2
5.0.3.048   GCC/4.9.3, iccifort/2015.2.164-GCC-4.9.2, iccifort/2015.3.187, iccifort/2015.3.187-GNU-4.9.3-2.25
5.1.0.079   iccifort/2015.3.187
5.1.1.109   iccifort/2016.0.109-GCC-4.9.3-2.25
5.1.2.150   iccifort/2015.5.223-GCC-4.9.3-2.25, iccifort/2016.1.150-GCC-4.9.3-2.25
5.1.3.181   iccifort/2016.2.181-GCC-4.9.3-2.25, iccifort/2016.2.181-GCC-5.3.0-2.26, iccifort/2016.3.210-GCC-4.9.3-2.25, iccifort/2016.3.210-GCC-5.3.0-2.26, iccifort/2016.3.210-GCC-5.4.0-2.26, iccifortcuda/2016.10
2017.0.098   iccifort/2017.0.098-GCC-5.4.0-2.26
2017.1.132   iccifort/2017.1.132-GCC-5.4.0-2.26, iccifort/2017.1.132-GCC-6.3.0-2.27
2017.2.174   iccifort/2017.2.174-GCC-6.3.0-2.27

IMPUTE2

IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009

homepage: http://mathgen.stats.ox.ac.uk/impute/impute_v2.html

version versionsuffix toolchain
2.3.0 _x86_64_dynamic dummy
2.3.0 _x86_64_static dummy
2.3.2 _x86_64_dynamic dummy
2.3.2 _x86_64_static dummy

Infernal

Infernal (‘INFERence of RNA ALignment’) is for searching DNA sequence databases for RNA structure and sequence similarities.

homepage: http://eddylab.org/infernal/

version toolchain
1.1 goolf/1.4.10, ictce/5.3.0
1.1rc1 goolf/1.4.10, ictce/5.3.0

inputproto

X.org InputProto protocol headers.

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

version toolchain
2.3 foss/2014b, goolf/1.4.10, goolf/1.5.14, ictce/5.3.0, intel/2014b, intel/2015a
2.3.1 foss/2016a, gimkl/2.11.5, goolf/1.5.14, intel/2015a, intel/2015b, intel/2016a
2.3.2 intel/2016a

Inspector

Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications

homepage: http://software.intel.com/en-us/intel-inspector-xe

version toolchain
2013_update6 dummy
2013_update7 dummy
2016_update3 dummy
2017_update1 dummy
2017_update2 dummy

Instant

Instant is a Python module that allows for instant inlining of C and C++ code in Python. It is a small Python module built on top of SWIG and Distutils.

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

version versionsuffix toolchain
1.0.0 -Python-2.7.3 goolf/1.4.10, ictce/5.3.0
1.6.0 -Python-2.7.11 intel/2015b

intel

Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.

homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/

version versionsuffix toolchain
2014.06   dummy
2014.10   dummy
2014.11   dummy
2014b   dummy
2015.02   dummy
2015.08   dummy
2015a   dummy
2015b   dummy
2016.00   dummy
2016.01   dummy
2016.02 -GCC-4.9 dummy
2016.02 -GCC-5.3 dummy
2016.03 -GCC-4.9 dummy
2016.03 -GCC-5.3 dummy
2016.03 -GCC-5.4 dummy
2016a   dummy
2016b   dummy
2017.00   dummy
2017.01   dummy
2017.02   dummy
2017a   dummy

intelcuda

Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit

homepage: (none)

version toolchain
2016.10 dummy

InterProScan

InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource.

homepage: http://www.ebi.ac.uk/interpro/

version toolchain
5.16-55.0 intel/2015b
5.21-60.0 intel/2015b

intltool

intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.

homepage: http://freedesktop.org/wiki/Software/intltool/

version versionsuffix toolchain
0.51.0   intel/2015b
0.51.0 -Perl-5.20.3 intel/2016a
0.51.0 -Perl-5.22.1 foss/2016a, intel/2016a
0.51.0 -Perl-5.24.0 GCCcore/4.9.3, intel/2016b

io_lib

Io_lib is a library of file reading and writing code to provide a general purpose trace file (and Experiment File) reading interface. The programmer simply calls the (eg) read_reading to create a “Read” C structure with the data loaded into memory. It has been compiled and tested on a variety of unix systems, MacOS X and MS Windows.

homepage: http://sourceforge.net/projects/staden/files/io_lib/

version toolchain
1.14.8 foss/2016a

iomkl

Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.

homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/

version toolchain
2015.01 dummy
2015.02 dummy
2015.03 dummy
2016.07 dummy
2016.09-GCC-4.9.3-2.25 dummy
2016.09-GCC-5.4.0-2.26 dummy
2017.01 dummy
2017a dummy

iompi

Intel C/C++ and Fortran compilers, alongside Open MPI.

homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/

version toolchain
2015.01 dummy
2015.02 dummy
2015.03 dummy
2016.07 dummy
2016.09-GCC-4.9.3-2.25 dummy
2016.09-GCC-5.4.0-2.26 dummy
2017.01 dummy
2017a dummy

IOR

The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, or HDF5 interfaces.

homepage: https://github.com/chaos/ior

version versionsuffix toolchain
2.10.3 -mpiio goolf/1.4.10, intel/2014b
3.0.1 -mpiio foss/2016a

IOzone

IOzone is a filesystem benchmark tool. The benchmark generates and measures a variety of file operations. Iozone has been ported to many machines and runs under many operating systems.

homepage: http://www.iozone.org/

version toolchain
3.434 foss/2016a

Iperf

Iperf-2.0.5: TCP and UDP bandwidth performance measurement tool

homepage: http://iperf.sourceforge.net/

version toolchain
2.0.5 goolf/1.4.10, ictce/5.3.0

ipp

Intel Integrated Performance Primitives (Intel IPP) is an extensive library of multicore-ready, highly optimized software functions for multimedia, data processing, and communications applications. Intel IPP offers thousands of optimized functions covering frequently used fundamental algorithms.

homepage: http://software.intel.com/en-us/articles/intel-ipp/

version toolchain
7.0.5.233 dummy
8.1.0.144 dummy
9.0.1.150 dummy
2017.1.132 dummy

IPy

Class and tools for handling of IPv4 and IPv6 addresses and networks

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

version toolchain
0.83 dummy

ipyrad

ipyrad is an interactive toolkit for assembly and analysis of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies.

homepage: https://ipyrad.readthedocs.io

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

IPython

IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. Support for interactive data visualization and use of GUI toolkits. Flexible, embeddable interpreters to load into your own projects. Easy to use, high performance tools for parallel computing.

homepage: http://ipython.org/index.html

version versionsuffix toolchain
1.1.0 -Python-2.7.3 goolf/1.4.10
3.1.0 -Python-2.7.9 intel/2015a
3.2.0 -Python-2.7.9 foss/2015a, intel/2015a
3.2.1 -Python-2.7.10 intel/2015a
3.2.3 -Python-2.7.10 intel/2015b
3.2.3 -Python-2.7.11 foss/2015a, foss/2016a, intel/2016a
4.0.0 -Python-2.7.10 intel/2015a
4.1.0 -Python-2.7.5 goolf/1.4.10
4.2.0 -Python-2.7.11 goolf/1.7.20, intel/2016a
5.0.0 -Python-2.7.11 foss/2016a
5.0.0 -Python-3.5.1 foss/2016a
5.1.0 -Python-2.7.12 foss/2016b, intel/2016b
5.1.0 -Python-3.5.2 intel/2016b
5.2.2 -Python-2.7.12 intel/2016b
5.3.0 -Python-2.7.13 intel/2017a

IronPython

IronPython is an open-source implementation of the Python programming language which is tightly integrated with the .NET Framework. IronPython can use the .NET Framework and Python libraries, and other .NET languages can use Python code just as easily.

homepage: http://ironpython.net/

version toolchain
2.7 intel/2016b

ISIS

ISIS is Computational Fluid Dynamics software based on CALIF3S and PELICANS libraries. It is intensively used for simulation of fires and copes with a wide range of applications, including laminar or turbulent flows, possibly reactive, governed by incompressible or low Mach number Navier-Stokes equations.

homepage: https://gforge.irsn.fr/gf/project/isis/

version toolchain
4.2.1 intel/2015b

ISL

isl is a library for manipulating sets and relations of integer points bounded by linear constraints.

homepage: http://isl.gforge.inria.fr/

version toolchain
0.14 GCC/4.9.2
0.15 GCC/4.9.3-2.25, GNU/4.9.3-2.25, foss/2016a
0.16 GCC/4.9.3-2.25
0.17 foss/2016a

IsoInfer

IsoInfer is a C/C++ program to infer isoforms based on short RNA-Seq (single-end and paired-end) reads, exon-intron boundary and TSS/PAS information. This version of IsoInfer uses a unified way to handle different types of short reads with different lengths.

homepage: http://www.cs.ucr.edu/~jianxing/IsoInfer.html

version toolchain
0.9.1 goolf/1.4.10, ictce/6.2.5

ispc

Intel SPMD Program Compilers; An open-source compiler for high-performance SIMD programming on the CPU. ispc is a compiler for a variant of the C programming language, with extensions for ‘single program, multiple data’ (SPMD) programming. Under the SPMD model, the programmer writes a program that generally appears to be a regular serial program, though the execution model is actually that a number of program instances execute in parallel on the hardware.

homepage: http://ispc.github.io/ , https://github.com/ispc/ispc/

version toolchain
1.6.0 dummy

itac

The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays.

homepage: http://software.intel.com/en-us/intel-trace-analyzer/

version toolchain
8.0.0.011 dummy
8.1.4.045 dummy
9.0.3.051 dummy
2017.1.024 dummy

J

JAGS - Jansson - JasPer - Java - Jellyfish - jemalloc - jhbuild - Jinja2 - jModelTest - JUBE - JUnit - jupyterhub - JWM

JAGS

JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation

homepage: http://mcmc-jags.sourceforge.net/

version toolchain
3.4.0 goolf/1.4.10, ictce/6.2.5, intel/2014b
4.2.0 foss/2016a, intel/2016a

Jansson

Jansson is a C library for encoding, decoding and manipulating JSON data. Its main features and design principles are: * Simple and intuitive API and data model * Comprehensive documentation * No dependencies on other libraries * Full Unicode support (UTF-8) * Extensive test suite

homepage: http://www.digip.org/jansson/

version toolchain
2.6 GCC/4.8.3

JasPer

The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.

homepage: http://www.ece.uvic.ca/~frodo/jasper/

version toolchain
1.900.1 CrayGNU/2015.06, CrayGNU/2015.11, CrayIntel/2015.11, foss/2015a, foss/2016a, foss/2016b, foss/2017a, goolf/1.4.10, goolf/1.5.14, ictce/5.3.0, ictce/5.5.0, intel/2014.06, intel/2014b, intel/2015a, intel/2015b, intel/2016a, intel/2016b, intel/2017a
2.0.10 intel/2016b
2.0.12 intel/2017a

Java

Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.

homepage: http://java.com/

version toolchain
1.6.0_24 dummy
1.7.0_10 dummy
1.7.0_15 dummy
1.7.0_21 dummy
1.7.0_40 dummy
1.7.0_45 dummy
1.7.0_60 dummy
1.7.0_75 dummy
1.7.0_76 dummy
1.7.0_79 dummy
1.7.0_80 dummy
1.8.0_20 dummy
1.8.0_25 dummy
1.8.0_31 dummy
1.8.0_40 dummy
1.8.0_45 dummy
1.8.0_60 dummy
1.8.0_65 dummy
1.8.0_66 dummy
1.8.0_72 dummy
1.8.0_74 dummy
1.8.0_77 dummy
1.8.0_92 dummy
1.8.0_112 dummy
1.8.0_121 dummy

Jellyfish

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.

homepage: http://www.genome.umd.edu/jellyfish.html

version toolchain
1.1.11 foss/2016a, foss/2016b
2.1.3 foss/2014b, goolf/1.4.10
2.2.3 intel/2015b
2.2.4 foss/2015b, intel/2015b
2.2.6 goolf/1.7.20

jemalloc

jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.

homepage: http://www.canonware.com/jemalloc

version toolchain
3.6.0 foss/2015a, intel/2015a
4.1.0 intel/2016a
4.2.0 foss/2016a, intel/2016a
4.2.1 intel/2016b
4.5.0 intel/2017a

jhbuild

JHBuild allows you to automatically download and compile “modules” (i.e. source code packages). Modules are listed in “module set” files, which also include dependency information so that JHBuild can discover what modules need to be built and in what order.

homepage: https://wiki.gnome.org/action/show/Projects/Jhbuild

version toolchain
3.15.92 GCCcore/4.9.3

Jinja2

Jinja2 is a template engine written in pure Python. It provides a Django inspired non-XML syntax but supports inline expressions and an optional sandboxed environment.

homepage: https://pypi.python.org/pypi/Jinja2

version versionsuffix toolchain
2.6 -Python-2.7.3 goolf/1.4.10, ictce/5.3.0

jModelTest

jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution.

homepage: https://github.com/ddarriba/jmodeltest2

version versionsuffix toolchain
2.1.9r20160115 -Java-1.7.0_75 goolf/1.4.10
2.1.10r20160303 -Java-1.8.0_92 dummy

JUBE

The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, run those sets on different computer systems and evaluate the results.

homepage: http://www.fz-juelich.de/jsc/jube

version toolchain
2.0.3 dummy
2.0.4 dummy
2.0.5 dummy

JUnit

A programmer-oriented testing framework for Java.

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

version versionsuffix toolchain
4.10 -Java-1.7.0_10 dummy
4.10 -Java-1.7.0_21 dummy
4.11 -Java-1.7.0_15 dummy
4.11 -Java-1.7.0_21 dummy
4.11 -Java-1.7.0_60 dummy
4.11 -Java-1.7.0_75 dummy
4.11 -Java-1.7.0_79 dummy
4.12 -Java-1.7.0_80 dummy
4.12 -Java-1.8.0_112 dummy
4.12 -Java-1.8.0_121 dummy
4.12 -Java-1.8.0_66 dummy
4.12 -Java-1.8.0_72 dummy
4.12 -Java-1.8.0_77 dummy
4.12 -Java-1.8.0_92 dummy

jupyterhub

JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed for centralized deployments in companies, university classrooms and research labs.

homepage: http://jupyter.org

version versionsuffix toolchain
0.6.1 -Python-3.5.1 foss/2016a

JWM

JWM is a light-weight window manager for the X11 Window System.

homepage: https://joewing.net/projects/jwm/

version toolchain
2.3.5 intel/2016a

K

Kaiju - kallisto - kbproto - KEALib - Kent_tools - Keras - Kerberos_V5 - khmer - Kraken

Kaiju

Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing experiments

homepage: http://kaiju.binf.ku.dk/

version toolchain
1.5.0 intel/2016b

kallisto

kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.

homepage: http://pachterlab.github.io/kallisto/

version toolchain
0.42.4 intel/2015b
0.42.5 foss/2016a
0.43.0 intel/2016b

kbproto

X.org KBProto protocol headers.

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

version toolchain
1.0.6 foss/2014b, goolf/1.4.10, goolf/1.5.14, ictce/5.3.0, intel/2014b, intel/2015a
1.0.7 foss/2016a, gimkl/2.11.5, intel/2015a, intel/2015b, intel/2016a

KEALib

KEALib provides an implementation of the GDAL data model. The format supports raster attribute tables, image pyramids, meta-data and in-built statistics while also handling very large files and compression throughout. Based on the HDF5 standard, it also provides a base from which other formats can be derived and is a good choice for long term data archiving. An independent software library (libkea) provides complete access to the KEA image format and a GDAL driver allowing KEA images to be used from any GDAL supported software.

homepage: http://www.kealib.org

version toolchain
1.4.4 foss/2015a

Kent_tools

Kent tools: collection of tools used by the UCSC genome browser.

homepage: http://genome.cse.ucsc.edu/

version versionsuffix toolchain
20130806 -linux.x86_64 dummy

Keras

Keras is a minimalist, highly modular neural networks library, written in Python and capable of running on top of either TensorFlow or Theano.

homepage: https://keras.io/

version versionsuffix toolchain
1.0.8 -Python-3.5.2 intel/2016b
1.1.0 -Python-3.5.2 intel/2016b
2.0.4 -Python-3.6.1 intel/2017a

Kerberos_V5

Kerberos is a network authentication protocol. It is designed to provide strong authentication for client/server applications by using secret-key cryptography. A free implementation of this protocol is available from the Massachusetts Institute of Technology.

homepage: http://web.mit.edu/kerberos/dist/index.html

version toolchain
1.12.2 intel/2014b

khmer

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

homepage: https://github.com/ged-lab/khmer/

version versionsuffix toolchain
1.1 -Python-2.7.5 goolf/1.4.10
1.4.1 -Python-2.7.12 foss/2016b

Kraken

Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.

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

version versionsuffix toolchain
0.10.5-beta -Perl-5.22.1 foss/2016a
0.10.5-beta -Perl-5.24.0 foss/2016b

L

L_RNA_scaffolder - LAMARC - LAME - LAPACK - LASTZ - lbzip2 - LeadIT - less - LevelDB - lftp - libbitmask - libcerf - libcircle - libcmaes - libconfig - libcpuset - libcroco - libctl - libdap - libdrm - libdwarf - libedit - libelf - libevent - libffi - libfontenc - libgcrypt - libgd - libglade - libGLU - libgpg-error - libgtextutils - libharu - libibmad - libibumad - libibverbs - libICE - libiconv - libidn - Libint - libjpeg-turbo - libmatheval - libpciaccess - libpng - libpsortb - libpthread-stubs - libQGLViewer - libreadline - librsvg - libsigc++ - libSM - libsmm - libsodium - libspatialindex - libspatialite - LIBSVM - libtasn1 - LibTIFF - libtool - libungif - libunistring - libunwind - LibUUID - libX11 - libXau - libXaw - libxc - libxcb - libXcursor - libXdamage - libXdmcp - libXext - libXfixes - libXfont - libXft - libXi - libXinerama - libxkbcommon - libxml2 - libXmu - libXp - libXpm - libXrandr - libXrender - libXScrnSaver - libxslt - libxsmm - libXt - libXtst - libXxf86vm - libyaml - likwid - LinBox - LittleCMS - LLVM - LMDB - Lmod - LoFreq - Log-Log4perl - log4cplus - Loki - LSMS - Lua - LuaJIT - LWM2 - lxml - lynx - LZO

L_RNA_scaffolder

L_RNA_scaffolder is a novel scaffolding tool using long trancriptome reads to scaffold genome fragments

homepage: http://www.fishbrowser.org/software/L_RNA_scaffolder/

version versionsuffix toolchain
20141124 -Perl-5.24.0 intel/2016b

LAMARC

LAMARC is a program which estimates population-genetic parameters such as population size, population growth rate, recombination rate, and migration rates.

homepage: http://evolution.genetics.washington.edu/lamarc/

version versionsuffix toolchain
2.1.9 -headless ictce/5.5.0

LAME

LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.

homepage: http://lame.sourceforge.net/

version toolchain
3.99.5 foss/2015a

LAPACK

LAPACK is written in Fortran90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems.

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

version toolchain
3.4.2 gompi/1.4.10
3.5.0 gompi/1.5.16

LASTZ

LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.

homepage: http://www.bx.psu.edu/~rsharris/lastz/

version toolchain
1.02.00 foss/2016a, goolf/1.7.20

lbzip2

lbzip2 is a free, multi-threaded compression utility with support for bzip2 compressed file format

homepage: http://lbzip2.org/

version toolchain
2.5 goolf/1.7.20

LeadIT

Visually Informed LeadOpt

homepage: http://www.biosolveit.de/LeadIT/index.html

version toolchain
2.1.9 dummy

less

Less is a free, open-source file pager. It can be found on most versions of Linux, Unix and Mac OS, as well as on many other operating systems.

homepage: http://www.greenwoodsoftware.com/less/

version toolchain
458 GCC/4.8.2

LevelDB

LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values.

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

version toolchain
1.18 foss/2016a

lftp

LFTP is a sophisticated ftp/http client, and a file transfer program supporting a number of network protocols. Like BASH, it has job control and uses the readline library for input. It has bookmarks, a built-in mirror command, and can transfer several files in parallel. It was designed with reliability in mind.

homepage: http://lftp.yar.ru

version toolchain
4.4.1 goolf/1.4.10
4.6.4 GNU/4.9.3-2.25

libbitmask

libbitmask provides a convenient, powerful bitmask data type

homepage: http://oss.sgi.com/projects/cpusets/

version toolchain
2.0 dummy

libcerf

libcerf is a self-contained numeric library that provides an efficient and accurate implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions.

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

version toolchain
1.4 foss/2016a, foss/2016b, intel/2016a
1.5 foss/2016b, intel/2016b

libcircle

An API to provide an efficient distributed queue on a cluster. libcircle is an API for distributing embarrassingly parallel workloads using self-stabilization.

homepage: https://github.com/hpc/libcircle/

version toolchain
0.2.0-rc.1 goolf/1.4.10, ictce/5.3.0

libcmaes

libcmaes is a multithreaded C++11 library for high performance blackbox stochastic optimization using the CMA-ES algorithm for Covariance Matrix Adaptation Evolution Strategy.

homepage: http://beniz.github.io/libcmaes/

version toolchain
0.9.5 foss/2016a

libconfig

Libconfig is a simple library for processing structured configuration files

homepage: http://www.hyperrealm.com/libconfig/

version toolchain
1.5 intel/2016b

libcpuset

libcpuset provides full access to cpuset capabilities

homepage: http://oss.sgi.com/projects/cpusets/

version toolchain
1.0 dummy

libcroco

Libcroco is a standalone css2 parsing and manipulation library.

homepage: https://github.com/GNOME/libcroco

version toolchain
0.6.11 intel/2016a

libctl

libctl is a free Guile-based library implementing flexible control files for scientific simulations.

homepage: http://ab-initio.mit.edu/libctl

version toolchain
3.2.1 goolf/1.4.10, ictce/5.3.0
3.2.2 foss/2016a, intel/2015a

libdap

A C++ SDK which contains an implementation of DAP 2.0 and the development versions of DAP3, up to 3.4. This includes both Client- and Server-side support classes.

homepage: http://opendap.org/download/libdap

version versionsuffix toolchain
3.14.0 -Python-2.7.10 intel/2015a, intel/2015b
3.18.1 -Python-2.7.11 foss/2016a

libdrm

Direct Rendering Manager runtime library.

homepage: http://dri.freedesktop.org

version toolchain
2.4.27 goolf/1.4.10, ictce/5.3.0, ictce/5.5.0
2.4.59 intel/2015a
2.4.64 intel/2015b
2.4.66 intel/2015b
2.4.67 foss/2016a, gimkl/2.11.5, intel/2016a
2.4.68 foss/2016a, intel/2016a
2.4.70 foss/2016b, intel/2016b
2.4.76 intel/2017a

libdwarf

The DWARF Debugging Information Format is of interest to programmers working on compilers and debuggers (and anyone interested in reading or writing DWARF information))

homepage: http://www.prevanders.net/dwarf.html

version toolchain
20140805 GCC/4.9.2
20150310 GCC/4.9.2

libedit

This BSD-style licensed command line editor library provides generic line editing, history, and tokenization functions, similar to those found in GNU Readline.

homepage: http://thrysoee.dk/editline/

version toolchain
20150325 GNU/4.9.3-2.25

libelf

libelf is a free ELF object file access library

homepage: http://www.mr511.de/software/english.html

version toolchain
0.8.13 GCC/4.8.3, GCC/4.9.2

libevent

The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts.

homepage: http://libevent.org/

version toolchain
2.0.21 intel/2014b
2.0.22 GCC/4.9.2, GCC/5.4.0-2.26, GCCcore/4.9.3, GNU/4.9.3-2.25
2.1.8 dummy

libffi

The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time.

homepage: http://sourceware.org/libffi/

version toolchain
3.0.11 goolf/1.4.10
3.0.13 foss/2015b, goolf/1.4.10, goolf/1.5.14, ictce/5.2.0, ictce/5.3.0, intel/2015a, intel/2015b
3.1 goolf/1.5.14, goolf/1.7.20, intel/2014.06, intel/2014b, intel/2015a, intel/2015b
3.2.1 GCC/4.9.2, GCC/4.9.3-2.25, GCC/5.4.0-2.26, GCCcore/6.3.0, GNU/4.9.3-2.25, foss/2015a, foss/2015b, foss/2016.04, foss/2016a, foss/2016b, gimkl/2.11.5, intel/2015a, intel/2015b, intel/2016a, intel/2016b

libfontenc

X11 font encoding library

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

version toolchain
1.1.3 foss/2016a, gimkl/2.11.5, intel/2015a, intel/2015b, intel/2016a

libgcrypt

Libgpg-error is a small library that defines common error values for all GnuPG components.

homepage: https://gnupg.org/related_software/libgcrypt/index.html

version toolchain
1.6.5 intel/2016a

libgd

GD is an open source code library for the dynamic creation of images by programmers.

homepage: http://libgd.bitbucket.org/

version toolchain
2.1.0 ictce/5.5.0
2.1.1 foss/2016a, intel/2015b, intel/2016a
2.2.3 foss/2016b, intel/2016b

libglade

Libglade is a library for constructing user interfaces dynamically from XML descriptions.

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

version toolchain
2.6.4 intel/2016a

libGLU

The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.

homepage: ftp://ftp.freedesktop.org/pub/mesa/glu/

version versionsuffix toolchain
9.0.0   foss/2016a, foss/2016b, gimkl/2.11.5, intel/2015b, intel/2016a, intel/2016b, intel/2017a
9.0.0 -Mesa-11.0.8 intel/2015b
9.0.0 -Mesa-11.2.1 foss/2016a, intel/2016a
9.0.0 -Python-2.7.10 intel/2015a

libgpg-error

Libgpg-error is a small library that defines common error values for all GnuPG components.

homepage: https://gnupg.org/related_software/libgpg-error/index.html

version toolchain
1.21 intel/2016a

libgtextutils

ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream

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

version toolchain
0.6.1 goolf/1.4.10, goolf/1.7.20, ictce/5.3.0, intel/2015a
0.7 foss/2015b, foss/2016a, foss/2016b

libharu

libHaru is a free, cross platform, open source library for generating PDF files.

homepage: http://libharu.org/

version toolchain
2.2.0 goolf/1.4.10, ictce/5.3.0
2.3.0 foss/2016a, foss/2016b

libibmad

libibmad is a convenience library to encode, decode, and dump IB MAD packets. It is implemented on top of and in conjunction with libibumad (the umad kernel interface library.)

homepage: http://www.openfabrics.org

version toolchain
1.3.9 GCC/4.6.3, GCC/4.7.2