Logiciels disponibles

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Le tableau présenté ci-dessous montre la liste des logiciels disponibles sur les systèmes nationaux de Calcul Canada. Cette liste est modifiée à l'ajout de tout nouveau logiciel. Pour demander l'installation ou la mise à jour d'un logiciel ou d'une bibliothèque, les utilisateurs peuvent communiquer avec le soutien technique.

Notes

À l'exception des programmes de base des systèmes, l'accès à la plupart des logiciels se fait par le chargement de modules. Pour plus d'information sur comment utiliser le système de modules Lmod, consultez la page Utiliser des modules. Prenez note que certains modules pré-requis sont chargés par défaut.

Points à retenir à propos des logiciels disponibles

  • La plupart des modules Python ne sont pas installés en tant que modules (Lmod), mais en tant qu'environnements binaires localisés sous /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/; TensorFlow est un exemple. Voyez la page Python pour des détails sur comment lister les paquets Python et les installer.
  • De même, la plupart des paquets R et Perl ne sont pas installés. Nous vous recommandons de les installer dans votre environnement personnel ou dans celui de votre groupe. Voyez les pages R et Perl pour des détails sur l'installation des paquets.
  • Voyez la page Algèbre symbolique où il est question de SageMath.
  • Notez que Docker n'est pas disponible sur les grappes de Calcul Canada, mais que Singularity peut être utilisé en chargeant le module singularity. Pour convertir les contenants Dockers, consultez le guide de l’utilisateur Singularity.
  • Certains logiciels listés dans le tableau sont sous licence et donc non accessibles directement à tous les utilisateurs; Calcul Canada peut vous en accorder l'accès au besoin. En tentant de charger le module d'un tel logiciel, vous recevrez les consignes sur comment en obtenir l'accès.
  • La plupart des paquets listés se trouvent sur toutes les grappes de Calcul Canada. Certains cependant ne sont disponibles que sur un site en particulier en raison des restrictions liées à l'octroi des licences; voir #Disponibles uniquement sur certaines grappes ci-dessous.
  • Plusieurs paquets reliés au système d’exploitation comme Autotools, Make et Git ne sont pas installés en tant que modules, mais font partie de l'environnement par défaut; ils ne paraissent pas dans le tableau.

Niagara (LP) fait exception; les logiciels disponibles sur cette grappe sont énumérés dans le Guide de démarrage pour Niagara. Vous pouvez toutefois accéder les modules listés ci-dessous en exécutant d'abord les commandes

  [name@server ~]$ module load CCEnv
  [name@server ~]$ module load StdEnv


Modules disponibles sur toutes les grappes

Le tableau suivant liste les logiciels pour lesquels un module d'environnement est disponible. Certains modules peuvent être chargés avec la commande module load alors que d'autres nécessitent des conditions particulières. Dans la colonne Description, cliquez sur Expand pour connaître les prérequis et lire une description sommaire du logiciel. Un lien dans la colonne Documentation conduit à la documentation spécifique sur le logiciel. Pour lister les logiciels selon leur type, effectuer un tri en cliquant sur l'entête de la colonne Type.

Les types sont :

  • ai (intelligence artificielle)
  • bio (biologie, bioinformatique)
  • chem (chimie)
  • geo (sciences de la Terre)
  • io (input/output)
  • math (mathématiques)
  • mpi (MPI)
  • phys (physique et génie)
  • tools (langages et bibliothèques)
  • vis (visualisation).
Module Type Documentation Description
abaqus/6.14.1 phys

Description: 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 Keyword:phys
Prerequisites: -
Description:
abinit/8.2.2 chem ABINIT

Description: 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/ Keyword:chem CC-Wiki: ABINIT
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description:
abinit/8.4.4 chem ABINIT

Description: 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/ Keyword:chem CC-Wiki: ABINIT
Prerequisites: intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
abyss/1.5.2 bio

Description: Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss Keyword:bio
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
abyss/1.9.0 bio

Description: Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler - Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss Keyword:bio
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1
Description:
abyss/2.0.2 bio

Description: Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss Keyword:bio
Prerequisites: gcc/7.3.0 and openmpi/3.1.2 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description:
admixture/1.3.0 bio

Description: 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 Keyword:bio
Prerequisites: -
Description:
advisor/2018.3 -

Description: Vectorization Optimization and Thread Prototyping - Vectorize and thread code or performance dies - Easy workflow + data + tips = faster code faster - Prioritize, Prototype and Predict performance gain Homepage: https://software.intel.com/intel-advisor-xe
Prerequisites: -
Description:
afni/20180404 -

Description: AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. Homepage: http://afni.nimh.nih.gov/
Prerequisites: gcc/5.4.0
Description:
alamode/1.0.2 -

Description: ALAMODE is an open source software designed for analyzing lattice anharmonicity and lattice thermal conductivity of solids. By using an external DFT package such as VASP and Quantum ESPRESSO, you can extract harmonic and anharmonic force constants straightforwardly with ALAMODE. Using the calculated anharmonic force constants, you can also estimate lattice thermal conductivity, phonon linewidth, and other anharmonic phonon properties from first principles. The binary alm is multi-threaded (OpenMP), add this command to your SLURM script: export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK Homepage: http://alamode.readthedocs.io/en/latest/index.html
Prerequisites: intel/2017.5 and openmpi/2.1.1
Description:
allpaths-lg/52488 bio

Description: ALLPATHS-LG, the new short read genome assembler. Homepage: http://www.broadinstitute.org/software/allpaths-lg/blog/ Keyword:bio
Prerequisites: gcc/4.8.5
Description:
alpscore/2.2.0 -

Description: The ALPSCore project, based on the ALPS (Algorithms and Libraries for Physics Simulations) project, provides generic algorithms and utilities for physics problems. It strives to increase software reuse in the physics community. For copyright see COPYRIGHT.TXT For licensing see LICENSE.TXT For acknowledgment in scientific publications see ACKNOWLEDGE.TXT Homepage: https://github.com/ALPSCore/ALPSCore
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
amber/18 chem

Description: Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. Homepage: http://ambermd.org/amber.html Keyword:chem
Prerequisites: gcc/5.4.0 and cuda/9.0.176 and openmpi/2.1.1 or gcc/5.4.0 and openmpi/2.1.1
Description:
angsd/0.918 bio

Description: Program for analysing NGS data. Homepage: http://www.popgen.dk/angsd Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
annovar/2017Jul16 bio

Description: 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/ Keyword:bio
Prerequisites: - or gcc/5.4.0 or intel/2016.4
Description:
ansys/17.2 phys ANSYS

Description: 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 Keyword:phys CC-Wiki: ANSYS
Prerequisites: -
Description:
ansys/18.1 phys ANSYS

Description: 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 Keyword:phys CC-Wiki: ANSYS
Prerequisites: -
Description:
ansys/18.2 phys ANSYS

Description: 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 Keyword:phys CC-Wiki: ANSYS
Prerequisites: -
Description:
ansys/19.1 phys ANSYS

Description: 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 Keyword:phys CC-Wiki: ANSYS
Prerequisites: -
Description:
ants/2.2.0 -

Description: 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/
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
appleseed/1.8.1-beta vis

Description: appleseed is an open source, physically-based global illumination rendering engine primarily designed for animation and visual effects. Homepage: https://github.com/appleseedhq/appleseed Keyword:vis
Prerequisites: gcc/5.4.0
Description:
arcs/1.0.1 bio

Description: Scaffolding genome sequence assemblies using 10X Genomics GemCode/Chromium data. Homepage: https://github.com/bcgsc/arcs Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
argtable/2.13 -

Description: Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. Homepage: http://argtable.sourceforge.net/
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
armadillo/7.950.1 math

Description: 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/ Keyword:math
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2017.5 or intel/2018.3
Description:
armadillo/8.500.1 math

Description: 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/ Keyword:math
Prerequisites: intel/2016.4 or intel/2018.3
Description:
arpack-ng/3.4.0 math

Description: ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. - Homepage: http://forge.scilab.org/index.php/p/arpack-ng/ Keyword:math
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description:
arpack-ng/3.5.0 math

Description: ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. Homepage: http://forge.scilab.org/index.php/p/arpack-ng/ Keyword:math
Prerequisites: gcc/5.4.0 or gcc/6.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2017.5 or intel/2018.3
Description:
arrow/0.8.0 tools

Description: Apache Arrow is a cross-language development platform for in-memory data. Homepage: https://arrow.apache.org Keyword:tools
Prerequisites: gcc/5.4.0
Description:
ascp/3.5.4 tools

Description: Aspera ASCP is a high speed file transfer software Homepage: http://downloads.asperasoft.com/ Keyword:tools
Prerequisites: -
Description:
atom/4.2.7_2 -

Description: ATOM is the name of a program originally written (circa 1982) by Sverre Froyen at the University of California at Berkeley, modified starting in 1990 by Norman Troullier and Jose Luis Martins at the University of Minnesota, and currently maintained by Alberto Garcia, who added some features and made substantial structural changes to the April 1990 (5.0) Minnesota version while at Berkeley and elsewhere. Homepage: https://departments.icmab.es/leem/siesta/Pseudopotentials/Code/downloads.html
Prerequisites: intel/2016.4 or intel/2018.3
Description:
atomicrex/1.0 -

Description: atomicrex is a versatile tool for the construction of advanced atomistic models. It is written in C++ and Python. It was primarily developed to fit interatomic potential models. Thanks to its flexible generic structure its application range, however, is much larger. In a general sense, it allows one to develop models that describe a given property as a function of an atomic (or atom-like) configuration. The property in question can be scalar or vectorial in nature, and could represent e.g., total energies and forces, or eventually electronic eigen energies. It thus provides already the basic framework for constructing in the future for example tight binding models. Homepage: http://atomicrex.gitlab.io/atomicrex/
Prerequisites: intel/2016.4
Description:
atomicrex/1.0.20181114 -

Description: atomicrex is a versatile tool for the construction of advanced atomistic models. It is written in C++ and Python. It was primarily developed to fit interatomic potential models. Thanks to its flexible generic structure its application range, however, is much larger. In a general sense, it allows one to develop models that describe a given property as a function of an atomic (or atom-like) configuration. The property in question can be scalar or vectorial in nature, and could represent e.g., total energies and forces, or eventually electronic eigen energies. It thus provides already the basic framework for constructing in the future for example tight binding models. Homepage: http://atomicrex.gitlab.io/atomicrex/
Prerequisites: intel/2018.3
Description:
augustus/3.2.3 bio

Description: AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences Homepage: http://bioinf.uni-greifswald.de/augustus/ Keyword:bio
Prerequisites: gcc/5.4.0
Description:
augustus/3.3 bio

Description: AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences Homepage: http://bioinf.uni-greifswald.de/augustus/ Keyword:bio
Prerequisites: intel/2016.4 or intel/2018.3
Description:
bamm/2.5.0 -

Description: BAMM is oriented entirely towards detecting and quantifying heterogeneity in evolutionary rates. It uses reversible jump Markov chain Monte Carlo to automatically explore a vast universe of candidate models of lineage diversification and trait evolution. Homepage: http://bamm-project.org/
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
bamtools/2.4.1 bio

Description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. - Homepage: https://github.com/pezmaster31/bamtools Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2018.3
Description:
bamutil/1.0.13 bio

Description: 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 Keyword:bio
Prerequisites: intel/2016.4
Description:
bamutil/1.0.14 bio

Description: 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 Keyword:bio
Prerequisites: intel/2018.3
Description:
bayesass/3.0.4 -

Description: BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes Homepage: http://www.rannala.org/?page_id=245
Prerequisites: intel/2016.4 or intel/2018.3
Description:
bayescan/2.1 -

Description: 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/
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2018.3
Description:
baypass/2.1 -

Description: The package 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). Homepage: http://www1.montpellier.inra.fr/CBGP/software/baypass/
Prerequisites: intel/2016.4 or intel/2018.3
Description:
bazel/0.11.1 tools

Description: 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/ Keyword:tools
Prerequisites: -
Description:
bazel/0.19.2 tools

Description: 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/ Keyword:tools
Prerequisites: -
Description:
bazel/0.5.2 tools

Description: 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/ Keyword:tools
Prerequisites: -
Description:
bazel/0.7.0 tools

Description: 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/ Keyword:tools
Prerequisites: -
Description:
bbmap/37.36 bio

Description: BBMap short read aligner, and other bioinformatic tools. Homepage: https://sourceforge.net/projects/bbmap/ Keyword:bio
Prerequisites: intel/2016.4 or intel/2018.3
Description:
bcftools/1.4 bio

Description: Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants - Homepage: http://www.htslib.org/ Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description:
bcftools/1.5 bio

Description: Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants Homepage: http://www.htslib.org/ Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
bcftools/1.9 bio

Description: Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants Homepage: http://www.htslib.org/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
bcl2fastq2/2.20 bio

Description: bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis. Homepage: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html Keyword:bio
Prerequisites: intel/2016.4
Description:
beagle-lib/2.1.2 bio

Description: beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. - Homepage: https://github.com/beagle-dev/beagle-lib Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2018.3
Description:
beagle-lib/3.1.1 bio

Description: beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. Homepage: https://github.com/beagle-dev/beagle-lib Keyword:bio
Prerequisites: intel/2016.4 or intel/2016.4 and cuda/8.0.44
Description:
beast/2.4.0 bio

Description: 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/ Keyword:bio
Prerequisites: intel/2016.4 or intel/2018.3
Description:
beast/2.5.1 bio BEAST

Description: 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. - CC-Wiki: BEAST Homepage: http://beast2.org/ Keyword:bio
Prerequisites: intel/2016.4
Description:
bedtools/2.26.0 bio

Description: 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 Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description:
bedtools/2.27.1 bio

Description: 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 Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
beef/0.1.1 -

Description: 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
Prerequisites: intel/2016.4 or intel/2017.1 or intel/2017.5 or intel/2018.3
Description:
berkeleygw/1.2.0 phys

Description: 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. We ask that you please cite the following papers when using results obtained from the BerkeleyGW package: - Mark S. Hybertsen and Steven G. Louie, Electron correlation in semiconductors and insulators: Band gaps and quasiparticle energies, Phys. Rev. B 34, 5390 (1986). - Michael Rohlfing and Steven G. Louie, Electron-hole excitations and optical spectra from first principles, Phys. Rev. B 62, 4927 (2000). - Jack Deslippe, Georgy Samsonidze, David A. Strubbe, Manish Jain, Marvin L. Cohen, and Steven G. Louie, BerkeleyGW: A Massively Parallel Computer Package for the Calculation of the Quasiparticle and Optical Properties of Materials and Nanostructures, Comput. Phys. Commun. 183, 1269 (2012) (http://arxiv.org/abs/1111.4429). Homepage: http://www.berkeleygw.org Keyword:phys
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2018.3 and openmpi/3.1.2
Description:
bigdft/1.7.6 -

Description: BigDFT is a DFT massively parallel electronic structure code using a wavelet basis set with the capability to use a linear scaling method. Wavelets form a real space basis set distributed on an adaptive mesh (two levels of resolution in our implementation). GTH or HGH pseudopotentials are used to remove the core electrons. The code BigDFT is available in ABINIT v5.5 and higher but can also be downloaded in a standalone version from the website. Thanks to our Poisson solver based on a Green function formalism, periodic systems, surfaces and isolated systems can be simulated with explicit boundary conditions. The Poisson solver can also be downloaded and used independently and is integrated in ABINIT, Octopus and CP2K. The code is free software, available under GNU-GPL license and the BigDFT developer community encourages anyone willing to contribute to join the team. Homepage: http://bigdft.org/Wiki/index.php?title=BigDFT_website
Prerequisites: intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
bioperl/1.7.1 bio

Description: 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/ Keyword:bio
Prerequisites: -
Description:
blacs/1.1 -

Description: 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/
Prerequisites: gcc/5.4.0 and openmpi/1.8.8 or gcc/7.3.0 and openmpi/3.1.2
Description:
blasr/1.3.1 bio

Description: 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 Keyword:bio
Prerequisites: intel/2016.4
Description:
blasr/5.3.0 bio

Description: 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 Keyword:bio
Prerequisites: intel/2016.4 or intel/2018.3
Description:
blasr_libcpp/20170426 bio

Description: 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 Keyword:bio
Prerequisites: intel/2016.4 or intel/2018.3
Description:
blast+/2.6.0 bio

Description: 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/ Keyword:bio
Prerequisites: gcc/5.4.0
Description:
blast+/2.7.1 bio

Description: 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/ Keyword:bio
Prerequisites: gcc/7.3.0
Description:
blat/3.5 bio

Description: 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 Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1
Description:
blender/2.79b -

Description: 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/
Prerequisites: intel/2018.3
Description:
blitz++/0.10 tools

Description: 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/ Keyword:tools
Prerequisites: gcc/5.4.0
Description:
blitz++/1.0.1 tools

Description: Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in C++ with a speed comparable to Fortran implementations, while preserving an object-oriented interface Homepage: https://github.com/blitzpp/blitz/ Keyword:tools
Prerequisites: gcc/7.3.0
Description:
bolt-lmm/2.2 bio

Description: The BOLT-LMM software package currently consists of two main algorithms, the BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML algorithm for variance components analysis (i.e., partitioning of SNP-heritability and estimation of genetic correlations). The BOLT-LMM algorithm computes statistics for testing association between phenotype and genotypes using a linear mixed model (LMM). The BOLT-REML algorithm estimates heritability explained by genotyped SNPs and genetic correlations among multiple traits measured on the same set of individuals. Like the GCTA software. Homepage: https://data.broadinstitute.org/alkesgroup/BOLT-LMM/ Keyword:bio
Prerequisites: -
Description:
boost-mpi/1.60.0 tools

Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: http://www.boost.org/ Keyword:tools
Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1
Description:
boost-mpi/1.65.1 tools

Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: http://www.boost.org/ Keyword:tools
Prerequisites: gcc/5.4.0 and cuda/8.0.44 and openmpi/2.1.1 or gcc/5.4.0 and cuda/9.0.176 and openmpi/2.1.1 or gcc/5.4.0 and openmpi/2.1.1 or gcc/6.4.0 and cuda/9.0.176 and openmpi/2.1.1 or gcc/6.4.0 and openmpi/2.1.1 or intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and cuda/9.0.176 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1 or intel/2017.5 and cuda/9.0.176 and openmpi/2.1.1 or intel/2017.5 and openmpi/2.1.1
Description:
boost-mpi/1.68.0 tools

Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: http://www.boost.org/ Keyword:tools
Prerequisites: gcc/7.3.0 and cuda/10.0.130 and openmpi/3.1.2 or gcc/7.3.0 and openmpi/3.1.2 or intel/2018.3 and cuda/10.0.130 and openmpi/3.1.2 or intel/2018.3 and openmpi/3.1.2
Description:
boost/1.54.0 tools

Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: http://www.boost.org/ Keyword:tools
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
boost/1.60.0 tools

Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: http://www.boost.org/ Keyword:tools
Prerequisites: gcc/4.8.5 or gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description:
boost/1.63.0 tools

Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: http://www.boost.org/ Keyword:tools
Prerequisites: intel/2016.4
Description:
boost/1.65.1 tools

Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: http://www.boost.org/ Keyword:tools
Prerequisites: gcc/5.4.0 or gcc/6.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2017.5
Description:
boost/1.66.0 tools

Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: http://www.boost.org/ Keyword:tools
Prerequisites: gcc/7.3.0
Description:
boost/1.68.0 tools

Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: http://www.boost.org/ Keyword:tools
Prerequisites: gcc/7.3.0 or intel/2018.3
Description:
bowtie/1.1.2 bio

Description: 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 Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2018.3
Description:
bowtie2/2.2.9 bio

Description: 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 Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
bowtie2/2.3.0 bio

Description: 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 Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description:
bowtie2/2.3.3.1 bio

Description: 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 Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
bowtie2/2.3.4.1 bio

Description: 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 Keyword:bio
Prerequisites: intel/2016.4
Description:
bowtie2/2.3.4.3 bio

Description: 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 Keyword:bio
Prerequisites: gcc/7.3.0 or intel/2018.3
Description:
bpp-core/2.4.0 -

Description: Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools. Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
Prerequisites: intel/2016.4 or intel/2018.3
Description:
bpp-phyl-omics/2.4.0 -

Description: Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools. Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
Prerequisites: intel/2016.4 or intel/2018.3
Description:
bpp-phyl/2.4.0 -

Description: Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools. Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
Prerequisites: intel/2016.4 or intel/2018.3
Description:
bpp-popgen/2.4.0 -

Description: Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools. Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
Prerequisites: intel/2016.4 or intel/2018.3
Description:
bpp-seq-omics/2.4.0 -

Description: Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools. Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
Prerequisites: intel/2016.4 or intel/2018.3
Description:
bpp-seq/2.4.0 -

Description: Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools. Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
Prerequisites: intel/2016.4 or intel/2018.3
Description:
breakdancer/1.4.5 bio

Description: 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 Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
bufrlib/10.2.3 -

Description: NCEP BUFRLIB software to encode or decode BUFR messages. It is not intended to be a primer on the BUFR code form itself. Homepage: http://www.nco.ncep.noaa.gov/sib/decoders/BUFRLIB/
Prerequisites: intel/2016.4 or intel/2018.3
Description:
busco/3.0.2 bio

Description: BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs Homepage: http://busco.ezlab.org/ Keyword:bio
Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or gcc/7.3.0 and openmpi/3.1.2
Description:
bwa/0.7.15 bio

Description: 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/ Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description:
bwa/0.7.17 bio

Description: 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/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2018.3
Description:
caffe/1.0 -

Description: 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
Prerequisites: gcc/5.4.0 or gcc/5.4.0 and cuda/8.0.44
Description:
caffe2/0.8.1 ai Caffe2

Description: Caffe2 is a lightweight, modular, and scalable deep learning framework. Building on the original Caffe, Caffe2 is designed with expression, speed, and modularity in mind. Homepage: https://github.com/caffe2/caffe2 Keyword:ai CC-Wiki: Caffe2
Prerequisites: gcc/5.4.0 and cuda/8.0.44
Description:
canu/1.5 bio

Description: 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 Keyword:bio
Prerequisites: gcc/5.4.0
Description:
canu/1.6 bio

Description: 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 Keyword:bio
Prerequisites: gcc/5.4.0
Description:
canu/1.7 bio

Description: 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 Keyword:bio
Prerequisites: gcc/5.4.0
Description:
canu/1.7.1 bio

Description: 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 Keyword:bio
Prerequisites: gcc/5.4.0
Description:
canu/1.8 bio

Description: 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 Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
canvas/1.25 bio

Description: Canvas is a tool for calling copy number variants (CNVs) from human DNA sequencing data. It can work either with germline data, or paired tumor/normal samples. Its primary input is aligned reads (in .bam format), and its primary output is a report (in a .vcf file) giving the copy number status of the genome. To run, do mono $EBROOTCANVAS/Canvas.dll ... Homepage: https://github.com/Illumina/canvas Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
cap3/20151002 -

Description: CAP3 assembly program Homepage: http://seq.cs.iastate.edu/
Prerequisites: -
Description:
casm/0.2.1 -

Description: CASM is an open source software package designed to perform first-principles statistical mechanical studies of multi-component crystalline solids. CASM interfaces with first-principles electronic structure codes, automates the construction and parameterization of effective Hamiltonians and subsequently builds highly optimized (kinetic) Monte Carlo codes to predict finite-temperature thermodynamic and kinetic properties. CASM uses group theoretic techniques that take full advantage of crystal symmetry in order to rigorously construct effective Hamiltonians for almost arbitrary degrees of freedom in crystalline solids. This includes cluster expansions for configurational disorder in multi-component solids and lattice-dynamical effective Hamiltonians for vibrational degrees of freedom involved in structural phase transitions. Homepage: https://github.com/prisms-center/CASMcode
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
casper/0.8.2 bio

Description: CASPER (Context-Aware Scheme for Paired-End Read) is state-of-the art merging tool in terms of accuracy and robustness. Using this sophisticated merging method, we could get elongated reads from the forward and reverse reads. Homepage: http://best.snu.ac.kr/casper/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4
Description:
ccfits/2.5 vis

Description: 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/ Keyword:vis
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2018.3
Description:
ccsm/4_0_a02 geo

Description: The Community Climate System Model (CCSM) is a coupled climate model for simulating the earth's climate system. Composed of four separate models simultaneously simulating the earth's atmosphere, ocean, land surface and sea-ice, and one central coupler component, the CCSM allows researchers to conduct fundamental research into the earth's past, present and future climate states. Homepage: http://www.cesm.ucar.edu/models/ccsm4.0/ Keyword:geo
Prerequisites: -
Description:
cd-hit/4.6.8 bio

Description: CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. Homepage: http://weizhong-lab.ucsd.edu/cd-hit/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/5.4.0 and openmpi/2.1.1 or gcc/7.3.0 or intel/2016.4 or intel/2016.4 and openmpi/2.1.1 or intel/2018.3
Description:
cdo/1.7.2 geo

Description: CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data. Homepage: https://code.zmaw.de/projects/cdo Keyword:geo
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
cdo/1.9.5 geo

Description: CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data. Homepage: https://code.zmaw.de/projects/cdo Keyword:geo
Prerequisites: intel/2018.3 and openmpi/3.1.2
Description:
cellranger/2.1.0 bio

Description: Cell Ranger is a set of analysis pipelines that process Chromium single cell 3-RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. Cell Ranger 1.2 and later support libraries generated by the Chromium Single Cell 3i-v1 and v2 reagent kits, whereas Cell Ranger 1.1 and earlier do not support v2 libraries. Cell Ranger includes four main gene expression pipelines: - cellranger mkfastq wraps Illumina's bcl2fastq to correctly demultiplex Chromium-prepared sequencing samples and to convert barcode and read data to FASTQ files. - cellranger count takes FASTQ files from cellranger mkfastq and performs alignment, filtering, and UMI counting. - cellranger aggr aggregates outputs from multiple runs of cellranger count, normalizing those runs to the same sequencing depth and then recomputing the gene-barcode matrices and analysis on the combined data. - cellranger reanalyze takes gene-barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction, clustering, and gene expression algorithms using tunable parameter settings. These pipelines combine Chromium-specific algorithms with the widely used RNA-seq aligner STAR. Output is delivered in standard BAM, MEX, CSV, HDF5 and HTML formats that are augmented with cellular information. Homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome Keyword:bio
Prerequisites: -
Description:
centrifuge/1.0.3-beta bio

Description: [Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.7 GB for all complete bacterial and viral genomes plus the human genome) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers Homepage: https://github.com/infphilo/centrifuge Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
centrifuge/1.0.4-beta bio

Description: [Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.7 GB for all complete bacterial and viral genomes plus the human genome) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers Homepage: https://github.com/infphilo/centrifuge Keyword:bio
Prerequisites: gcc/7.3.0
Description:
cesm/1_2_2 geo

Description: The Community Earth System Model (CESM) is a fully-coupled, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states. Homepage: http://www.cesm.ucar.edu/models/cesm1.2/ Keyword:geo
Prerequisites: -
Description:
cfitsio/3.42 vis

Description: 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/ Keyword:vis
Prerequisites: intel/2016.4 or intel/2018.3
Description:
cfour-mpi/1.0 -

Description: CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a program package for performing high-level quantum chemical calculations on atoms and molecules. The major strength of the program suite is its rather sophisticated arsenal of high-level ab initio methods for the calculation of atomic and molecular properties. Virtually all approaches based on Muller-Plesset (MP) perturbation theory and the coupled-cluster approximation (CC) are available; most of these have complementary analytic derivative approaches within the package as well. CFOUR is not a commercial code. It is rather a program that is undergoing development; new techniques and improvements are constantly being made (mainly in the groups of John F. Stanton (until the end of 2016 at the University of Texas at Austin, USA, now at the Quantum Theory Project of the University of Florida at Gainesville, USA) and Juergen Gauss (Universitat Mainz, Germany)). For non-commercial purposes there is no charge to obtain CFOUR; one must simply sign a license agreement. http://slater.chemie.uni-mainz.de/cfour/index.php?n=Main.Download Homepage: http://www.cfour.de/
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
cgal/4.9 math

Description: 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/ Keyword:math
Prerequisites: gcc/4.8.5 or gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2018.3
Description:
cgns/3.3.1 phys

Description: The CGNS system is designed to facilitate the exchange of data between sites and applications, and to help stabilize the archiving of aerodynamic data. Homepage: https://cgns.github.io/ Keyword:phys
Prerequisites: gcc/5.4.0 and openmpi/2.1.1 or gcc/7.3.0 and openmpi/3.1.2 or intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
chapel-single/1.15.0 tools

Description: 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 MPIMessage Passing Interface. Homepage: http://chapel.cray.com Keyword:tools
Prerequisites: gcc/5.4.0
Description:
chapel-slurm-gasnetrun_ibv/1.15.0 tools

Description: 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 MPIMessage Passing Interface. Homepage: http://chapel.cray.com Keyword:tools
Prerequisites: gcc/5.4.0
Description:
chemps2/1.8 chem

Description: 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 Keyword:chem
Prerequisites: intel/2016.4
Description:
chemps2/1.8.9 chem

Description: 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 Keyword:chem
Prerequisites: intel/2018.3
Description:
circos/0.69-6 vis

Description: 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. There are other reasons why a circular layout is advantageous, not the least being the fact that it is attractive. Circos is ideal for creating publication-quality infographics and illustrations with a high data-to-ink ratio, richly layered data and pleasant symmetries. You have fine control each element in the figure to tailor its focus points and detail to your audience. Homepage: http://circos.ca/documentation/ Keyword:vis
Prerequisites: -
Description:
clang/3.8.1 tools

Description: C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCCGNU Compiler Collection, an open source compiler collection. Homepage: http://clang.llvm.org/ Keyword:tools
Prerequisites: -
Description:
clang/3.9.0 tools

Description: C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCCGNU Compiler Collection, an open source compiler collection. Homepage: http://clang.llvm.org/ Keyword:tools
Prerequisites: -
Description:
clhep/2.1.3.1 math

Description: 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/ Keyword:math
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
clhep/2.3.1.1 math

Description: 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/ Keyword:math
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
clhep/2.3.4.3 math

Description: 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/ Keyword:math
Prerequisites: gcc/5.4.0
Description:
clhep/2.4.1.0 math

Description: 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/ Keyword:math
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
clustal-omega/1.2.4 -

Description: 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/
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
cmake/3.12.3 -

Description: 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
Prerequisites: -
Description:
cnvnator/0.3.3 bio

Description: a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads Homepage: https://github.com/abyzovlab/CNVnator Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2018.3
Description:
comsol/5.3a phys

Description: COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems. Homepage: https://www.comsol.com Keyword:phys
Prerequisites: -
Description:
comsol/5.4 phys

Description: COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems. Homepage: https://www.comsol.com Keyword:phys
Prerequisites: -
Description:
corset/1.07 -

Description: Corset is a command-line software program to go from a de novo transcriptome assembly to gene-level counts. Our software takes a set of reads that have been multi-mapped to the transcriptome (where multiple alignments per read were reported) and hierarchically clusters the transcripts based on the proportion of shared reads and expression patterns. It will report the clusters and gene-level counts for each sample, which are easily tested for differential expression with count based tools such as edgeR and DESeq. Homepage: https://github.com/Oshlack/Corset/wiki
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
cp2k/4.1 chem

Description: 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/ Keyword:chem
Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or gcc/7.3.0 and openmpi/3.1.2 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
cp2k/5.1 chem

Description: 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/ Keyword:chem
Prerequisites: gcc/5.4.0 and cuda/8.0.44 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.1.1
Description:
cp2k/6.1 chem

Description: 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/ Keyword:chem
Prerequisites: intel/2017.1 and openmpi/2.1.1
Description:
cpmd/3.17.1 chem

Description: The CPMD code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. Homepage: http://cpmd.org Keyword:chem
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
cppunit/1.12.1 -

Description: CppUnit is the C++ port of the famous JUnit framework for unit testing. Homepage: http://sourceforge.net/projects/cppunit/
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
cromwell/34 -

Description: Scientific workflow engine designed for simplicity and scalability. Trivially transition between one off use cases to massive scale production environments http://cromwell.readthedocs.io/ Homepage: https://cromwell.readthedocs.io/
Prerequisites: -
Description:
cst/2017 phys

Description: CST offers accurate, efficient computational solutions for electromagnetic design and analysis. CST simulation is user-friendly and enables users to choose the most appropriate method for the design and optimization of devices operating in a wide range of frequencies. Please note that we installed only Graphic frontend and command line interface. You need to provide your own license server in order to be able to run CST. Homepage: https://www.cst.com/ Keyword:phys
Prerequisites: -
Description:
cst/2018 phys

Description: CST offers accurate, efficient computational solutions for electromagnetic design and analysis. CST simulation is user-friendly and enables users to choose the most appropriate method for the design and optimization of devices operating in a wide range of frequencies. Please note that we installed only Graphic frontend and command line interface. You need to provide your own license server in order to be able to run CST. Homepage: https://www.cst.com/ Keyword:phys
Prerequisites: -
Description:
ctffind/4.1.10 -

Description: program for finding CTFs of electron micrographs Homepage: http://grigoriefflab.janelia.org/ctffind4
Prerequisites: gcc/5.4.0
Description:
ctffind/4.1.8 -

Description: program for finding CTFs of electron micrographs Homepage: http://grigoriefflab.janelia.org/ctffind4
Prerequisites: gcc/5.4.0
Description:
cuda/10.0.130 tools CUDA

Description: 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 Keyword:tools CC-Wiki: CUDA
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
cuda/7.5.18 tools CUDA

Description: 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 Keyword:tools CC-Wiki: CUDA
Prerequisites: gcc/4.8.5
Description:
cuda/8.0.44 tools CUDA

Description: 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 Keyword:tools CC-Wiki: CUDA
Prerequisites: gcc/5.4.0 or intel/2016.4 or pgi/17.3
Description:
cuda/9.0.176 tools CUDA

Description: 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 Keyword:tools CC-Wiki: CUDA
Prerequisites: gcc/5.4.0 or gcc/6.4.0 or intel/2016.4 or intel/2017.5 or pgi/17.3
Description:
cudnn/5.1 math

Description: 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 Keyword:math
Prerequisites: gcc/5.4.0 and cuda/8.0.44 or intel/2016.4 and cuda/8.0.44
Description:
cudnn/6.0 math

Description: 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 Keyword:math
Prerequisites: gcc/5.4.0 and cuda/8.0.44 or intel/2016.4 and cuda/8.0.44
Description:
cudnn/7.0 math

Description: 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 Keyword:math
Prerequisites: gcc/5.4.0 and cuda/8.0.44 or gcc/5.4.0 and cuda/9.0.176 or intel/2016.4 and cuda/8.0.44 or intel/2016.4 and cuda/9.0.176
Description:
cudnn/7.4 math

Description: 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 Keyword:math
Prerequisites: gcc/7.3.0 and cuda/10.0.130 or intel/2018.3 and cuda/10.0.130
Description:
cufflinks/2.2.1 bio

Description: Transcript assembly, differential expression, and differential regulation for RNA-Seq - Homepage: http://cole-trapnell-lab.github.io/cufflinks/ Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1 or intel/2018.3
Description:
cunit/2.1-3 -

Description: Automated testing framework for C. Homepage: https://sourceforge.net/projects/cunit/
Prerequisites: -
Description:
cwp_su/44R11 geo

Description: Seismic Unix is a seismic processing and research environment developed at the Center for Wave Phenomena. Homepage: http://www.cwp.mines.edu/cwpcodes/ Keyword:geo
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
dakota/6.8 -

Description: The Dakota project delivers both state-of-the-art research and robust, usable software for optimization and UQ. Broadly, the Dakota software's advanced parametric analyses enable design exploration, model calibration, risk analysis, and quantification of margins and uncertainty with computational models. The Dakota toolkit provides a flexible, extensible interface between such simulation codes and its iterative systems analysis methods, which include: - optimization with gradient and nongradient-based methods; - uncertainty quantification with sampling, reliability, stochastic expansion, and epistemic methods; - parameter estimation using nonlinear least squares (deterministic) or Bayesian inference (stochastic); and - sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as hybrid optimization, surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. Homepage: https://dakota.sandia.gov/
Prerequisites: intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
dalton/2017-alpha -

Description: The Dalton suite consists of two separate executables, Dalton and LSDalton. The Dalton code is a powerful tool for a wide range of molecular properties at different levels of theory, whereas LSDalton is a linear-scaling HF and DFT code suitable for large molecular systems, now also with some CCSD capabilites. Any published work arising from use of one of the Dalton programs must acknowledge that by a proper reference. The following list of capabilities of the Dalton programs should give you some indication of whether or not the Dalton suite is able to meet your requirements.. Homepage: http://daltonprogram.org/
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2018.3 and openmpi/3.1.2
Description:
dcm2niix/1.0.20180622 -

Description: dcm2nii DICOM to NIfTI converter: compiled versions available from NITRC Homepage: https://github.com/rordenlab/dcm2niix
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
ddt-cpu/18.3 tools ARM software

Description: Profiler and debugger, combining Arm MAP and Arm DDT. Homepage: http://www.allinea.com CC-Wiki: ARM software
Prerequisites: -
Description:
ddt-cpu/7.1 tools ARM software

Description: Profiler and debugger, combining Allinea MAP and Allinea DDT. Homepage: http://www.allinea.com CC-Wiki: ARM software
Prerequisites: -
Description:
ddt-gpu/18.3 tools ARM software

Description: Profiler and debugger, combining Arm MAP and Arm DDT, with support for CUDA. Homepage: http://www.allinea.com CC-Wiki: ARM software
Prerequisites: -
Description:
ddt-gpu/7.1 tools ARM software

Description: Profiler and debugger, combining Allinea MAP and Allinea DDT, with support for CUDA. Homepage: http://www.allinea.com CC-Wiki: ARM software
Prerequisites: -
Description:
dealii-petsc/8.5.0 -

Description: A C++ software library supporting the creation of finite element codes and an open community of users and developers. Homepage: http://www.dealii.org/
Prerequisites: intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
dealii/8.5.0 math

Description: A C++ software library supporting the creation of finite element codes and an open community of users and developers. Homepage: http://www.dealii.org/ Keyword:math
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
demon2k/4.4.4 chem

Description: deMon (density of Montreal) is a software package for density functional theory (DFT) [1-3] calculations. It uses the linear combination of Gaussian-type orbital (LCGTO) approach for the self-consistent solution of the Kohn-Sham (KS) DFT equations. The calculation of the four-center electron repulsion integrals is avoided by introducing an auxiliary function basis for the variational fitting of the Coulomb potential [4-6]. Homepage: http://www.demon-software.com/public_html/index.html Keyword:chem
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
detonate/1.11 bio

Description: DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation) consists of two component packages, RSEM-EVAL and REF-EVAL. Both packages are mainly intended to be used to evaluate de novo transcriptome assemblies, although REF-EVAL can be used to compare sets of any kinds of genomic sequences. Homepage: http://deweylab.biostat.wisc.edu/detonate/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
diamond/0.9.8 bio

Description: Accelerated BLAST compatible local sequence aligner Homepage: https://github.com/bbuchfink/diamond Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
discosnp/2.3.X bio

Description: DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, from raw set(s) of reads. The number of input read sets is not constrained, it can be one, two, or more. No reference genome is needed. Homepage: https://github.com/GATB/DiscoSnp Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
discovardenovo/52488 -

Description: DISCOVAR de novo is a short read genome assembly developed by the Broad Institute. It can generate high quality assemblies from the latest 250 base Illumina paired-end PCR-free fragment read' Homepage: https://software.broadinstitute.org/software/discovar/blog/?page_id=98
Prerequisites: gcc/4.8.5
Description:
dl_poly4/4.08 chem

Description: DL_POLY is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory by I.T. Todorov and W. Smith. Homepage: http://www.scd.stfc.ac.uk/SCD/44516.aspx Keyword:chem
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description:
dmalloc/5.5.2 -

Description: The debug memory allocation or dmalloc library has been designed as a drop in replacement for the system s malloc, realloc, calloc, free and other memory management routines while providing powerful debugging facilities configurable at runtime. These facilities include such things as memory-leak tracking, fence-post write detection, file/line number reporting, and general logging of statistics. The library is reasonably portable having been run successfully on at least the following operating systems: AIX, BSD/OS, DG/UX, Free/Net/OpenBSD, GNU/Hurd, HPUX, Irix, Linux, MS-DOG, NeXT, OSF, SCO, Solaris, SunOS, Ultrix, Unixware, Windoze, and even Unicos on a Cray T3E. It also provides support for the debugging of threaded programs. The package includes the library, configuration scripts, debug utility application, test program, and documentation. Homepage: http://dmalloc.com/
Prerequisites: intel/2016.4 or intel/2018.3
Description:
dotnet-core-runtime/1.1.8 -

Description: .NET is a free, cross-platform, open source developer platform for building many different types of applications. With .NET, you can use multiple languages, editors, and libraries to build for web, mobile, desktop, gaming, and IoT. Homepage: https://www.microsoft.com/net/
Prerequisites: -
Description:
dotnet-core-runtime/2.0.7 -

Description: .NET is a free, cross-platform, open source developer platform for building many different types of applications. Homepage: https://www.microsoft.com/net/
Prerequisites: -
Description:
dtiprep/1.2.9 -

Description: DTIPrep performs a "Study-specific Protocol" based automatic pipeline for DWI/DTI quality control and preparation. This is both a GUI and command line tool. Homepage: https://www.nitrc.org/projects/dtiprep/
Prerequisites: gcc/5.4.0
Description:
eccodes/2.8.2 -

Description: ecCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding). Homepage: https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home
Prerequisites: intel/2018.3
Description:
eclipse/4.6.0 tools

Description: Eclipse is an integrated development environment (IDE) used in computer programming, and is the most widely used Java IDE.[6] It contains a base workspace and an extensible plug-in system for customizing the environment. Eclipse is written mostly in Java and its primary use is for developing Java applications, but it may also be used to develop applications in other programming languages via plug-ins, including: Ada, ABAP, C, C++, COBOL, D, Fortran, Haskell, JavaScript, Julia,[7] Lasso, Lua, NATURAL, Perl, PHP, Prolog, Python, R, Ruby (including Ruby on Rails framework), Rust, Scala, Clojure, Groovy, Scheme, and Erlang. It can also be used to develop documents with LaTeX (via a TeXlipse plug-in) and packages for the software Mathematica. Development environments include the Eclipse Java development tools (JDT) for Java and Scala, Eclipse CDT for C/C++, and Eclipse PDT for PHP, among others. - Homepage: https://www.perl.org/ Keyword:tools
Prerequisites: -
Description:
eems/20171011 bio

Description: This repository contains an implementation of the EEMS method for analyzing and visualizing spatial population structure from geo-referenced genetic samples. EEMS uses the concept of effective migration to model the relationship between genetics and geography, and it outputs an estimated effective migration surface (hence, EEMS) - a visual representation of population structure that can highlight potential regions of higher-than-average and lower-than-average historic gene flow. Homepage: https://github.com/dipetkov/eems Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
eigen/3.2.10 math

Description: 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 Keyword:math
Prerequisites: -
Description:
eigen/3.2.2 math

Description: 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 Keyword:math
Prerequisites: -
Description:
eigen/3.3.2 math

Description: 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 Keyword:math
Prerequisites: -
Description:
eigen/3.3.5 math

Description: 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 Keyword:math
Prerequisites: -
Description:
eigensoft/7.2.1 bio

Description: 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/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
elixir/1.5 tools

Description: Elixir is a dynamic, functional language designed for building scalable and maintainable applications. Homepage: https://elixir-lang.org/ Keyword:tools
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
elk/5.2.10 -

Description: An all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features. Written originally at Karl-Franzens-Universitt 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/
Prerequisites: intel/2016.4 and openmpi/2.0.2
Description:
elk/5.2.14 -

Description: An all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features. Written originally at Karl-Franzens-Universitt 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/
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2018.3 and openmpi/3.1.2
Description:
elpa/2017.11.001 math

Description: Eigenvalue SoLvers for Petaflop-Applications . Homepage: http://elpa.rzg.mpg.de Keyword:math
Prerequisites: intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
emboss/6.6.0 bio

Description: 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/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
erds/1.1 bio

Description: ERDS is an open-source software free to academia and nor-profit organization, designed for inferring copy number variants (CNVs) in high-coverage human genomes using next generation sequence (NGS) data. When a CNV presents in a test genome, multiple signatures, weak or strong, would present in the alignment data. ERDS starts from read depth (RD) information, and integrates other information including paired end mapping (PEM) and soft-clip signature to call CNVS sensitively and accurately. Homepage: http://www.utahresearch.org/mingfuzhu/erds/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
erlangotp/20.0 tools

Description: Erlang is a general-purpose concurrent, garbage-collected programming language and runtime system. Homepage: http://www.erlang.org/ Keyword:tools
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
esmf/7.0.1 geo

Description: The Earth System Modeling Framework (ESMF) is software for building and coupling weather, climate, and related models. Homepage: http://sourceforge.net/projects/esmf Keyword:geo
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
esmf/7.1.0r geo

Description: The Earth System Modeling Framework (ESMF) is software for building and coupling weather, climate, and related models. Homepage: http://sourceforge.net/projects/esmf Keyword:geo
Prerequisites: intel/2018.3 and openmpi/3.1.2
Description:
etsf_io/1.0.4 io

Description: 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 Keyword:io
Prerequisites: intel/2016.4 or intel/2018.3
Description:
exonerate/2.4.0 bio

Description: 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/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
expat/2.2.5 -

Description: 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/
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
expat/2.2.6 -

Description: 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/
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2018.3
Description:
falcon/1.8.8 bio

Description: Falcon: a set of tools for fast aligning long reads for consensus and assembly Homepage: https://github.com/PacificBiosciences/FALCON Extensions: FALCON-1.8.8, networkx-1.10, pypeFLOW-20170504 Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
fast-gbs/2017-01-25 bio

Description: A bioinformatic pipeline designed to extract a high-quality SNP catalog starting from FASTQ files obtained from sequencing genotyping-by-sequencing (GBS) libraries. Homepage: https://bitbucket.org/jerlar73/fast-gbs Keyword:bio
Prerequisites: -
Description:
fasta/36.3.8g -

Description: 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
Prerequisites: gcc/5.4.0
Description:
fastme/2.1.6.1 -

Description: FastME: a comprehensive, accurate and fast distance-based phylogeny inference program. Homepage: http://www.atgc-montpellier.fr/fastme/
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
fastp/0.12.4 bio

Description: A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. Homepage: https://github.com/OpenGene/fastp Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
fastp/0.19.5 bio

Description: A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. Homepage: https://github.com/OpenGene/fastp Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
fastq_screen/0.11.4 -

Description: FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect. Homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
fastqc/0.11.5 bio

Description: 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/ Keyword:bio
Prerequisites: -
Description:
fastsimcoal2/2.6.0.3 bio

Description: While preserving all the simulation flexibility of simcoal2, fastsimcoal is now implemented under a faster continous-time sequential Markovian coalescent approximation, allowing it to efficiently generate genetic diversity for different types of markers along large genomic regions, for both present or ancient samples. It includes a parameter sampler allowing its integration into Bayesian or likelihood parameter estimation procedure. fastsimcoal can handle very complex evolutionary scenarios including an arbitrary migration matrix between samples, historical events allowing for population resize, population fusion and fission, admixture events, changes in migration matrix, or changes in population growth rates. The time of sampling can be specified independently for each sample, allowing for serial sampling in the same or in different populations. Homepage: http://cmpg.unibe.ch/software/fastsimcoal2/ Keyword:bio
Prerequisites: -
Description:
fasttree/2.1.10 bio

Description: 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/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
fastx-toolkit/0.0.14 bio

Description: The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. Homepage: http://hannonlab.cshl.edu/fastx_toolkit/ Extensions: GD-2.67, GD::Graph-1.43, GD::Text-0.86, PerlIO::gzip-0.20 Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2018.3
Description:
feko/2018 -

Description: FEKO is a comprehensive computational electromagnetics (CEM) code used widely in the telecommunications, automobile, space and defense industries. Homepage: https://altairhyperworks.com/product/FEKO
Prerequisites: -
Description:
ferret/7.3 -

Description: 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/
Prerequisites: gcc/5.4.0 and openmpi/2.1.1
Description:
fftw-mpi/2.1.5 math

Description: 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 Keyword:math
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
fftw-mpi/3.3.6 math

Description: 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 Keyword:math
Prerequisites: gcc/5.4.0 and openmpi/1.8.8 or gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or gcc/6.4.0 and cuda/9.0.176 and openmpi/2.1.1 or gcc/6.4.0 and openmpi/2.1.1 or intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1 or intel/2017.5 and impi/2017.4.239 or intel/2017.5 and openmpi/2.1.1
Description:
fftw-mpi/3.3.8 math

Description: 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 Keyword:math
Prerequisites: gcc/7.3.0 and cuda/10.0.130 and openmpi/3.1.2 or gcc/7.3.0 and openmpi/3.1.2 or intel/2018.3 and cuda/10.0.130 and openmpi/3.1.2 or intel/2018.3 and openmpi/3.1.2
Description:
fftw/3.3.6 math

Description: 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 Keyword:math
Prerequisites: gcc/4.8.5 or gcc/5.4.0 or gcc/6.4.0 or intel/2016.4 or intel/2017.1
Description:
fftw/3.3.8 math

Description: 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 Keyword:math
Prerequisites: gcc/7.3.0 or intel/2018.3
Description:
filtlong/0.2.0 -

Description: Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter Homepage: https://github.com/rrwick/Filtlong
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
flint/2.5.2 math

Description: FLINT is a C library for doing number theory, maintained by William Hart. FLINT supports arithmetic with numbers, polynomials, power series and matrices over many base rings, including: - Multiprecision integers and rationals - Integers modulo n - p-adic numbers - Finite fields (prime and non-prime order) - Real and complex numbers (via the Arb extension library) Homepage: http://www.flintlib.org/ Keyword:math
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
fluent/16.1 - ANSYS

Description: 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. Fluent covers a broad reach, including special models with capabilities to model in-cylinder combustion, aero-acoustics, turbomachinery and multiphase systems. Homepage: https://www.ansys.com/products/fluids/ansys-fluent CC-Wiki: ANSYS
Prerequisites: -
Description:
fpc/3.0.0 tools

Description: A 32/64/16-bit Pascal compiler for Win32/64/CE, Linux, Mac OS X/iOS, FreeBSD, OS/2, Game Boy Advance, Nintendo NDS and DOS; semantically compatible with Delphi, Borland Pascal and Mac Pascal (partially) with extra features, e.g. operator overloading. Homepage: https://sourceforge.net/projects/freepascal/ Keyword:tools
Prerequisites: -
Description:
fraggenescan/1.19 -

Description: FragGeneScan is an application for finding (fragmented) genes in short reads. Homepage: http://omics.informatics.indiana.edu/FragGeneScan/
Prerequisites: intel/2016.4
Description:
fraggenescan/1.30 -

Description: FragGeneScan is an application for finding (fragmented) genes in short reads. Homepage: http://omics.informatics.indiana.edu/FragGeneScan/
Prerequisites: intel/2016.4
Description:
fraggenescan/1.31 -

Description: FragGeneScan is an application for finding (fragmented) genes in short reads. Homepage: http://omics.informatics.indiana.edu/FragGeneScan/
Prerequisites: intel/2018.3
Description:
frealign/9.11 -

Description: Frealign is a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles. Homepage: http://grigoriefflab.janelia.org/frealign
Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.0.2 or intel/2018.3
Description:
freebayes/1.1.0 bio

Description: Bayesian haplotype-based polymorphism discovery and genotyping. Homepage: https://github.com/ekg/freebayes Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
freebayes/1.2.0 bio

Description: Bayesian haplotype-based polymorphism discovery and genotyping. Homepage: https://github.com/ekg/freebayes Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
freesurfer/5.3.0 -

Description: FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data. Homepage: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki
Prerequisites: -
Description:
freexl/1.0.3 -

Description: 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
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
fsl/5.0.11 -

Description: FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. Homepage: http://www.fmrib.ox.ac.uk/fsl/
Prerequisites: intel/2016.4
Description:
fsl/5.0.9 -

Description: FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. Homepage: http://www.fmrib.ox.ac.uk/fsl/
Prerequisites: intel/2016.4
Description:
fusioncatcher/0.99.7c-beta bio

Description: Finder of somatic fusion-genes in RNA-seq data. The database is installed in $EBROOTFUSIONCATCHER/data/current. Homepage: https://github.com/ndaniel/fusioncatcher Keyword:bio
Prerequisites: intel/2016.4
Description:
g2clib/1.6.0 geo

Description: Library contains GRIB2 encoder/decoder ('C' version). Homepage: http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ Keyword:geo
Prerequisites: -
Description:
g2lib/1.4.0 geo

Description: Library contains GRIB2 encoder/decoder and search/indexing routines. Homepage: http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ Keyword:geo
Prerequisites: -
Description:
gamess-us/20170420-R1 chem

Description: 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 Keyword:chem
Prerequisites: intel/2016.4 or intel/2018.3 and openmpi/3.1.2
Description:
gapfiller/2.1.1 bio

Description: 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 Keyword:bio
Prerequisites: intel/2016.4
Description:
gate/8.0 -

Description: 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/
Prerequisites: gcc/5.4.0
Description:
gatk-queue/3.8-0 bio

Description: 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/ Keyword:bio
Prerequisites: -
Description:
gatk/3.7 bio

Description: 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/ Keyword:bio
Prerequisites: -
Description:
gatk/3.8 bio

Description: 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/ Keyword:bio
Prerequisites: -
Description:
gatk/4.0.0.0 bio

Description: 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/ Keyword:bio
Prerequisites: -
Description:
gatk/4.0.8.1 bio

Description: 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/ Keyword:bio
Prerequisites: -
Description:
gcc/4.8.5 tools

Description: 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/ Keyword:tools
Prerequisites: -
Description:
gcc/4.9.4 tools

Description: 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/ Keyword:tools
Prerequisites: -
Description:
gcc/5.4.0 tools

Description: 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/ Keyword:tools
Prerequisites: -
Description:
gcc/6.4.0 tools

Description: 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/ Keyword:tools
Prerequisites: -
Description:
gcc/7.3.0 tools

Description: 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/ Keyword:tools
Prerequisites: -
Description:
gcta/1.26.0 -

Description: GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits. GCTA currently supports the following analyses. Homepage: http://cnsgenomics.com/software/gcta/
Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or gcc/7.3.0 or intel/2016.4 and openmpi/2.0.2 or intel/2018.3
Description:
gctf/1.06 -

Description: Gctf: real-time CTF determination and correction Homepage: https://www.mrc-lmb.cam.ac.uk/kzhang/
Prerequisites: intel/2016.4
Description:
gctf/1.18 -

Description: Gctf: real-time CTF determination and correction Homepage: https://www.mrc-lmb.cam.ac.uk/kzhang/
Prerequisites: intel/2016.4
Description:
gdal-mpi/1.10.1 geo

Description: 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/ Keyword:geo
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
gdal-mpi/1.11.5 geo

Description: 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/ Keyword:geo
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
gdal/2.1.3 geo

Description: 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/ Keyword:geo
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2018.3
Description:
gdal/2.2.1 geo

Description: 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/ Keyword:geo
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
geant4/10.02.p03 phys

Description: 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/ Keyword:phys
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
geant4/10.04.p02 phys

Description: 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/ Keyword:phys
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
geant4/9.6.p04 phys

Description: 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/ Keyword:phys
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4
Description:
gemma/0.97 bio

Description: GEMMA is a software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets. Homepage: http://veda.cs.uiuc.edu/Seq2Expr/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
genometools/1.5.10 -

Description: The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named libgenometools which contains a wide variety of classes for efficient and convenient implementation of sequence and annotation processing software. Homepage: https://github.com/genometools/genometools
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
geos/3.4.3 geo

Description: GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) Homepage: http://trac.osgeo.org/geos Keyword:geo
Prerequisites: intel/2016.4
Description:
geos/3.6.1 geo

Description: GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) Homepage: http://trac.osgeo.org/geos Keyword:geo
Prerequisites: gcc/5.4.0 or gcc/6.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2017.5 or intel/2018.3
Description:
git-annex/6.20180807 -

Description: git-annex allows managing files with git, without checking the file contents into git. While that may seem paradoxical, it is useful when dealing with files larger than git can currently easily handle, whether due to limitations in memory, time, or disk space. Homepage: http://git-annex.branchable.com/
Prerequisites: -
Description:
glm/0.9.7.2 vis

Description: 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 Keyword:vis
Prerequisites: gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
glost/0.3.1 -

Description: This is GLOST, the Greedy Launcher Of Small Tasks. Homepage: https://github.com/cea-hpc/glost
Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or gcc/7.3.0 and openmpi/3.1.2 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
glpk/4.61 math

Description: 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/ Keyword:math
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2018.3
Description:
gmap-gsnap/2017-04-13 bio

Description: 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/ Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
gmap-gsnap/2018-07-04 bio

Description: 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/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
gmsh/3.0.6 -

Description: Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor. Homepage: http://geuz.org/gmsh
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4
Description:
gmt/5.4.2 geo

Description: 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/ Keyword:geo
Prerequisites: intel/2016.4 or intel/2018.3
Description:
gnuplot/5.2.2 vis

Description: Portable interactive, function plotting utility Homepage: http://gnuplot.sourceforge.net/ Keyword:vis
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
go/1.10.3 -

Description: Go is an open source programming language that makes it easy to build simple, reliable, and efficient software. Homepage: http://www.golang.org
Prerequisites: -
Description:
googletest/1.8.0 tools

Description: Welcome to Google Test, Google-s C++ test framework! Please see the project page for more information as well as the mailing list for questions, discussions, and development. There is also an IRC channel on OFTC. Getting started information for Google Test is available in the Google Test Primer documentation. Google Mock is an extension to Google Test for writing and using C++ mock classes. See the separate Google Mock documentation. More detailed documentation for googletest (including build instructions) are in its interior googletest/README.md file. Homepage: https://github.com/google/googletest Keyword:tools
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
gossamer/0.1 -

Description: Gossamer bioinformatics suite Homepage: https://github.com/data61/gossamer
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
grace/5.1.25 -

Description: Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif. Homepage: http://freecode.com/projects/grace
Prerequisites: intel/2016.4
Description:
grace/5.99.0 -

Description: Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif. Homepage: http://freecode.com/projects/grace
Prerequisites: intel/2016.4 or intel/2018.3
Description:
grackle/2.1 phys

Description: Grackle is a chemistry and radiative cooling library for astrophysical simulations and models. Homepage: http://grackle.readthedocs.io Keyword:phys
Prerequisites: intel/2016.4
Description:
grackle/3.1 phys

Description: Grackle is a chemistry and radiative cooling library for astrophysical simulations and models. Homepage: http://grackle.readthedocs.io Keyword:phys
Prerequisites: intel/2016.4 or intel/2018.3
Description:
grass/7.4.0 geo

Description: GRASS: Geographic Resources Analysis Support System, commonly referred to as GRASS, is a Geographic Information System (GIS) used for geospatial data management and analysis, image processing, graphics/maps production, spatial modeling, and visualization. GRASS is currently used in academic and commercial settings around the world, as well as by many governmental agencies and environmental consulting companies. Homepage: https://grass.osgeo.org/download/software/sources/ Keyword:geo
Prerequisites: intel/2016.4
Description:
grnboost/20171009 bio

Description: GRNBoost is a library built on top of Apache Spark that implements a scalable strategy for gene regulatory network (GRN) inference. Inferring a gene regulatory network (GRN) from gene expression data is a computationally expensive task, exacerbated by increasing data sizes due to advances in high-throughput gene profiling technology. GRNBoost was inspired by GENIE3, a popular algorithm for GRN inference. GENIE3 breaks up the inference problem into a number of tree-based ensemble (Random Forest) nonlinear regressions, building a predictive model for the expression profile of each gene in the dataset in function of the expression profiles of a collection of candidate regulatory genes (transcription factors). The regression models act as a feature selection mechanism, they yield the most predictive regulators for the target genes as candidate links in the resulting gene regulatory network.. Homepage: https://github.com/aertslab/GRNBoost Keyword:bio
Prerequisites: gcc/6.4.0
Description:
gromacs-plumed/2016.3 chem GROMACS

Description: GROMACS is a versatile package to perform molecular dynamics. This version contains the PLUMED patches in order to run metadynamics. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org Keyword:chem CC-Wiki: GROMACS
Prerequisites: intel/2016.4 and cuda/8.0.44 and openmpi/2.0.2 or intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description:
gromacs-plumed/2018.1 chem GROMACS

Description: GROMACS is a versatile package to perform molecular dynamics. This version contains the PLUMED patches in order to run metadynamics. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org Keyword:chem CC-Wiki: GROMACS
Prerequisites: gcc/6.4.0 and cuda/9.0.176 and openmpi/2.1.1 or gcc/6.4.0 and openmpi/2.1.1
Description:
gromacs/2016.3 chem GROMACS

Description: GROMACS is a versatile package to perform molecular dynamics. i.e. simulating the Newtonian equations of motion for systems with hundreds to millions of particles. - CC-Wiki: GROMACS - Homepage: http://www.gromacs.org Keyword:chem CC-Wiki: GROMACS
Prerequisites: intel/2016.4 and cuda/8.0.44 and openmpi/2.0.2 or intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and cuda/9.0.176 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description:
gromacs/2016.5 - GROMACS

Description: GROMACS is a versatile package to perform molecular dynamics. i.e. simulating the Newtonian equations of motion for systems with hundreds to millions of particles. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org
Prerequisites: gcc/6.4.0 and cuda/9.0.176 and openmpi/2.1.1 or gcc/6.4.0 and openmpi/2.1.1
Description:
gromacs/2018 chem GROMACS

Description: GROMACS is a versatile package to perform molecular dynamics. i.e. simulating the Newtonian equations of motion for systems with hundreds to millions of particles. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org Keyword:chem CC-Wiki: GROMACS
Prerequisites: intel/2016.4 and cuda/9.0.176 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1
Description:
gromacs/2018.1 - GROMACS

Description: GROMACS is a versatile package to perform molecular dynamics. i.e. simulating the Newtonian equations of motion for systems with hundreds to millions of particles. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org
Prerequisites: gcc/6.4.0 and cuda/9.0.176 and openmpi/2.1.1 or gcc/6.4.0 and openmpi/2.1.1
Description:
gromacs/2018.2 - GROMACS

Description: GROMACS is a versatile package to perform molecular dynamics. i.e. simulating the Newtonian equations of motion for systems with hundreds to millions of particles. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org
Prerequisites: gcc/6.4.0 and cuda/9.0.176 and openmpi/2.1.1 or gcc/6.4.0 and openmpi/2.1.1
Description:
gromacs/2018.3 - GROMACS

Description: GROMACS is a versatile package to perform molecular dynamics. i.e. simulating the Newtonian equations of motion for systems with hundreds to millions of particles. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org Keyword:chem CC-Wiki: GROMACS
Prerequisites: gcc/6.4.0 and cuda/9.0.176 and openmpi/2.1.1 or gcc/6.4.0 and openmpi/2.1.1 or gcc/7.3.0 and openmpi/3.1.2
Description:
gromacs/4.6.7 chem GROMACS

Description: GROMACS is a versatile package to perform molecular dynamics. i.e. simulating the Newtonian equations of motion for systems with hundreds to millions of particles. - CC-Wiki: GROMACS - Homepage: http://www.gromacs.org Keyword:chem CC-Wiki: GROMACS
Prerequisites: intel/2016.4 and cuda/8.0.44 and openmpi/2.0.2 or intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description:
gromacs/5.0.7 chem GROMACS

Description: GROMACS is a versatile package to perform molecular dynamics. i.e. simulating the Newtonian equations of motion for systems with hundreds to millions of particles. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org Keyword:chem CC-Wiki: GROMACS
Prerequisites: intel/2016.4 and cuda/8.0.44 and openmpi/2.0.2 or intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description:
gromacs/5.1.4 chem GROMACS

Description: GROMACS is a versatile package to perform molecular dynamics. i.e. simulating the Newtonian equations of motion for systems with hundreds to millions of particles. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org Keyword:chem CC-Wiki: GROMACS
Prerequisites: intel/2016.4 and cuda/8.0.44 and openmpi/2.0.2 or intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1
Description:
gromacs/5.1.5 chem GROMACS

Description: GROMACS is a versatile package to perform molecular dynamics. i.e. simulating the Newtonian equations of motion for systems with hundreds to millions of particles. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org Keyword:chem CC-Wiki: GROMACS
Prerequisites: intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1
Description:
gromacs/gromacs/2016.5 - GROMACS

Description: GROMACS is a versatile package to perform molecular dynamics. i.e. simulating the Newtonian equations of motion for systems with hundreds to millions of particles. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org
Prerequisites: gcc/6.4.0 and cuda/9.0.176 and openmpi/2.1.1 or gcc/6.4.0 and openmpi/2.1.1
Description:
gromacs/gromacs/2018.1 - GROMACS

Description: GROMACS is a versatile package to perform molecular dynamics. i.e. simulating the Newtonian equations of motion for systems with hundreds to millions of particles. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org
Prerequisites: gcc/6.4.0 and cuda/9.0.176 and openmpi/2.1.1 or gcc/6.4.0 and openmpi/2.1.1
Description:
gromacs/gromacs/2018.2 - GROMACS

Description: GROMACS is a versatile package to perform molecular dynamics. i.e. simulating the Newtonian equations of motion for systems with hundreds to millions of particles. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org
Prerequisites: gcc/6.4.0 and openmpi/2.1.1
Description:
gromacs/gromacs/5.1.4 - GROMACS

Description: GROMACS is a versatile package to perform molecular dynamics. i.e. simulating the Newtonian equations of motion for systems with hundreds to millions of particles. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org
Prerequisites: intel/2017.1 and openmpi/2.1.1
Description:
gsl/1.16 math

Description: 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/ Keyword:math
Prerequisites: gcc/4.8.5 or gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2018.3
Description:
gsl/2.2.1 math

Description: 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/ Keyword:math
Prerequisites: gcc/4.8.5 or gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description:
gsl/2.3 math

Description: 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/ Keyword:math
Prerequisites: gcc/4.8.5 or gcc/5.4.0 or gcc/6.4.0 or intel/2016.4 or intel/2017.1 or intel/2017.5
Description:
gsl/2.4 math

Description: 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/ Keyword:math
Prerequisites: gcc/7.3.0
Description:
gsl/2.5 math

Description: 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/ Keyword:math
Prerequisites: gcc/7.3.0 or intel/2018.3
Description:
gtk+3/3.20.9 -

Description: GTK+, or the GIMP Toolkit, is a multi-platform toolkit for creating graphical user interfaces. Offering a complete set of widgets, GTK+ is suitable for projects ranging from small one-off tools to complete application suites. Homepage: https://www.gtk.org/
Prerequisites: -
Description:
guile/1.8.8 tools

Description: Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system. Homepage: http://www.gnu.org/software/guile Keyword:tools
Prerequisites: - or intel/2016.4
Description:
h4toh5/2.2.2 io

Description: 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/ Keyword:io
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description:
hal/20180814 -

Description: Hierarchical Alignment (HAL) is a structure to efficiently store and index multiple genome alignments and ancestral reconstructions. Homepage: https://github.com/ComparativeGenomicsToolkit/hal
Prerequisites: gcc/5.4.0
Description:
harminv/1.4 math

Description: 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 Keyword:math
Prerequisites: intel/2016.4 or intel/2018.3
Description:
hdf/4.2.12 io

Description: 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/ Keyword:io
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2018.3
Description:
hdf5-mpi/1.10.3 io

Description: HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. Homepage: http://portal.hdfgroup.org/display/support Keyword:io
Prerequisites: gcc/7.3.0 and openmpi/3.1.2 or intel/2018.3 and openmpi/3.1.2
Description:
hdf5-mpi/1.8.18 io

Description: HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections. Homepage: https://support.hdfgroup.org/HDF5/ Keyword:io
Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or gcc/6.4.0 and openmpi/2.1.1 or intel/2014.6 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1 or intel/2017.5 and impi/2017.4.239 or pgi/17.3 and openmpi/2.1.1
Description:
hdf5/1.10.1 io

Description: HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections. Homepage: http://www.hdfgroup.org/HDF5/ Keyword:io
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
hdf5/1.10.3 io

Description: HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. Homepage: http://portal.hdfgroup.org/display/support Keyword:io
Prerequisites: gcc/7.3.0 or intel/2017.5 or intel/2018.3
Description:
hdf5/1.8.18 io

Description: HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections. Homepage: http://www.hdfgroup.org/HDF5/ Keyword:io
Prerequisites: gcc/4.8.5 or gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description:
hdf5/1.8.20 io

Description: HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections. Homepage: http://www.hdfgroup.org/HDF5/ Keyword:io
Prerequisites: gcc/7.3.0 or intel/2018.3
Description:
heasoft/6.22.1 phys

Description: A Unified Release of the FTOOLS and XANADU Software Packages XANADU High-level, multi-mission tasks for X-ray astronomical spectral, timing, and imaging data analysis FTOOLS General and mission-specific tools to manipulate FITS files FITSIO Core library responsible for reading and writing FITS files (distributed with FTOOLS) fv General FITS file browser/editor/plotter with a graphical user interface (distributed with FTOOLS) XSTAR Tool for calculating the physical conditions and emission spectra of photoionized gases Homepage: https://heasarc.nasa.gov/lheasoft/ Keyword:phys
Prerequisites: gcc/5.4.0
Description:
hh-suite/2.0.16 -

Description: 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
Prerequisites: gcc/5.4.0
Description:
hh-suite/3.0-beta.3 -

Description: The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). Homepage: https://github.com/soedinglab/hh-suite
Prerequisites: intel/2018.3
Description:
hisat2/2.1.0 bio

Description: 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 Keyword:bio
Prerequisites: intel/2016.4 or intel/2018.3
Description:
hmmer/2.3.2 bio

Description: 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/ Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
hmmer/3.1b2 bio

Description: 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/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
hpl/2.2 -

Description: 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/
Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or gcc/7.3.0 and openmpi/3.1.2 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2 or pgi/17.3 and openmpi/2.0.2 or pgi/17.3 and openmpi/2.1.1
Description:
htslib/1.4 bio

Description: A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix - Homepage: http://www.htslib.org/ Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description:
htslib/1.5 bio

Description: A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix Homepage: http://www.htslib.org/ Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
htslib/1.9 bio

Description: A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix Homepage: http://www.htslib.org/ Keyword:bio
Prerequisites: gcc/7.3.0 or intel/2018.3
Description:
hyphy/2.3.13 -

Description: HyPhy: Hypothesis testing using Phylogenies. HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for parallel computing environments (via message passing interface (MPIMessage Passing Interface)) and it can be compiled as a shared library and called from other programming environments such as Python and R. Homepage: https://veg.github.io/hyphy-site/
Prerequisites: gcc/5.4.0 and openmpi/2.0.2
Description:
hyphy/2.3.14 -

Description: HyPhy: Hypothesis testing using Phylogenies. HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for parallel computing environments (via message passing interface (MPIMessage Passing Interface)) and it can be compiled as a shared library and called from other programming environments such as Python and R. Homepage: https://veg.github.io/hyphy-site/
Prerequisites: gcc/7.3.0 and openmpi/3.1.2
Description:
hypre/2.10.0b -

Description: 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
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
hypre/2.15.1 -

Description: Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences. Homepage: https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods
Prerequisites: intel/2018.3 and openmpi/3.1.2
Description:
igblast/1.7.0 bio

Description: IgBLAST was developed at NCBI to facilitate analysis of immunoglobulin variable domain sequences (IgBLAST has recently been extended to perform analysis for T cell receptor (TR) sequences). It uses BLAST search algorithm. Homepage: https://www.ncbi.nlm.nih.gov/igblast/intro.html Keyword:bio
Prerequisites: gcc/5.4.0
Description:
igblast/1.8.0 bio

Description: IgBLAST was developed at NCBI to facilitate analysis of immunoglobulin variable domain sequences (IgBLAST has recently been extended to perform analysis for T cell receptor (TR) sequences). It uses BLAST search algorithm. Homepage: https://www.ncbi.nlm.nih.gov/igblast/intro.html Keyword:bio
Prerequisites: gcc/4.8.5 or gcc/5.4.0
Description:
igblast/1.9.0 bio

Description: IgBLAST was developed at NCBI to facilitate analysis of immunoglobulin variable domain sequences (IgBLAST has recently been extended to perform analysis for T cell receptor (TR) sequences). It uses BLAST search algorithm. Homepage: https://www.ncbi.nlm.nih.gov/igblast/intro.html Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
igraph/0.7.1 math

Description: 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 Keyword:math
Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or gcc/7.3.0 and openmpi/3.1.2 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
imkl/11.1.4.214 math

Description: 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/ Keyword:math
Prerequisites: -
Description:
imkl/11.3.4.258 math

Description: 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/ Keyword:math
Prerequisites: -
Description:
imkl/2017.1.132 math

Description: 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/ Keyword:math
Prerequisites: -
Description:
imkl/2017.4.239 math

Description: 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/ Keyword:math
Prerequisites: -
Description:
imkl/2018.1.163 math

Description: 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/ Keyword:math
Prerequisites: -
Description:
imkl/2018.3.222 math

Description: 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/ Keyword:math
Prerequisites: -
Description:
impi/2017.4.239 mpi

Description: Intel MPIMessage Passing Interface Library, compatible with MPICH ABI Homepage: http://software.intel.com/en-us/intel-mpi-library/
Prerequisites: intel/2017.5
Description:
impi/2018.3.222 mpi

Description: Intel MPIMessage Passing Interface Library, compatible with MPICH ABI Homepage: http://software.intel.com/en-us/intel-mpi-library/
Prerequisites: intel/2018.3
Description:
impute2/2.3.2 bio

Description: 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 Keyword:bio
Prerequisites: -
Description:
infernal/1.1.2 bio

Description: Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. Homepage: http://eddylab.org/infernal/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
inspector/2018.3 -

Description: 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
Prerequisites: -
Description:
intel/2014.6 tools

Description: Intel C, C++ and Fortran compilers Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ Keyword:tools
Prerequisites: -
Description:
intel/2016.4 tools

Description: Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPIMessage Passing Interface and Intel MKLIntel Math Kernel Library, a software library of optimized math routines Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ Keyword:tools
Prerequisites: -
Description:
intel/2017.1 tools

Description: Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPIMessage Passing Interface and Intel MKLIntel Math Kernel Library, a software library of optimized math routines Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ Keyword:tools
Prerequisites: -
Description:
intel/2017.5 tools

Description: Intel C, C++ and Fortran compilers Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ Keyword:tools
Prerequisites: -
Description:
intel/2018.3 tools

Description: Intel C, C++ and Fortran compilers Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ Keyword:tools
Prerequisites: -
Description:
interproscan/5.23-62.0 bio

Description: 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/ Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
ipp/2017.1.132 tools

Description: 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/ Keyword:tools
Prerequisites: -
Description:
ipp/9.0.4 tools

Description: 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/ Keyword:tools
Prerequisites: -
Description:
iq-tree/1.5.5 bio

Description: Efficient phylogenomic software by maximum likelihood Homepage: http://www.iqtree.org/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
itac/2018.3.022 -

Description: 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/
Prerequisites: -
Description:
itk/4.12.2 -

Description: Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data. Homepage: https://itk.org
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
itk/4.13.1 -

Description: Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data. Homepage: https://itk.org
Prerequisites: gcc/7.3.0 or intel/2018.3
Description:
jags/4.2.0 math

Description: 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/ Keyword:math
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description:
jags/4.3.0 math

Description: 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/ Keyword:math
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2018.3
Description:
jasper/1.900.1 vis

Description: 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/ Keyword:vis
Prerequisites: -
Description:
java/1.7.0_80 tools Java

Description: Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. Homepage: http://java.com/ Keyword:tools CC-Wiki: Java
Prerequisites: -
Description:
java/1.8.0_121 tools Java

Description: Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. - Homepage: http://java.com/ Keyword:tools CC-Wiki: Java
Prerequisites: -
Description:
jdftx/1.4.2 -

Description: JDFTx is a plane-wave density-functional theory (DFT) code designed to be as easy to develop with as it is easy to use. It is distributed under the GPL license (version 3 or higher) and publications resulting from its use must cite: R. Sundararaman, K. Letchworth-Weaver, K.A. Schwarz, D. Gunceler, Y. Ozhabes and T.A. Arias, 'JDFTx: software for joint density-functional theory Homepage: http://jdftx.org/index.html
Prerequisites: intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1
Description:
jellyfish/1.1.11 bio

Description: Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. Homepage: http://www.cbcb.umd.edu/software/jellyfish/ Keyword:bio
Prerequisites: intel/2016.4
Description:
jellyfish/2.2.6 bio

Description: Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. - Homepage: http://www.genome.umd.edu/jellyfish.html Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2018.3
Description:
julia/0.5.1 tools

Description: A high-level, high-performance dynamic language for technical computing. Homepage: http://julialang.org Keyword:tools
Prerequisites: intel/2016.4
Description:
julia/0.6.0 tools

Description: A high-level, high-performance dynamic language for technical computing. Homepage: http://julialang.org Keyword:tools
Prerequisites: intel/2016.4
Description:
julia/0.6.2 tools

Description: A high-level, high-performance dynamic language for technical computing. Homepage: http://julialang.org Keyword:tools
Prerequisites: intel/2016.4
Description:
julia/1.0.0 tools

Description: A high-level, high-performance dynamic language for technical computing. Homepage: http://julialang.org Keyword:tools
Prerequisites: intel/2016.4
Description:
julia/1.0.2 tools

Description: A high-level, high-performance dynamic language for technical computing. Homepage: http://julialang.org Keyword:tools
Prerequisites: gcc/7.3.0
Description:
kaiju/1.6.2 -

Description: 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/
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
kallisto/0.44.0 bio

Description: 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/ Keyword:bio
Prerequisites: intel/2016.4 or intel/2018.3
Description:
kentutils/20180716 -

Description: Kent utilities: collection of tools used by the UCSC genome browser. Homepage: http://genome.cse.ucsc.edu/
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4
Description:
kim/1.8.2 chem

Description: OpenKIM is an online suite of open source tools for molecular simulation of materials. These tools help to make molecular simulation more accessible and more reliable. Within OpenKIM, you will find an online resource for standardized testing and long-term warehousing of interatomic models and data, and an application programming interface (API) standard for coupling atomistic simulation codes and interatomic potential subroutines. Homepage: https://openkim.org/ Keyword:chem
Prerequisites: intel/2016.4 or intel/2018.3
Description:
kim/1.9.7 chem

Description: OpenKIM is an online suite of open source tools for molecular simulation of materials. These tools help to make molecular simulation more accessible and more reliable. Within OpenKIM, you will find an online resource for standardized testing and long-term warehousing of interatomic models and data, and an application programming interface (API) standard for coupling atomistic simulation codes and interatomic potential subroutines. Homepage: https://openkim.org/ Keyword:chem
Prerequisites: intel/2018.3
Description:
kraken/0.10.5-beta bio

Description: 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/ Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
kraken/1.1 bio

Description: 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/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
kraken2/2.0.7-beta -

Description: 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/
Prerequisites: gcc/7.3.0
Description:
lammps-omp/20170331 chem

Description: LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics simulation. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. It can be coupled to various programs. The following packages are not included within this version: -MSCG, -GPU, -KOKKOS, -KIM, -USER-QUIP, -USER-INTEL, -USER-VTK Homepage: http://lammps.sandia.gov/ Keyword:chem
Prerequisites: intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1
Description:
lammps-omp/20170811 chem

Description: LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics simulation. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. It can be coupled to various programs. The following packages are not included within this version: -GPU, -KOKKOS, -MSCG, -USER-INTEL, -USER-QUIP Homepage: http://lammps.sandia.gov/ Keyword:chem
Prerequisites: intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1
Description:
lammps-user-intel/20170331 chem

Description: LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics simulation. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. It can be coupled to various programs. The following packages are not included within this version: -MSCG, -GPU, -KOKKOS, -KIM, -USER-QUIP, -USER-VTK, -QEQ, -USER-ATC, -MANYBODY Homepage: http://lammps.sandia.gov/ Keyword:chem
Prerequisites: intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1
Description:
lammps-user-intel/20170811 chem

Description: LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics simulation. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. It can be coupled to various programs. The following packages are not included within this version: -GPU, -KOKKOS, -MANYBODY, -MSCG, -QEQ, -USER-ATC, -USER-QUIP Homepage: http://lammps.sandia.gov/ Keyword:chem
Prerequisites: intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1
Description:
lammps/20170331 chem

Description: LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics simulation. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. It can be coupled to various programs. The following packages are not included within this version: -MSCG, -GPU, -KOKKOS, -KIM, -USER-QUIP, -USER-OMP, -OPT, -USER-MISC, -USER-INTEL, -USER-VTK Homepage: http://lammps.sandia.gov/ Keyword:chem
Prerequisites: intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description:
last/959 -

Description: LAST finds similar regions between sequences. Homepage: http://last.cbrc.jp/
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
leveldb/1.18 tools

Description: 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 Keyword:tools
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
libcerf/1.5 math

Description: 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://apps.jcns.fz-juelich.de/src/libcerf/ Keyword:math
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
libconfig/1.7.2 -

Description: Libconfig is a simple library for processing structured configuration files Homepage: http://www.hyperrealm.com/libconfig/
Prerequisites: gcc/7.3.0
Description:
libctl/3.2.2 tools

Description: libctl is a free Guile-based library implementing flexible control files for scientific simulations. Homepage: http://ab-initio.mit.edu/libctl Keyword:tools
Prerequisites: intel/2016.4 or intel/2018.3
Description:
libgd/2.2.5 -

Description: GD is an open source code library for the dynamic creation of images by programmers. Homepage: https://libgd.github.io/
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
libgpuarray/0.6.9 math

Description: Homepage: http://deeplearning.net/software/libgpuarray Keyword:math
Prerequisites: gcc/5.4.0 and cuda/8.0.44 or intel/2016.4 and cuda/8.0.44
Description:
libgpuarray/0.7.5 math

Description: Homepage: http://deeplearning.net/software/libgpuarray Keyword:math
Prerequisites: gcc/5.4.0 and cuda/8.0.44
Description:
libgridxc/0.8.0 -

Description: A library to compute the exchange and correlation energy and potential in spherical (i.e. an atom) or periodic systems. It is based on SiestaXC. Homepage: https://launchpad.net/libgridxc
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
libgtextutils/0.7 bio

Description: ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream Homepage: http://hannonlab.cshl.edu/fastx_toolkit/ Keyword:bio
Prerequisites: - or gcc/7.3.0 or intel/2018.3
Description:
libint/1.1.6 chem

Description: Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. - Homepage: https://sourceforge.net/p/libint/ Keyword:chem
Prerequisites: gcc/5.4.0 or gcc/6.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2017.5 or intel/2018.3
Description:
libint/2.2.0 chem

Description: Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. Homepage: https://github.com/evaleev/libint Keyword:chem
Prerequisites: gcc/7.3.0
Description:
libmaus2/2.0.499 -

Description: libmaus2 is a collection of data structures and algorithms. Homepage: https://github.com/gt1/libmaus2
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2018.3
Description:
libmesh/1.2.1 math

Description: The libMesh library provides a framework for the numerical simulation of partial differential equations using arbitrary unstructured discretizations on serial and parallel platforms. A major goal of the library is to provide support for adaptive mesh refinement (AMR) computations in parallel while allowing a research scientist to focus on the physics they are modeling. Homepage: https://github.com/libMesh/libmesh Keyword:math
Prerequisites: intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
libplinkio/0.9.5 bio

Description: A small C and Python library for reading PLINK genotype files. Homepage: https://github.com/mfranberg/libplinkio Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
libspatialindex/1.8.5 -

Description: C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API Homepage: http://libspatialindex.github.io
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
libspatialite/4.3.0a -

Description: SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities. Homepage: https://www.gaia-gis.it/fossil/libspatialite/home
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
libtricubic/1.0 -

Description: Library implementing tricubic interpolation. Homepage: https://github.com/nbigaouette/libtricubic
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
libxc/3.0.0 chem

Description: Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. - Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Libxc Keyword:chem
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2017.5 or intel/2018.3
Description:
libxc/3.0.1 chem

Description: Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Libxc Keyword:chem
Prerequisites: gcc/6.4.0
Description:
libxc/4.2.1 chem

Description: Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Libxc Keyword:chem
Prerequisites: gcc/5.4.0 or gcc/6.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2017.5
Description:
libxc/4.2.3 chem

Description: Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Libxc Keyword:chem
Prerequisites: intel/2018.3
Description:
libxsmm/1.8 math

Description: LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86). - Homepage: https://github.com/hfp/libxsmm Keyword:math
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2017.5 or intel/2018.3
Description:
libxsmm/1.8.2 math

Description: LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86). Homepage: https://github.com/hfp/libxsmm Keyword:math
Prerequisites: gcc/6.4.0 or gcc/7.3.0 or intel/2018.3
Description:
links/1.8.5 bio

Description: LINKS is a scalable genomics application for scaffolding or re-scaffolding genome assembly drafts with long reads, such as those produced by Oxford Nanopore Technologies Ltd and Pacific Biosciences. It provides a generic alignment-free framework for scaffolding and can work on any sequences. It is versatile and supports not only long sequences as a source of long-range information, but also MPET pairs and linked-reads, such as those from the 10X Genomics GemCode and Chromium platform, via ARCS (http://www.bcgsc.ca/platform/bioinfo/software/arcs). Fill gaps in LINKS-derived scaffolds using Sealer (http://www.bcgsc.ca/platform/bioinfo/software/sealer). Homepage: http://www.bcgsc.ca/platform/bioinfo/software/links Keyword:bio
Prerequisites: -
Description:
lis/2.0.10 -

Description: Lis, a Library of Iterative Solvers for linear systems, is a parallel library for solving linear equations and eigenvalue problems that arise in the numerical solution of partial differential equations using iterative methods. The installation of Lis requires a C compiler. The Fortran interface requires a Fortran compiler, and the algebraic multigrid preconditioner requires a Fortran 90 compiler. For parallel computing environments, an OpenMP or MPIMessage Passing Interface-1 library is used. Both the Harwell-Boeing and Matrix Market formats are supported to import and export user data. Homepage: http://www.netlib.org/misc/lis/
Prerequisites: gcc/5.4.0 and openmpi/2.1.1 or gcc/7.3.0 and openmpi/3.1.2 or intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
llvm/6.0.1 -

Description: The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator. Homepage: http://llvm.org/
Prerequisites: -
Description:
lobstr/4.0.6 -

Description: lobSTR is a tool for profiling Short Tandem Repeats (STRs) from high throughput sequencing data. Homepage: http://lobstr.teamerlich.org/
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
locarna/1.9.2.1 -

Description: LocARNA is a collection of alignment tools for the structural analysis of RNA. Given a set of RNA sequences, LocARNA simultaneously aligns and predicts common structures for your RNAs. In this way, LocARNA performs Sankoff-like alignment and is in particular suited for analyzing sets of related RNAs without known common structure. Homepage: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4
Description:
lpsolve/5.5.2.5 math

Description: Mixed Integer Linear Programming (MILP) solver Homepage: https://sourceforge.net/projects/lpsolve/ Keyword:math
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
ls-dyna-mpi/10.0 phys

Description: LS-DYNA is a general-purpose finite element program capable of simulating complex real world problems. It is used by the automobile, aerospace, construction, military, manufacturing, and bioengineering industries. LS-DYNA is optimized for shared and distributed memory Unix, Linux, and Windows based, platforms, and it is fully QA'd by LSTC. The code's origins lie in highly nonlinear, transient dynamic finite element analysis using explicit time integration. Homepage: http://www.lstc.com/products/ls-dyna Keyword:phys
Prerequisites: intel/2016.4 and openmpi/1.10.7
Description:
ls-dyna-mpi/7.1.2 phys

Description: LS-DYNA is a general-purpose finite element program capable of simulating complex real world problems. It is used by the automobile, aerospace, construction, military, manufacturing, and bioengineering industries. LS-DYNA is optimized for shared and distributed memory Unix, Linux, and Windows based, platforms, and it is fully QA'd by LSTC. The code's origins lie in highly nonlinear, transient dynamic finite element analysis using explicit time integration. Homepage: http://www.lstc.com/products/ls-dyna Keyword:phys
Prerequisites: intel/2016.4 and openmpi/1.6.5
Description:
ls-dyna-mpi/7.1.3 phys

Description: LS-DYNA is a general-purpose finite element program capable of simulating complex real world problems. It is used by the automobile, aerospace, construction, military, manufacturing, and bioengineering industries. LS-DYNA is optimized for shared and distributed memory Unix, Linux, and Windows based, platforms, and it is fully QA'd by LSTC. The code's origins lie in highly nonlinear, transient dynamic finite element analysis using explicit time integration. Homepage: http://www.lstc.com/products/ls-dyna Keyword:phys
Prerequisites: intel/2016.4 and openmpi/1.6.5
Description:
ls-dyna-mpi/8.1 phys

Description: LS-DYNA is a general-purpose finite element program capable of simulating complex real world problems. It is used by the automobile, aerospace, construction, military, manufacturing, and bioengineering industries. LS-DYNA is optimized for shared and distributed memory Unix, Linux, and Windows based, platforms, and it is fully QA'd by LSTC. The code's origins lie in highly nonlinear, transient dynamic finite element analysis using explicit time integration. Homepage: http://www.lstc.com/products/ls-dyna Keyword:phys
Prerequisites: intel/2016.4 and openmpi/1.8.8
Description:
ls-dyna-mpi/9.1 phys

Description: LS-DYNA is a general-purpose finite element program capable of simulating complex real world problems. It is used by the automobile, aerospace, construction, military, manufacturing, and bioengineering industries. LS-DYNA is optimized for shared and distributed memory Unix, Linux, and Windows based, platforms, and it is fully QA'd by LSTC. The code's origins lie in highly nonlinear, transient dynamic finite element analysis using explicit time integration. Homepage: http://www.lstc.com/products/ls-dyna Keyword:phys
Prerequisites: intel/2016.4 and openmpi/1.8.8
Description:
ls-dyna-mpi/9.2 phys

Description: LS-DYNA is a general-purpose finite element program capable of simulating complex real world problems. It is used by the automobile, aerospace, construction, military, manufacturing, and bioengineering industries. LS-DYNA is optimized for shared and distributed memory Unix, Linux, and Windows based, platforms, and it is fully QA'd by LSTC. The code's origins lie in highly nonlinear, transient dynamic finite element analysis using explicit time integration. Homepage: http://www.lstc.com/products/ls-dyna Keyword:phys
Prerequisites: intel/2016.4 and openmpi/1.8.8
Description:
ls-dyna/10.0 phys

Description: LS-DYNA is a general-purpose finite element program capable of simulating complex real world problems. It is used by the automobile, aerospace, construction, military, manufacturing, and bioengineering industries. LS-DYNA is optimized for shared and distributed memory Unix, Linux, and Windows based, platforms, and it is fully QA'd by LSTC. The code's origins lie in highly nonlinear, transient dynamic finite element analysis using explicit time integration. Homepage: http://www.lstc.com/products/ls-dyna Keyword:phys
Prerequisites: intel/2016.4
Description:
ls-dyna/7.1.2 phys

Description: LS-DYNA is a general-purpose finite element program capable of simulating complex real world problems. It is used by the automobile, aerospace, construction, military, manufacturing, and bioengineering industries. LS-DYNA is optimized for shared and distributed memory Unix, Linux, and Windows based, platforms, and it is fully QA'd by LSTC. The code's origins lie in highly nonlinear, transient dynamic finite element analysis using explicit time integration. Homepage: http://www.lstc.com/products/ls-dyna Keyword:phys
Prerequisites: intel/2016.4
Description:
ls-dyna/7.1.3 phys

Description: LS-DYNA is a general-purpose finite element program capable of simulating complex real world problems. It is used by the automobile, aerospace, construction, military, manufacturing, and bioengineering industries. LS-DYNA is optimized for shared and distributed memory Unix, Linux, and Windows based, platforms, and it is fully QA'd by LSTC. The code's origins lie in highly nonlinear, transient dynamic finite element analysis using explicit time integration. Homepage: http://www.lstc.com/products/ls-dyna Keyword:phys
Prerequisites: intel/2016.4
Description:
ls-dyna/8.1 phys

Description: LS-DYNA is a general-purpose finite element program capable of simulating complex real world problems. It is used by the automobile, aerospace, construction, military, manufacturing, and bioengineering industries. LS-DYNA is optimized for shared and distributed memory Unix, Linux, and Windows based, platforms, and it is fully QA'd by LSTC. The code's origins lie in highly nonlinear, transient dynamic finite element analysis using explicit time integration. Homepage: http://www.lstc.com/products/ls-dyna Keyword:phys
Prerequisites: intel/2016.4
Description:
ls-dyna/9.1 phys

Description: LS-DYNA is a general-purpose finite element program capable of simulating complex real world problems. It is used by the automobile, aerospace, construction, military, manufacturing, and bioengineering industries. LS-DYNA is optimized for shared and distributed memory Unix, Linux, and Windows based, platforms, and it is fully QA'd by LSTC. The code's origins lie in highly nonlinear, transient dynamic finite element analysis using explicit time integration. Homepage: http://www.lstc.com/products/ls-dyna Keyword:phys
Prerequisites: intel/2016.4
Description:
ls-dyna/9.2 phys

Description: LS-DYNA is a general-purpose finite element program capable of simulating complex real world problems. It is used by the automobile, aerospace, construction, military, manufacturing, and bioengineering industries. LS-DYNA is optimized for shared and distributed memory Unix, Linux, and Windows based, platforms, and it is fully QA'd by LSTC. The code's origins lie in highly nonlinear, transient dynamic finite element analysis using explicit time integration. Homepage: http://www.lstc.com/products/ls-dyna Keyword:phys
Prerequisites: intel/2016.4
Description:
ls-opt/5.2.1 -

Description: LS-OPT is a standalone Design Optimization and Probabilistic Analysis package with an interface to LS-DYNA. Homepage: http://www.lstc.com/products/ls-opt
Prerequisites: -
Description:
lumpy/0.2.13 bio

Description: A probabilistic framework for structural variant discovery. Homepage: https://github.com/arq5x/lumpy-sv Keyword:bio
Prerequisites: gcc/5.4.0 and openmpi/2.1.1 or gcc/7.3.0 or intel/2016.4 and openmpi/2.1.1 or intel/2018.3
Description:
mach/1.0.18 bio

Description: MACH 1.0 is a Markov Chain based haplotyper that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals. - Homepage: http://csg.sph.umich.edu/abecasis/MACH/ Keyword:bio
Prerequisites: -
Description:
mafft/7.310 bio

Description: MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of < ~200 sequences), FFT-NS-2 (fast; for alignment of < ~10,000 sequences), etc. Homepage: http://mafft.cbrc.jp/alignment/software/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
mafft/7.397 bio

Description: MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <200 sequences), FFT-NS-2 (fast; for alignment of <10,000 sequences), etc. Homepage: https://mafft.cbrc.jp/alignment/software/ Keyword:bio
Prerequisites: gcc/7.3.0 or intel/2018.3
Description:
magma/2.2.0 math

Description: The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems. Homepage: http://icl.cs.utk.edu/magma/ Keyword:math
Prerequisites: gcc/5.4.0 and cuda/8.0.44 or intel/2016.4 and cuda/8.0.44
Description:
magma/2.4.0 math

Description: The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems. Homepage: http://icl.cs.utk.edu/magma/ Keyword:math
Prerequisites: gcc/7.3.0 and cuda/10.0.130 or intel/2018.3 and cuda/10.0.130
Description:
make/3.82 -

Description: make-3.82: GNU version of make utility Homepage: http://www.gnu.org/software/make/make.html
Prerequisites: -
Description:
maker/2.31.9 bio

Description: MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. Homepage: http://www.yandell-lab.org/software/maker.html Keyword:bio
Prerequisites: gcc/5.4.0 and openmpi/2.1.1
Description:
manta/1.2.2 bio

Description: Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow. The method is designed for rapid analysis on standard compute hardware: NA12878 at 50x genomic coverage is analyzed in less than 20 minutes on a 20 core server, and most WGS tumor/normal analyses can be completed within 2 hours. Manta combines paired and split-read evidence during SV discovery and scoring to improve accuracy, but does not require split-reads or successful breakpoint assemblies to report a variant in cases where there is strong evidence otherwise. It provides scoring models for germline variants in small sets of diploid samples and somatic variants in matched tumor/normal sample pairs. There is experimental support for analysis of unmatched tumor samples as well. Manta accepts input read mappings from BAM or CRAM files and reports all SV and indel inferences in VCF 4.1 format. See the user guide for a full description of capabilities and limitations. Homepage: https://github.com/Illumina/manta Keyword:bio
Prerequisites: -
Description:
mariadb/10.1.21 -

Description: MariaDB An enhanced, drop-in replacement for MySQL. Homepage: https://mariadb.org/
Prerequisites: -
Description:
marvel/1.0 -

Description: MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads. Homepage: https://github.com/schloi/MARVEL
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
masurca/3.2.4 bio

Description: MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore). Homepage: http://www.genome.umd.edu/masurca.html Keyword:bio
Prerequisites: gcc/5.4.0
Description:
masurca/3.2.6 bio

Description: MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore). Homepage: http://www.genome.umd.edu/masurca.html Keyword:bio
Prerequisites: gcc/5.4.0
Description:
masurca/3.2.7 bio

Description: MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore). Homepage: http://www.genome.umd.edu/masurca.html Keyword:bio
Prerequisites: gcc/5.4.0
Description:
masurca/3.2.8 bio

Description: MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore). Homepage: http://www.genome.umd.edu/masurca.html Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
matio/1.5.2 io

Description: matio is an C library for reading and writing Matlab MAT files. Homepage: http://sourceforge.net/projects/matio/ Keyword:io
Prerequisites: gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
matlab/2014a tools MATLAB

Description: MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. Homepage: http://www.mathworks.com/products/matlab Keyword:tools CC-Wiki: MATLAB
Prerequisites: -
Description:
matlab/2016b tools MATLAB

Description: MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. Homepage: http://www.mathworks.com/products/matlab Keyword:tools CC-Wiki: MATLAB
Prerequisites: -
Description:
matlab/2017a tools MATLAB

Description: MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. Homepage: http://www.mathworks.com/products/matlab Keyword:tools CC-Wiki: MATLAB
Prerequisites: -
Description:
matlab/2018a tools MATLAB

Description: MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. Homepage: http://www.mathworks.com/products/matlab Keyword:tools CC-Wiki: MATLAB
Prerequisites: -
Description:
maven/3.5.0 tools

Description: Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information. Homepage: http://maven.apache.org/index.html Keyword:tools
Prerequisites: -
Description:
maxbin/2.2.4 bio

Description: MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Users can understand the underlying bins (genomes) of the microbes in their metagenomes by simply providing assembled metagenomic sequences and the reads coverage information or sequencing reads. For users convenience MaxBin will report genome-related statistics, including estimated completeness, GC content and genome size in the binning summary page. Users can use MEGAN or similar software on MaxBin bins to find the taxonomy of each bin after the binning process is finished. Homepage: https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html Keyword:bio
Prerequisites: gcc/5.4.0
Description:
mcl/14.137 math

Description: The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for networks (also known as graphs) based on simulation of (stochastic) flow in graphs. The algorithm was invented/discovered by Stijn van Dongen at the Centre for Mathematics and Computer Science (also known as CWI) in the Netherlands. MCL has been applied in a number of different domains, mostly in bioinformatics. Homepage: http://micans.org/mcl/ Keyword:math
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
mcr/R2013a tools MATLAB

Description: The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. Homepage: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools CC-Wiki: MATLAB
Prerequisites: -
Description:
mcr/R2013b tools MATLAB

Description: The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. Homepage: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools CC-Wiki: MATLAB
Prerequisites: -
Description:
mcr/R2014a tools MATLAB

Description: The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. Homepage: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools CC-Wiki: MATLAB
Prerequisites: -
Description:
mcr/R2014b tools MATLAB

Description: The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. Homepage: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools CC-Wiki: MATLAB
Prerequisites: -
Description:
mcr/R2015a tools MATLAB

Description: The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. Homepage: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools CC-Wiki: MATLAB
Prerequisites: -
Description:
mcr/R2015b tools MATLAB

Description: The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. Homepage: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools CC-Wiki: MATLAB
Prerequisites: -
Description:
mcr/R2016a tools MATLAB

Description: The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. Homepage: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools CC-Wiki: MATLAB
Prerequisites: -
Description:
mcr/R2016b tools MATLAB

Description: The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. Homepage: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools CC-Wiki: MATLAB
Prerequisites: -
Description:
mcr/R2017a tools MATLAB

Description: The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. Homepage: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools CC-Wiki: MATLAB
Prerequisites: -
Description:
mcr/R2017b tools MATLAB

Description: The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. Homepage: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools CC-Wiki: MATLAB
Prerequisites: -
Description:
mcr/R2018a tools MATLAB

Description: The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. Homepage: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools CC-Wiki: MATLAB
Prerequisites: -
Description:
mcr/R2018b tools MATLAB

Description: The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. Homepage: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools CC-Wiki: MATLAB
Prerequisites: -
Description:
meep/1.3 phys

Description: Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems. Homepage: http://ab-initio.mit.edu/wiki/index.php/Meep Keyword:phys
Prerequisites: intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
mefit/1.0 bio

Description: MeFiT (Merging and Filtering Tool for Paired-End Reads): This pipeline will merge overlapping paired-end reads, calculate merge statistics, and filter reads for quality. Homepage: https://github.com/nisheth/MeFiT Extensions: HTSeq-0.9.1, pysam-0.14 Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
megahit/1.1.1 bio

Description: MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. Homepage: https://github.com/voutcn/megahit Keyword:bio
Prerequisites: gcc/5.4.0 and cuda/8.0.44
Description:
meraculous/2.2.4 bio

Description: Distributed and scalable assembler for eukaryotic genomes. Meraculous is a whole genome assembler for Next Generation Sequencing data geared for large genomes. It is a hybrid k-mer/read-based assembler that capitalizes on the high accuracy of Illumina sequence by eschewing an explicit error correction step which we argue to be redundant with the assembly process. Meraculous achieves high performance with large datasets by utilizing lightweight data structures and multi-threaded parallelization, allowing to assemble human-sized genomes on commodity clusters in under a day. The process pipeline implements a highly transparent and portable model of job control and monitoring where different assembly stages can be executed and re-executed separately or in unison on a wide variety of architectures. Homepage: http://jgi.doe.gov/data-and-tools/meraculous/ Keyword:bio
Prerequisites: gcc/4.8.5
Description:
meraculous/2.2.5.1-1-ga103cd6 bio

Description: Meraculous is a whole genome assembler for Next Generation Sequencing data geared for large genomes. It is a hybrid k-mer/read-based assembler that capitalizes on the high accuracy of Illumina sequence by eschewing an explicit error correction step which we argue to be redundant with the assembly process. Meraculous achieves high performance with large datasets by utilizing lightweight data structures and multi-threaded parallelization, allowing to assemble human-sized genomes on commodity clusters in under a day. The process pipeline implements a highly transparent and portable model of job control and monitoring where different assembly stages can be executed and re-executed separately or in unison on a wide variety of architectures. Homepage: https://jgi.doe.gov/data-and-tools/meraculous/ Keyword:bio
Prerequisites: gcc/5.4.0
Description:
mesa-astrophysics/r10108 phys

Description: MESA Modules for Experiments in Stellar Astrophysics, Homepage: http://mesa.sourceforge.net/ Keyword:phys
Prerequisites: gcc/5.4.0
Description:
mesa/18.0.0 -

Description: Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. Homepage: http://www.mesa3d.org/
Prerequisites: intel/2018.3
Description:
mesquite/2.3.0 -

Description: Mesh-Quality Improvement Library Homepage: https://software.sandia.gov/mesquite/
Prerequisites: intel/2016.4 or intel/2018.3
Description:
met/8.0_bugfix -

Description: Model Evaluation Tools (MET) is a highly configurable, state-of-the-art suite of verification tools designed for the verification and evaluation of numerical weather forecasts. Although MET was developed at the Developmental Testbed Center (DTC) to be used with the Weather Research and Forecasting (WRF) modeling system, the data formats and standards used allow MET to be run on the output of other modeling systems as well. Homepage: ihttps://dtcenter.org/met/users/support/online_tutorial/METv6.1/index.php
Prerequisites: intel/2018.3 and openmpi/3.1.2
Description:
metabat/2.12.1 bio

Description: MetaBAT: A robust statistical framework for reconstructing genomes from metagenomic data Homepage: https://bitbucket.org/berkeleylab/metabat Keyword:bio
Prerequisites: -
Description:
metal/2011-03-25 bio

Description: METAL provides a computationally efficient tool for meta-analysis of genome-wide association scans, which is a commonly used approach for improving power complex traits gene mapping studies. METAL provides a rich scripting interface and implements efficient memory management to allow analyses of very large data sets and to support a variety of input file formats. Availability and implementation: METAL, including source code, documentation, examples, and executables, is available at: http://www.sph.umich.edu/csg/abecasis/metal/ If you use Metal please fill out the registration form on the page: http://csg.sph.umich.edu/abecasis/metal/download/ Contact: goncalo@umich.edu Homepage: http://www.sph.umich.edu/csg/abecasis/metal/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
metaphlan/2.2.0 bio

Description: MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. Homepage: https://bitbucket.org/biobakery/metaphlan2 Keyword:bio
Prerequisites: intel/2016.4 or intel/2018.3
Description:
metis/4.0.3 math

Description: METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. - Homepage: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview Keyword:math
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
metis/5.1.0 math

Description: METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. - Homepage: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview Keyword:math
Prerequisites: gcc/4.8.5 or gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2018.3
Description:
mfem/3.4 -

Description: MFEM is a free, lightweight, scalable C++ library for finite element methods. Homepage: http://mfem.org/
Prerequisites: intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
minc-toolkit/1.9.16 -

Description: Medical Imaging NetCDF Toolkit Homepage: http://bic-mni.github.io/
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
minia/2.0.7 bio

Description: Minia is a short-read assembler based on a de Bruijn graph - Homepage: http://minia.genouest.org/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
miniasm/0.3 -

Description: Ultrafast de novo assembly for long noisy reads (though having no consensus step). Homepage: https://github.com/lh3/miniasm
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4
Description:
minimac2/2014.9.15 bio

Description: minimac2 is an improved version of Minimac. It is designed to work on phased genotypes and can handle very large reference panels with hundreds or thousands of haplotypes. The name has two parts. The first, mini, refers to the modest amount of computational resources it requires. The second, mac, is short hand for MaCH, our widely used algorithm for genotype imputation. - Homepage: http://genome.sph.umich.edu/wiki/Minimac2 Keyword:bio
Prerequisites: -
Description:
minimac3/2.0.1 bio

Description: Minimac3 is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac and minimac2. Minimac3 is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy. Homepage: http://genome.sph.umich.edu/wiki/Minimac3 Keyword:bio
Prerequisites: intel/2016.4 or intel/2018.3
Description:
minimap2/2.13 -

Description: Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited test data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replace BWA-MEM for long reads and contig alignment. Homepage: https://github.com/lh3/minimap2
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
mira/4.0.2 bio

Description: MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the latter at the moment only CCS and error-corrected CLR reads). Homepage: https://sourceforge.net/projects/mira-assembler/ Keyword:bio
Prerequisites: gcc/4.8.5
Description:
mitobim/1.9 bio

Description: This document contains instructions on how to use the MITObim pipeline described in Hahn et al. 2013. The full article c an be found [here](http://nar.oxfordjournals.org/content/41/13/e129 "MITObim full article at NAR"). Kindly cite the arti cle if you are using MITObim in your work. Homepage: https://github.com/chrishah/MITObim/ Keyword:bio
Prerequisites: gcc/4.8.5
Description:
mitsuba/0.1.1 -

Description: Mitsuba is a research-oriented rendering system in the style of PBRT, from which it derives much inspiration. It is written in portable C++, implements unbiased as well as biased techniques, and contains heavy optimizations targeted towards current CPU architectures. Mitsuba is extremely modular: it consists of a small set of core libraries and over 100 different plugins that implement functionality ranging from materials and light sources to complete rendering algorithms. Homepage: https://www.mitsuba-renderer.org/index.html
Prerequisites: gcc/5.4.0 and openmpi/2.1.1
Description:
mixcr/2.1.10 bio

Description: MiXCR is a universal framework that processes big immunome data from raw sequences to quantitated clonotypes. MiXCR efficiently handles paired- and single-end reads, considers sequence quality, corrects PCR errors and identifies germline hypermutations. The software supports both partial- and full-length profiling and employs all available RNA or DNA information, including sequences upstream of V and downstream of J gene segments. Homepage: http://mixcr.readthedocs.io/en/latest/quickstart.html Keyword:bio
Prerequisites: -
Description:
mixcr/2.1.5 bio

Description: MiXCR is a universal framework that processes big immunome data from raw sequences to quantitated clonotypes. MiXCR efficiently handles paired- and single-end reads, considers sequence quality, corrects PCR errors and identifies germline hypermutations. The software supports both partial- and full-length profiling and employs all available RNA or DNA information, including sequences upstream of V and downstream of J gene segments. Homepage: http://mixcr.readthedocs.io/en/latest/quickstart.html Keyword:bio
Prerequisites: -
Description:
mkl-dnn/0.14 -

Description: Intel(R) Math Kernel Library for Deep Neural Networks (Intel(R) MKLIntel Math Kernel Library, a software library of optimized math routines-DNN) Homepage: https://01.org/mkl-dnn
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
mkl-dnn/0.16 -

Description: Intel(R) Math Kernel Library for Deep Neural Networks (Intel(R) MKLIntel Math Kernel Library, a software library of optimized math routines-DNN) Homepage: https://01.org/mkl-dnn
Prerequisites: gcc/7.3.0 or intel/2018.3
Description:
molden/5.7 chem

Description: Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac Homepage: http://www.cmbi.ru.nl/molden/ Keyword:chem
Prerequisites: intel/2016.4 or intel/2017.1 or intel/2018.3
Description:
mono/4.6.2.7 tools

Description: An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET. - Homepage: http://mono-framework.com Keyword:tools
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2018.3
Description:
mono/5.16.0.179 tools

Description: An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET. Homepage: http://www.mono-project.com/ Keyword:tools
Prerequisites: gcc/7.3.0
Description:
mono/5.4.0.56 tools

Description: An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET. Homepage: http://www.mono-project.com/ Keyword:tools
Prerequisites: gcc/5.4.0
Description:
mothur/1.39.4 bio

Description: Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. Homepage: http://www.mothur.org/ Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
mothur/1.40.4 bio

Description: Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. Homepage: http://www.mothur.org/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4
Description:
mothur/1.41.0 bio

Description: Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. Homepage: http://www.mothur.org/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
motioncor2/1.0.5 bio

Description: Correction of electron beam-induced sample motion is one of the major factors contributing to the recent resolution breakthroughs in cryo-electron microscopy. Based on observations that the electron beam induces doming of the thin vitreous ice layer, we developed an algorithm to correct anisotropic image motion at the single pixel level across the whole frame, suitable for both single particle and tomographic images. Iterative, patch-based motion detection is combined with spatial and temporal constraints and dose weighting. Homepage: http://msg.ucsf.edu/em/software/motioncor2.html Keyword:bio
Prerequisites: intel/2016.4
Description:
mpe2/2.4.9b mpi

Description: MPE is a software package for MPIMessage Passing Interface (Message Passing Interface) programmers. The package provides users with a number of useful tools for their MPIMessage Passing Interface programs. The latest version is called MPE2. Current available tools under MPE2 are the following: 1. A set of profiling libraries to collect information about the behavior of MPIMessage Passing Interface programs. Linking the user MPIMessage Passing Interface program with the libraries will generate logfile for postmortem visualization when the user program is executed. 2. Convenient compiler wrapper, mpecc and mpefc, are provided to compile/link with the related profiled libraries, e.g. "mpecc -mpilog" enables automatic MPIMessage Passing Interface and user-defined MPE logging, "mpecc -mpicheck" enables collective and datatype checking of the user MPIMessage Passing Interface program, and "mpecc -help" shows available options. 3. A SLOG-2 viewer, Jumpshot, for the various logfiles. 4. A set of CLOG-2 and SLOG-2 utilities programs. 5. An MPIMessage Passing Interface collective and datatype checking library. 6. A shared-display parallel X graphics library. 7. A profiling wrapper generator for MPIMessage Passing Interface interface. 8. Routines for sequentializing a section of code being executed in parallel. 9. Debugger setup routines. Homepage: http://www.mcs.anl.gov/research/projects/perfvis/download/index.htm Keyword:mpi
Prerequisites: gcc/5.4.0 and openmpi/2.1.1 or gcc/7.3.0 and openmpi/3.1.2 or intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
mpfi/1.5.1 math

Description: MPFI, a multiple precision interval arithmetic library based on MPFR MPFI stands for Multiple Precision Floating-point Interval library. Homepage: http://perso.ens-lyon.fr/nathalie.revol/software.html Keyword:math
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4
Description:
mpi.net/13-08-2017 mpi

Description: MPIMessage Passing Interface.NET is a high-performance, easy-to-use implementation of the Message Passing Interface (MPIMessage Passing Interface) for Microsoft's .NET environment. Homepage: https://github.com/jmp75/MPI.NET Keyword:mpi
Prerequisites: gcc/5.4.0 and openmpi/2.1.1
Description:
mpi4py/3.0.0 tools

Description: MPIMessage Passing Interface for Python (mpi4py) provides bindings of the Message Passing Interface (MPIMessage Passing Interface) standard for the Python programming language, allowing any Python program to exploit multiple processors. Homepage: https://bitbucket.org/mpi4py/mpi4py Keyword:tools
Prerequisites: gcc/5.4.0 and cuda/8.0.44 and openmpi/2.1.1 or gcc/5.4.0 and openmpi/2.1.1 or gcc/6.4.0 and cuda/9.0.176 and openmpi/2.1.1 or gcc/7.3.0 and openmpi/3.1.2 or intel/2016.4 and cuda/8.0.44 and openmpi/2.0.2 or intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and cuda/9.0.176 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1 or intel/2017.5 and cuda/9.0.176 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
mrbayes/3.2.6 bio

Description: MrBayes is a program for the Bayesian estimation of phylogeny. - Homepage: http://mrbayes.csit.fsu.edu Keyword:bio
Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
mrtrix/3.0_RC3 -

Description: MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines. Homepage: http://www.brain.org.au/software/index.html#mrtrix
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
mscg/1.7.3.1 -

Description: The Multiscale Coarse-Graining (MS-CG) method is a variational force-matching technique developed by the Voth group. This project serves as the workhorse implementation of the method used as a standard force-matching code. The development of MS-CG is supported by academic research grants. If you use this package, please cite at least one of these papers: - S. Izvekov and G. A. Voth, J. Chem. Phys. 123, 134105 (2005). - W. G. Noid, et al., J. Chem. Phys. 128, 244114 (2008). - W. G. Noid et al., J. Chem. Phys. 128, 244115 (2008). - L. Lu, S. Izvekov, A. Das, H. C. Andersen, and G. A. Voth, Journal of Chemical Theory and Computation, 6(3), 954-965 (2010). Homepage: https://github.com/uchicago-voth/MSCG-release
Prerequisites: intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
msmc/1.0.1 -

Description: This software implements MSMC, a method to infer population size and gene flow from multiple genome sequences (Schiffels and Durbin, 2014, Nature Genetics, or Preprint). In short, msmc can infer the scaled population size of a single population as a function of time the timing and nature of population separations between two populations from multiple phased haplotypes. When only two haplotypes are given, MSMC is similar to PSMC, and we call it PSMC' because of subtle differences in the method and the underlying model, which allows PSMC' to infer more accurately the recombination rate. Homepage: https://github.com/stschiff/msmc
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
multiwfn/3.5 -

Description: A multifunctional wavefunction analyzer. Homepage: http://sobereva.com/multiwfn/
Prerequisites: -
Description:
multiwfn/3.6 -

Description: A multifunctional wavefunction analyzer. Homepage: http://sobereva.com/multiwfn/
Prerequisites: intel/2016.4 or intel/2018.3
Description:
multovl/1.3.8203e7d bio

Description: The MULTOVL suite of programs finds multiple overlaps among genomic regions. The MULTOVL algorithm can detect several kinds of region overlaps. In addition to the N-fold overlaps you can detect solitary regions which are the input regions that do not overlap with any other region in the input data set, and union overlaps that is the union of the input regions that overlap at least once somewhere. Homepage: https://sourceforge.net/projects/multovl/ Keyword:bio
Prerequisites: intel/2016.4 or intel/2018.3
Description:
mummer-64bit/3.23 bio

Description: MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it. Homepage: http://mummer.sourceforge.net/ Keyword:bio
Prerequisites: gcc/5.4.0
Description:
mummer/3.23 bio

Description: MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it. Homepage: http://mummer.sourceforge.net/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
mummer/4.0.0beta2 bio

Description: MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it. Homepage: http://mummer.sourceforge.net/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
mumps-metis/5.1.2 -

Description: A parallel sparse direct solver Homepage: http://graal.ens-lyon.fr/MUMPS/
Prerequisites: intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
mumps-parmetis/5.1.2 -

Description: A parallel sparse direct solver Homepage: http://graal.ens-lyon.fr/MUMPS/
Prerequisites: intel/2016.4 and openmpi/2.1.1 or intel/2017.5 and impi/2017.4.239 or intel/2018.3 and openmpi/3.1.2
Description:
muparser/2.2.5 -

Description: muParser is an extensible high performance math expression parser library written in C++. It works by transforming a mathematical expression into bytecode and precalculating constant parts of the expression. Homepage: http://beltoforion.de/article.php?a=muparser
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4
Description:
muparser/2.2.6 -

Description: muParser is an extensible high performance math expression parser library written in C++. It works by transforming a mathematical expression into bytecode and precalculating constant parts of the expression. Homepage: http://beltoforion.de/article.php?a=muparser
Prerequisites: intel/2018.3
Description:
muscle/3.8.31 bio

Description: MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes-only a handful of command-line options are needed to perform common alignment tasks. Homepage: http://drive5.com/muscle/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4
Description:
mysql/5.7 -

Description: MySQL is (as of March 2014) the world's second most widely used open-source relational database management system (RDBMS). Homepage: http://www.mysql.com/
Prerequisites: -
Description:
namd-mpi/2.12 chem NAMD

Description: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Homepage: http://www.ks.uiuc.edu/Research/namd/ Keyword:chem CC-Wiki: NAMD
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
namd-multicore/2.12 chem NAMD

Description: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Homepage: http://www.ks.uiuc.edu/Research/namd/ Keyword:chem CC-Wiki: NAMD
Prerequisites: intel/2016.4 or intel/2016.4 and cuda/8.0.44
Description:
namd-verbs-smp/2.12 chem NAMD

Description: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Homepage: http://www.ks.uiuc.edu/Research/namd/ Keyword:chem CC-Wiki: NAMD
Prerequisites: intel/2016.4 and cuda/8.0.44
Description:
namd-verbs/2.12 chem NAMD

Description: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Homepage: http://www.ks.uiuc.edu/Research/namd/ Keyword:chem CC-Wiki: NAMD
Prerequisites: intel/2016.4
Description:
nanopolish/0.8.5 bio

Description: Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more. Homepage: https://github.com/jts/nanopolish Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
nccl/2.3.5 -

Description: The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs. Homepage: https://developer.nvidia.com/nccl
Prerequisites: gcc/5.4.0 and cuda/9.0.176 or gcc/7.3.0 and cuda/10.0.130 or intel/2018.3 and cuda/10.0.130
Description:
ncl/6.4.0 vis

Description: NCL is an interpreted language designed specifically for scientific data analysis and visualization. Homepage: http://www.ncl.ucar.edu Keyword:vis
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
nco/4.6.6 io

Description: manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5 Homepage: http://nco.sourceforge.net Keyword:io
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2018.3
Description:
ncview/2.1.7 vis

Description: Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc. Homepage: http://meteora.ucsd.edu/~pierce/ncview_home_page.html Keyword:vis
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
nektar++/4.4.1 math

Description: Nektar++ is a tensor product based finite element package designed to allow one to construct efficient classical low polynomial order h-type solvers (where h is the size of the finite element) as well as higher p-order piecewise polynomial order solvers. Homepage: https://www.nektar.info/ Keyword:math
Prerequisites: intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
netcdf-c++-mpi/4.2 io

Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. - Homepage: http://www.unidata.ucar.edu/software/netcdf/ Keyword:io
Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or gcc/7.3.0 and openmpi/3.1.2 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
netcdf-c++/4.2 io

Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. - Homepage: http://www.unidata.ucar.edu/software/netcdf/ Keyword:io
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2018.3
Description:
netcdf-c++4-mpi/4.3.0 io

Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. - Homepage: http://www.unidata.ucar.edu/software/netcdf/ Keyword:io
Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or gcc/7.3.0 and openmpi/3.1.2 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
netcdf-c++4/4.3.0 -

Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: http://www.unidata.ucar.edu/software/netcdf/
Prerequisites: gcc/7.3.0 or intel/2018.3
Description:
netcdf-fortran-mpi/4.4.4 io

Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. - Homepage: http://www.unidata.ucar.edu/software/netcdf/ Keyword:io
Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or gcc/6.4.0 and openmpi/2.1.1 or gcc/7.3.0 and openmpi/3.1.2 or intel/2014.6 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
netcdf-fortran/4.4.4 io

Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: http://www.unidata.ucar.edu/software/netcdf/ Keyword:io
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2018.3
Description:
netcdf-mpi/4.1.3 io

Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: http://www.unidata.ucar.edu/software/netcdf/ Keyword:io
Prerequisites: gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1
Description:
netcdf-mpi/4.4.1.1 io

Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. - Homepage: http://www.unidata.ucar.edu/software/netcdf/ Keyword:io
Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or gcc/6.4.0 and openmpi/2.1.1 or intel/2014.6 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1 or pgi/17.3 and openmpi/2.1.1
Description:
netcdf-mpi/4.6.1 io

Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: http://www.unidata.ucar.edu/software/netcdf/ Keyword:io
Prerequisites: gcc/7.3.0 and openmpi/3.1.2 or intel/2018.3 and openmpi/3.1.2
Description:
netcdf/4.4.1.1 io

Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. - Homepage: http://www.unidata.ucar.edu/software/netcdf/ Keyword:io
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description:
netcdf/4.6.1 io

Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: http://www.unidata.ucar.edu/software/netcdf/ Keyword:io
Prerequisites: gcc/7.3.0 or intel/2018.3
Description:
networkx/1.1 tools

Description: NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. Homepage: https://pypi.python.org/pypi/networkx Keyword:tools
Prerequisites: - or intel/2016.4 or intel/2018.3
Description:
networkx/2.1 tools

Description: Bundle which contains networkx for different Python versions Homepage: http://python.org/ Keyword:tools
Prerequisites: -
Description:
nextgenmap/0.5.0 bio

Description: NextGenMap (NGM) is a flexible and fast read mapping program that is more than twice as fast as BWA, while achieving a mapping sensitivity similar to Stampy or Bowtie2. Homepage: http://cibiv.github.io/NextGenMap/ Keyword:bio
Prerequisites: gcc/5.4.0 and cuda/8.0.44 or gcc/7.3.0
Description:
nextgenmap/0.5.4 bio

Description: NextGenMap (NGM) is a flexible and fast read mapping program that is more than twice as fast as BWA, while achieving a mapping sensitivity similar to Stampy or Bowtie2. Homepage: http://cibiv.github.io/NextGenMap/ Keyword:bio
Prerequisites: gcc/5.4.0 and cuda/8.0.44
Description:
ngs-bits/2018_10 -

Description: ngs-bits contains a lot of tools that are used for NGS-based diagnostics Homepage: https://github.com/imgag/ngs-bits Extensions: kiwisolver-1.0.1, matplotlib-3.0.2, pyparsing-2.3.0, subprocess32-3.5.3
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
ngstools/1.0.1 bio

Description: ngsTools is a collection of programs for population genetics analyses from NGS data, taking into account data statistical uncertainty. The methods implemented in these programs do not rely on SNP or genotype calling, and are particularly suitable for low sequencing depth data. An application note illustrating its application has published (Fumagalli et al., 2014). Homepage: https://github.com/mfumagalli/ngsTools Keyword:bio
Prerequisites: intel/2016.4 or intel/2018.3
Description:
nlopt/2.4.2 math

Description: NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. Homepage: http://ab-initio.mit.edu/wiki/index.php/NLopt Keyword:math
Prerequisites: intel/2016.4 or intel/2018.3
Description:
nodejs/11.1.0 -

Description: Node.js is a platform built on Chrome's JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices. Homepage: http://nodejs.org
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
ntl/11.3.0 -

Description: NTL is a high-performance, portable C++ library providing data structures and algorithms for manipulating signed, arbitrary length integers, and for vectors, matrices, and polynomials over the integers and over finite fields. Homepage: http://www.shoup.net/ntl/
Prerequisites: - or gcc/5.4.0 or gcc/7.3.0
Description:
nwchem/6.6.revision27746 chem

Description: NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity. Homepage: http://www.nwchem-sw.org Keyword:chem
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
oasys-ls-dyna/14.1 -

Description: The Oasys Suite of software, exclusively written for LS-DYNA, is at the leading edge of the pre- and post-processing markets and is used worldwide by many of the largest LS-DYNA customers. Homepage: http://www.oasys-software.com/dyna/en/
Prerequisites: -
Description:
octave/4.2.1 tools

Description: GNU Octave is a high-level interpreted language, primarily intended for numerical computations. - Homepage: http://www.gnu.org/software/octave/ Keyword:tools
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description:
octave/4.2.2 tools

Description: GNU Octave is a high-level interpreted language, primarily intended for numerical computations. Homepage: http://www.gnu.org/software/octave/ Keyword:tools
Prerequisites: gcc/7.3.0
Description:
octopus/7.2 -

Description: Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully ever-increasing range of system types. Electrons are described quantum-mechanically within density-functional theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the pseudopotential approximation. Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Main_Page
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2018.3 and openmpi/3.1.2
Description:
open3dqsar/2.3 chem

Description: Open3DQSAR is an open-source tool aimed at pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields (MIFs). Open3DQSAR can generate steric potential, electron density and MM/QM electrostatic potential fields; furthermore, it can import GRIDKONT binary files produced by GRID, CoMFA/CoMSIA fields (exported from SYBYL with the aid of a small SPL script), and MOE grid interaction fields (exported from and MOE with the aid of a small SVL script). Homepage: http://open3dqsar.sourceforge.net/?Home Keyword:chem
Prerequisites: intel/2016.4 or intel/2018.3
Description:
openbabel/2.4.1 chem

Description: Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Homepage: http://openbabel.org Keyword:chem
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
openblas/0.2.20 math

Description: OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. Homepage: http://xianyi.github.com/OpenBLAS/ Keyword:math
Prerequisites: gcc/5.4.0 or gcc/6.4.0 or gcc/7.3.0 or intel/2016.4
Description:
openblas/0.3.4 math

Description: OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. Homepage: http://xianyi.github.com/OpenBLAS/ Keyword:math
Prerequisites: gcc/7.3.0 or intel/2018.3
Description:
opencolorio/1.0.9 vis

Description: OpenColorIO (OCIO) is a complete color management solution geared towards motion picture production with an emphasis on visual effects and computer animation. Homepage: http://opencolorio.org/ Keyword:vis
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
opencv/2.4.13.3 vis

Description: OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. Homepage: http://opencv.org/ Keyword:vis
Prerequisites: gcc/5.4.0 or gcc/5.4.0 and cuda/8.0.44
Description:
opencv/3.3.0 vis

Description: OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. Homepage: http://opencv.org/ Keyword:vis
Prerequisites: gcc/5.4.0 or gcc/5.4.0 and cuda/8.0.44
Description:
opencv/3.4.3 vis

Description: OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. Homepage: http://opencv.org/ Keyword:vis
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
opencv_contrib/3.4.3 -

Description: OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. Homepage: http://opencv.org/
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
openexr/2.2.1 vis

Description: OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light and Magic for use in computer imaging applications Homepage: http://www.openexr.com/ Keyword:vis
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
openfoam-extend/4.0 -

Description: OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. Homepage: http://www.extend-project.de/
Prerequisites: intel/2016.4 and openmpi/2.0.2
Description:
openfoam/2.3.1 phys OpenFOAM

Description: OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. Homepage: http://www.openfoam.com/ Keyword:phys CC-Wiki: OpenFOAM
Prerequisites: gcc/4.8.5 and openmpi/2.1.1
Description:
openfoam/2.4.0 phys OpenFOAM

Description: OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. Homepage: http://www.openfoam.com/ Keyword:phys CC-Wiki: OpenFOAM
Prerequisites: gcc/5.4.0 and openmpi/2.1.1
Description:
openfoam/3.0.1 phys OpenFOAM

Description: OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. Homepage: http://www.openfoam.com/ Keyword:phys CC-Wiki: OpenFOAM
Prerequisites: gcc/5.4.0 and openmpi/2.1.1 or gcc/7.3.0 and openmpi/3.1.2 or intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
openfoam/4.1 phys OpenFOAM

Description: OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. Homepage: http://www.openfoam.org/ Keyword:phys CC-Wiki: OpenFOAM
Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or gcc/7.3.0 and openmpi/3.1.2 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
openfoam/5.0 phys OpenFOAM

Description: OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. Homepage: http://www.openfoam.org/ Keyword:phys CC-Wiki: OpenFOAM
Prerequisites: gcc/5.4.0 and openmpi/2.1.1 or gcc/7.3.0 and openmpi/3.1.2 or intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
openfoam/6 phys OpenFOAM

Description: OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. Homepage: http://www.openfoam.org/ Keyword:phys CC-Wiki: OpenFOAM
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
openfoam/6.20180813 phys OpenFOAM

Description: OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. Homepage: http://www.openfoam.org/ Keyword:phys CC-Wiki: OpenFOAM
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
openfoam/v1712 phys OpenFOAM

Description: OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. Homepage: http://www.openfoam.com/ Keyword:phys CC-Wiki: OpenFOAM
Prerequisites: gcc/5.4.0 and openmpi/2.1.1 or gcc/7.3.0 and openmpi/3.1.2 or intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
openimageio/1.8.15 vis

Description: OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, and applications. Homepage: http://openimageio.org/ Keyword:vis
Prerequisites: gcc/7.3.0 or intel/2018.3
Description:
openimageio/1.8.7 vis

Description: OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, and applications. Homepage: http://openimageio.org/ Keyword:vis
Prerequisites: gcc/5.4.0
Description:
openmm/7.1.1 chem OpenMM

Description: OpenMM is a toolkit for molecular simulation. - CC-Wiki: OpenMM Homepage: https://simtk.org/home/openmm Keyword:chem
Prerequisites: intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
openmpi/1.10.7 mpi MPI

Description: The Open MPIMessage Passing Interface Project is an open source MPIMessage Passing Interface-2 implementation. Homepage: http://www.open-mpi.org/ Keyword:mpi CC-Wiki: MPIMessage Passing Interface
Prerequisites: intel/2016.4
Description:
openmpi/1.6.5 mpi MPI

Description: The Open MPIMessage Passing Interface Project is an open source MPIMessage Passing Interface-2 implementation. Homepage: http://www.open-mpi.org/ Keyword:mpi CC-Wiki: MPIMessage Passing Interface
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
openmpi/1.8.8 mpi MPI

Description: The Open MPIMessage Passing Interface Project is an open source MPIMessage Passing Interface-2 implementation. Homepage: http://www.open-mpi.org/ Keyword:mpi CC-Wiki: MPIMessage Passing Interface
Prerequisites: gcc/4.8.5 or gcc/5.4.0 or intel/2016.4
Description:
openmpi/2.0.2 mpi MPI

Description: The Open MPIMessage Passing Interface Project is an open source MPIMessage Passing Interface-2 implementation. Homepage: http://www.open-mpi.org/ Keyword:mpi CC-Wiki: MPIMessage Passing Interface
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2016.4 and cuda/8.0.44 or intel/2017.1 or pgi/17.3
Description:
openmpi/2.1.1 mpi MPI

Description: The Open MPIMessage Passing Interface Project is an open source MPIMessage Passing Interface-2 implementation. Homepage: http://www.open-mpi.org/ Keyword:mpi CC-Wiki: MPIMessage Passing Interface
Prerequisites: gcc/4.8.5 or gcc/5.4.0 or gcc/5.4.0 and cuda/10.0.130 or gcc/5.4.0 and cuda/8.0.44 or gcc/5.4.0 and cuda/9.0.176 or gcc/6.4.0 or gcc/6.4.0 and cuda/9.0.176 or gcc/7.3.0 or intel/2014.6 or intel/2016.4 or intel/2016.4 and cuda/10.0.130 or intel/2016.4 and cuda/8.0.44 or intel/2016.4 and cuda/9.0.176 or intel/2017.1 or intel/2017.5 or intel/2017.5 and cuda/9.0.176 or pgi/13.10 or pgi/17.3
Description:
openmpi/3.1.2 mpi MPI

Description: The Open MPIMessage Passing Interface Project is an open source MPIMessage Passing Interface-3 implementation. Homepage: http://www.open-mpi.org/ Keyword:mpi CC-Wiki: MPIMessage Passing Interface
Prerequisites: gcc/7.3.0 or gcc/7.3.0 and cuda/10.0.130 or intel/2018.3 or intel/2018.3 and cuda/10.0.130
Description:
openmpi/openmpi/2.1.1 mpi

Description: The Open MPIMessage Passing Interface Project is an open source MPIMessage Passing Interface-2 implementation. Homepage: http://www.open-mpi.org/
Prerequisites: gcc/5.4.0 and cuda/10.0.130
Description:
openmpi/openmpi/openmpi/2.1.1 mpi

Description: The Open MPIMessage Passing Interface Project is an open source MPIMessage Passing Interface-2 implementation. Homepage: http://www.open-mpi.org/
Prerequisites: gcc/5.4.0 and cuda/10.0.130
Description:
openslide/3.4.1 vis

Description: OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides). Homepage: http://openslide.org/ Keyword:vis
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
orca/3.0.3 chem ORCA

Description: ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. Homepage: http://cec.mpg.de/forum/ Keyword:chem CC-Wiki: ORCA
Prerequisites: intel/2016.4 and openmpi/1.6.5
Description:
orca/4.0.0.2 chem ORCA

Description: ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. Homepage: http://cec.mpg.de/forum/ Keyword:chem CC-Wiki: ORCA
Prerequisites: intel/2016.4 and openmpi/2.0.2
Description:
orca/4.0.1.2 chem ORCA

Description: ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. Homepage: http://cec.mpg.de/forum/ Keyword:chem CC-Wiki: ORCA
Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.0.2
Description:
orthomcl/2.0.9 -

Description: OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. Homepage: http://orthomcl.org/
Prerequisites: - or gcc/5.4.0 or intel/2018.3
Description:
osl/1.9.6 vis

Description: Advanced shading language for production GI renderers Homepage: https://github.com/imageworks/OpenShadingLanguage Keyword:vis
Prerequisites: gcc/5.4.0
Description:
osu-micro-benchmarks/5.3.2 -

Description: OSU Micro-Benchmarks Homepage: http://mvapich.cse.ohio-state.edu/benchmarks/
Prerequisites: intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
p4est/1.1 math

Description: The p4est software library enables the dynamic management of a collection of adaptive octrees, conveniently called a forest of octrees. p4est is designed to work in parallel and scales to hundreds of thousands of processor cores. It is free software released under GNU General Public Licence version 2, or (at your option) any later version. Homepage: http://www.p4est.org/ Keyword:math
Prerequisites: gcc/5.4.0 and openmpi/2.1.1 or gcc/7.3.0 and openmpi/3.1.2 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
p4vasp/0.3.30 -

Description: p4vasp is the VASP Visualization Tool that can be used to display structure, unitcell, supercell, charge/probability/spin density, local potential, forces, velocities, dynamics, measure distances and angles, .... It can be used also to analyze electronic properties, total and local DOS and band structure Homepage: http://www.p4vasp.at
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
paml/4.9h -

Description: PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2018.3
Description:
papi/5.6.0 -

Description: PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack. Homepage: http://icl.cs.utk.edu/projects/papi/
Prerequisites: -
Description:
parallel/20160722 -

Description: parallel: Build and execute shell commands in parallel Homepage: http://savannah.gnu.org/projects/parallel/
Prerequisites: -
Description:
parallel/20170622 -

Description: parallel: Build and execute shell commands in parallel Homepage: http://savannah.gnu.org/projects/parallel/
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
paraview-offscreen-gpu/5.4.0 vis Visualization

Description: ParaView is a scientific parallel visualizer. Homepage: http://www.paraview.org Keyword:vis CC-Wiki: Visualization
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
paraview-offscreen-gpu/5.4.1 vis Visualization

Description: ParaView is a scientific parallel visualizer. Homepage: http://www.paraview.org Keyword:vis CC-Wiki: Visualization
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
paraview-offscreen/5.3.0 vis Visualization

Description: ParaView is a scientific parallel visualizer. - Homepage: http://www.paraview.org Keyword:vis CC-Wiki: Visualization
Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1
Description:
paraview-offscreen/5.5.2 vis Visualization

Description: ParaView is a scientific parallel visualizer. Homepage: http://www.paraview.org Keyword:vis CC-Wiki: Visualization
Prerequisites: intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
paraview/5.3.0 vis Visualization

Description: ParaView is a scientific parallel visualizer. - Homepage: http://www.paraview.org Keyword:vis CC-Wiki: Visualization
Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1
Description:
paraview/5.5.2 vis Visualization

Description: ParaView is a scientific parallel visualizer. Homepage: http://www.paraview.org Keyword:vis CC-Wiki: Visualization
Prerequisites: gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1
Description:
parmetis/4.0.3 math

Description: ParMETIS is an MPIMessage Passing Interface-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes. Homepage: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview Keyword:math
Prerequisites: gcc/5.4.0 and openmpi/2.1.1 or gcc/7.3.0 and openmpi/3.1.2 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
parmgridgen/1.0 -

Description: ParMGridGen is an MPIMessage Passing Interface-based parallel library that is based on the serial package MGridGen, that implements (serial) algorithms for obtaining a sequence of successive coarse grids that are well-suited for geometric multigrid methods. Homepage: http://www-users.cs.umn.edu/~moulitsa/software.html
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
pbbam/20170508 bio

Description: The pbbam software package provides components to create, query, and edit PacBio BAM files and associated indices. Homepage: http://pbbam.readthedocs.io/ Keyword:bio
Prerequisites: intel/2016.4 or intel/2018.3
Description:
pbdagcon/20170330 bio

Description: pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus) which is a sequence consensus algorithm based on using directed acyclic graphs to encode multiple sequence alignment. Homepage: https://github.com/PacificBiosciences/pbdagcon Keyword:bio
Prerequisites: intel/2016.4 or intel/2018.3
Description:
pbsuite/15.8.24 bio

Description: PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. Homepage: https://sourceforge.net/p/pb-jelly/wiki/Home/ Keyword:bio
Prerequisites: intel/2016.4
Description:
pcl/1.8.1 math

Description: The Point Cloud Library (PCL) is a standalone, large scale, open project for 2D/3D image and point cloud processing. Homepage: http://pointclouds.org/ Keyword:math
Prerequisites: gcc/5.4.0
Description:
pcmsolver/1.1.10 chem

Description: An API for the Polarizable Continuum Model. Homepage: https://pcmsolver.readthedocs.org Keyword:chem
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
pcmsolver/1.2.1 chem

Description: An API for the Polarizable Continuum Model. Homepage: https://pcmsolver.readthedocs.org Keyword:chem
Prerequisites: intel/2018.3
Description:
pear/0.9.10 bio

Description: PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. Homepage: http://sco.h-its.org/exelixis/web/software/pear/ Keyword:bio
Prerequisites: intel/2016.4 or intel/2018.3
Description:
penncnv/1.0.4 -

Description: PennCNV is a free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays. Homepage: http://penncnv.openbioinformatics.org/en/latest/
Prerequisites: -
Description:
percolator/3-02 -

Description: Semi-supervised learning for peptide identification from shotgun proteomics datasets Homepage: https://github.com/percolator
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4
Description:
perl/5.16.3 tools Perl

Description: Larry Wall's Practical Extraction and Report Language Homepage: http://www.perl.org/ Extensions: AnyEvent-7.04, B::LintSubs-0.06, Bio::Perl-1.6.901, boolean-0.30, Class::Load-0.20, Class::Singleton-1.4, Data::OptList-0.107, Data::Stag-0.11, Data::Types-0.09, DateTime-1.01, DateTime::Locale-0.45, DateTime::TimeZone-1.58, DateTime::Tiny-1.04, DB_File-1.827, DBI-1.625, Devel::GlobalDestruction-0.11, Dist::CheckConflicts-0.02, Eval::Closure-0.08, File::Slurp-9999.19, HTML::Entities-3.70, HTML::Tagset-3.20, HTTPHyperText Transfer Protocol::Date-6.02, HTTPHyperText Transfer Protocol::Request-6.06, IO::HTML-1.00, IO::String-1.08, IO::Tty-1.10, IPC::Run-0.92, List::MoreUtils-0.33, LWP::MediaTypes-6.02, Module::Implementation-0.06, Module::Runtime-0.013, Moose-2.0801, Mouse-1.05, MRO::Compat-0.12, Package::DeprecationManager-0.13, Package::Stash-0.34, Params::Util-1.07, Params::Validate-1.07, Sub::Exporter-0.985, Sub::Exporter::Progressive-0.001010, Sub::Install-0.926, Sub::Name-0.05, Sub::Uplevel-0.24, Test::Exception-0.31, Test::Fatal-0.010, Test::Harness-3.28, Test::Output-1.01, Test::Requires-0.06, Test::Simple-0.98, Test::Tester-0.108, Test::Warn-0.24, Tie::IxHash-1.23, Tree::DAG_Node-1.11, Try::Tiny-0.12, URI-1.60, XML::NamespaceSupport-1.11, XML::SAX-0.99, XML::SAX::Base-1.08 Keyword:tools CC-Wiki: Perl
Prerequisites: -
Description:
perl/5.22.2 tools Perl

Description: Perl 5 is a highly capable, feature-rich programming language with over 29 years of development. Homepage: https://www.perl.org/ Keyword:tools CC-Wiki: Perl
Prerequisites: -
Description:
perl/5.22.4 tools Perl

Description: Larry Wall's Practical Extraction and Report Language Homepage: http://www.perl.org/ Extensions: Acme::Damn-0.08, Algorithm::Dependency-1.110, Algorithm::Diff-1.1903, aliased-0.34, AnyData-0.12, AnyEvent-7.12, AppConfig-1.71, Archive::Extract-0.76, Authen::SASL-2.16, B::Lint-1.20, Bit::Vector-7.4, boolean-0.45, Bundle::BioPerl-2.1.9, Canary::Stability-2011, Capture::Tiny-0.40, Carp-1.38, Class::Accessor-0.34, Class::Data::Inheritable-0.08, Class::DBI-3.0.17, Class::DBI::SQLite-0.11, Class::Inspector-1.28, Class::ISA-0.36, Class::Load-0.23, Class::Load::XS-0.09, Class::Singleton-1.5, Class::Trigger-0.14, Clone-0.38, Config::General-2.61, CPANPLUS-0.9160, Crypt::DES-2.07, Crypt::Rijndael-1.13, Cwd::Guard-0.05, Data::Dumper::Concise-2.022, Data::Grove-0.08, Data::OptList-0.110, Data::Section::Simple-0.07, Data::Stag-0.14, Data::Types-0.09, Data::UUID-1.221, Date::Handler-1.2, Date::Language-2.30, DateTime-1.28, DateTime::Locale-1.03, DateTime::TimeZone-1.98, DateTime::Tiny-1.04, DBD::AnyData-0.110, DBD::SQLite-1.50, DBI-1.636, DBIx::Admin::TableInfo-3.01, DBIx::ContextualFetch-1.03, DBIx::Simple-1.35, Devel::CheckCompiler-0.06, Devel::GlobalDestruction-0.13, Devel::StackTrace-2.01, Digest::HMAC-1.03, Digest::SHA1-2.13, Dist::CheckConflicts-0.11, Email::Date::Format-1.005, Encode::Locale-1.05, Error-0.17024, Eval::Closure-0.13, Exception::Class-1.40, Expect-1.32, Exporter-5.72, Exporter::Declare-0.114, Exporter::Tiny-0.042, ExtUtils::Config-0.008, ExtUtils::Helpers-0.022, ExtUtils::InstallPaths-0.011, ExtUtils::MakeMaker-7.18, Fennec::Lite-0.004, File::CheckTree-4.42, File::Copy::Recursive-0.38, File::Find::Rule-0.34, File::Find::Rule::Perl-1.15, File::HomeDir-1.00, File::Listing-6.04, File::ShareDir::Install-0.11, File::Slurp-9999.19, File::Slurp::Tiny-0.004, File::Spec-3.62, File::Which-1.21, Font::TTF-1.05, forks-0.36, FreezeThaw-0.5001, GD-2.68, GD::Graph-1.52, Getopt::Long-2.48, Git-0.41, GO-0.04, GO::Utils-0.15, Graph-0.9704, Hash::Merge-0.200, HTML::Entities::Interpolate-1.09, HTML::Form-6.03, HTML::Parser-3.72, HTML::Tagset-3.20, HTML::Tree-5.03, HTTPHyperText Transfer Protocol::Cookies-6.01, HTTPHyperText Transfer Protocol::Daemon-6.01, HTTPHyperText Transfer Protocol::Date-6.02, HTTPHyperText Transfer Protocol::Negotiate-6.01, HTTPHyperText Transfer Protocol::Request-6.11, HTTPHyperText Transfer Protocol::Tiny-0.058, Ima::DBI-0.35, Import::Into-1.002005, Inline-0.80, Inline::C-0.78, IO::All-0.87, IO::HTML-1.001, IO::Socket::SSL-2.027, IO::String-1.08, IO::Stringy-2.111, IO::Tty-1.12, IPC::Run-0.94, IPC::Run3-0.048, JSON-2.90, Lingua::EN::PluralToSingular-0.18, List::AllUtils-0.10, List::MoreUtils-0.415, Log::Handler-0.84, Log::Message-0.08, Log::Message::Simple-0.10, LWP::MediaTypes-6.02, LWP::Simple-6.15, Mail::Util-2.18, Math::Bezier-0.01, Math::Round-0.07, Math::VecStat-0.08, Meta::Builder-0.003, MIME::Lite-3.030, MIME::Types-2.13, Mock::Quick-1.110, Module::Build-0.4218, Module::Build::Tiny-0.039, Module::Build::XSUtil-0.16, Module::Implementation-0.09, Module::Pluggable-5.2, Module::Runtime-0.014, Moo-2.001001, Moose-2.1801, Mouse-v2.4.5, MRO::Compat-0.12, Net::HTTPHyperText Transfer Protocol-6.09, Net::SMTP::SSL-1.03, Net::SNMP-v6.0.1, Number::Compare-0.03, Number::Format-1.75, Object::Accessor-0.48, Package::DeprecationManager-0.16, Package::Stash-0.37, Package::Stash::XS-0.28, Params::Util-1.07, Params::Validate-1.24, Parse::RecDescent-1.967013, Perl::Unsafe::Signals-0.03, Pod::LaTeX-0.61, Pod::Plainer-1.04, Pod::POM-2.01, Readonly-2.04, Regexp::Common-2016020301, Scalar::Util-1.45, Set::Array-0.30, Set::IntSpan-1.19, Set::IntSpan::Fast-1.15, Set::Scalar-1.29, Shell-0.73, SQL::Abstract-1.81, SQL::Statement-1.410, Statistics::Basic-1.6611, Statistics::Descriptive-3.0612, strictures-2.000003, Sub::Exporter-0.987, Sub::Exporter::Progressive-0.001011, Sub::Install-0.928, Sub::Name-0.15, Sub::Uplevel-0.25, Sub::Uplevel-0.25, SVG-2.77, Switch-2.17, Sys::SigAction-0.23, Template-2.26, Template::Plugin::Number::Format-1.06, Term::ReadKey-2.33, Term::UI-0.46, Test::ClassAPI-1.06, Test::Deep-1.120, Test::Differences-0.64, Test::Exception-0.43, Test::Exception::LessClever-0.006, Test::Fatal-0.014, Test::Harness-3.36, Test::LeakTrace-0.15, Test::Most-0.34, Test::NoWarnings-1.04, Test::Output-1.03, Test::Pod-1.51, Test::Requires-0.10, Test::Simple-1.302019, Test::Version-2.03, Test::Warn-0.30, Test::Warnings-0.026, Text::Balanced-2.03, Text::CSV-1.33, Text::Diff-1.44, Text::Format-0.59, Text::Glob-0.09, Text::Iconv-1.7, Text::Soundex-3.05, Text::Table-1.130, Tie::Function-0.02, Tie::IxHash-1.23, Time::HiRes-1.9754, Time::Piece-1.31, Time::Piece::MySQL-0.06, Tree::DAG_Node-1.29, Try::Tiny-0.24, UNIVERSAL::moniker-0.08, URI-1.71, version-0.9916, Want-0.29, WWW::RobotRules-6.02, XML::Bare-0.53, XML::DOM-1.46, XML::LibXML-2.0132, XML::NamespaceSupport-1.11, XML::SAX-0.99, XML::SAX-1.00, XML::SAX::Base-1.08, XML::SAX::Writer-0.56, XML::Simple-2.22, XML::Tiny-2.06, XML::Twig-3.49, XML::Writer-0.625, XML::XPath-1.36 Keyword:tools CC-Wiki: Perl
Prerequisites: -
Description:
perl4-corelibs/0.003 tools

Description: Libraries historically supplied with Perl 4 Homepage: https://metacpan.org/pod/Perl4::CoreLibs Keyword:tools
Prerequisites: -
Description:
petsc-64bits/3.10.2 tools

Description: PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. Homepage: http://www.mcs.anl.gov/petsc Keyword:tools
Prerequisites: intel/2018.3 and openmpi/3.1.2
Description:
petsc-64bits/3.7.5 tools

Description: PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. Homepage: http://www.mcs.anl.gov/petsc Keyword:tools
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1
Description:
petsc-complex/3.9.0 -

Description: PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. Homepage: http://www.mcs.anl.gov/petsc
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
petsc-debug/3.8.2 tools

Description: PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. Homepage: http://www.mcs.anl.gov/petsc Keyword:tools
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
petsc/2.3.3 tools

Description: PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. Homepage: http://www.mcs.anl.gov/petsc Keyword:tools
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
petsc/3.1-p8 tools

Description: PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. Homepage: http://www.mcs.anl.gov/petsc Keyword:tools
Prerequisites: gcc/5.4.0 and openmpi/1.8.8
Description:
petsc/3.10.2 tools

Description: PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. Homepage: http://www.mcs.anl.gov/petsc Keyword:tools
Prerequisites: intel/2018.3 and openmpi/3.1.2
Description:
petsc/3.7.5 tools

Description: PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. Homepage: http://www.mcs.anl.gov/petsc Keyword:tools
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1
Description:
petsc/3.8.2 tools

Description: PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. Homepage: http://www.mcs.anl.gov/petsc Keyword:tools
Prerequisites: intel/2016.4 and openmpi/2.1.1 or intel/2017.5 and impi/2017.4.239
Description:
petsc/3.9.0 tools

Description: PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. Homepage: http://www.mcs.anl.gov/petsc Keyword:tools
Prerequisites: gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1
Description:
pfft/1.0.8-alpha math

Description: PFFT is a software library for computing massively parallel, fast Fourier transformations on distributed memory architectures. PFFT can be understood as a generalization of FFTW-MPIMessage Passing Interface to multidimensional data decomposition. Homepage: https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software.php.en Keyword:math
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2018.3 and openmpi/3.1.2
Description:
pgi/13.10 tools

Description: C, C++ and Fortran compilers from The Portland Group - PGI Homepage: http://www.pgroup.com/
Prerequisites: -
Description:
pgi/17.3 tools

Description: C, C++ and Fortran compilers from The Portland Group - PGI - Homepage: http://www.pgroup.com/
Prerequisites: -
Description:
pgplot/5.2 vis

Description: The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs. It is intended for making graphical images of publication quality with minimum effort on the part of the user. For most applications, the program can be device-independent, and the output can be directed to the appropriate device at run time. Homepage: http://www.astro.caltech.edu/~tjp/pgplot/ Keyword:vis
Prerequisites: intel/2016.4
Description:
phana/20150831 -

Description: This program reads the binary file created by fix_phonon and helps to analyse the phonon related info. Homepage: https://github.com/lingtikong/phana
Prerequisites: gcc/5.4.0
Description:
phylip/3.697 bio

Description: PHYLIP is a free package of programs for inferring phylogenies. Homepage: http://evolution.genetics.washington.edu/phylip Keyword:bio
Prerequisites: intel/2016.4 or intel/2018.3
Description:
phylobayes-mpi/20180420 -

Description: A Bayesian software for phylogenetic reconstruction using mixture models Homepage: https://github.com/bayesiancook/pbmpi
Prerequisites: intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
phylobayes/4.1c bio

Description: A Bayesian software for phylogenetic reconstruction using mixture models Homepage: http://megasun.bch.umontreal.ca/People/lartillot/www/download.html Keyword:bio
Prerequisites: intel/2016.4
Description:
phyx/0.999 -

Description: phyx performs phylogenetics analyses on trees and sequences. Homepage: https://github.com/FePhyFoFum/phyx
Prerequisites: intel/2016.4 or intel/2018.3
Description:
picard/2.1.1 bio

Description: A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format. - Homepage: http://broadinstitute.github.io/picard/ Keyword:bio
Prerequisites: -
Description:
picard/2.10.7 bio

Description: A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format. Homepage: http://broadinstitute.github.io/picard/ Keyword:bio
Prerequisites: -
Description:
picard/2.17.3 bio

Description: A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format. Homepage: http://broadinstitute.github.io/picard/ Keyword:bio
Prerequisites: -
Description:
picard/2.18.9 bio

Description: A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format. Homepage: http://broadinstitute.github.io/picard/ Keyword:bio
Prerequisites: -
Description:
pilon/1.22 bio

Description: Pilon is an automated genome assembly improvement and variant detection tool To run pilon, please use: java -jar $EBROOTPILON/pilon-1.22.jar ... Use -Xmx Java option to adjust memory as in: java -Xmx8G -jar $EBROOTPILON/pilon-1.22.jar ... Homepage: https://github.com/broadinstitute/pilon Keyword:bio
Prerequisites: -
Description:
pindel/0.2.5b8 bio

Description: Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads. Homepage: http://gmt.genome.wustl.edu/packages/pindel/ Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
plast/2.3.2 -

Description: PLAST is a parallel alignment search tool for comparing large protein banks Homepage: http://www.irisa.fr/symbiose/projects/plast/
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
platanus/1.2.4 -

Description: PLATform for Assembling NUcleotide Sequences Homepage: http://platanus.bio.titech.ac.jp/
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
platypus/0.8.1 bio

Description: Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. Homepage: http://www.well.ox.ac.uk/platypus Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
plink/1.07 bio

Description: PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results. Homepage: http://pngu.mgh.harvard.edu/~purcell/plink/ Keyword:bio
Prerequisites: intel/2016.4 or intel/2018.3
Description:
plink/1.9b_4.1-x86_64 bio

Description: plink-1.9-x86_64: Whole-genome association analysis toolset Homepage: https://www.cog-genomics.org/plink/1.9/ Keyword:bio
Prerequisites: -
Description:
plink/1.9b_5.2-x86_64 bio

Description: plink-1.9-x86_64: Whole-genome association analysis toolset Homepage: https://www.cog-genomics.org/plink/1.9/ Keyword:bio
Prerequisites: -
Description:
plumed/2.3.0 chem

Description: PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. - Homepage: http://www.plumed-code.org Keyword:chem
Prerequisites: gcc/5.4.0 and cuda/8.0.44 and openmpi/2.1.1 or gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1 or intel/2017.5 and cuda/9.0.176 and openmpi/2.1.1 or intel/2017.5 and openmpi/2.1.1
Description:
plumed/2.3.2 chem

Description: PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. Homepage: http://www.plumed-code.org Keyword:chem
Prerequisites: intel/2016.4 and cuda/8.0.44 and openmpi/2.0.2 or intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description:
plumed/2.3.7 chem

Description: PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. Homepage: http://www.plumed-code.org Keyword:chem
Prerequisites: gcc/7.3.0 and openmpi/3.1.2 or intel/2018.3 and openmpi/3.1.2
Description:
plumed/2.4.2 chem

Description: PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. Homepage: http://www.plumed-code.org Keyword:chem
Prerequisites: gcc/6.4.0 and cuda/9.0.176 and openmpi/2.1.1 or gcc/6.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1
Description:
plumed/2.4.3 chem

Description: PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. Homepage: http://www.plumed-code.org Keyword:chem
Prerequisites: intel/2018.3 and openmpi/3.1.2
Description:
pnetcdf/1.8.1 io

Description: PnetCDF is a high-performance parallel I/O library for accessing files in format compatibility with Unidata's NetCDF, specifically the formats of CDF-1, 2, and 5. The CDF-5 file format, an extension of CDF-2, supports unsigned data types and uses 64-bit integers to allow users to define large dimensions, attributes, and variables (> 2B array elements). Homepage: https://trac.mcs.anl.gov/projects/parallel-netcdf Keyword:io
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description:
pnetcdf/1.9.0 io

Description: PnetCDF is a high-performance parallel I/O library for accessing files in format compatibility with Unidata's NetCDF, specifically the formats of CDF-1, 2, and 5. The CDF-5 file format, an extension of CDF-2, supports unsigned data types and uses 64-bit integers to allow users to define large dimensions, attributes, and variables (> 2B array elements). Homepage: https://trac.mcs.anl.gov/projects/parallel-netcdf Keyword:io
Prerequisites: intel/2018.3 and openmpi/3.1.2
Description:
postgresql/10.2 tools

Description: PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation. Homepage: https://www.postgresql.org/ Keyword:tools
Prerequisites: -
Description:
postgresql/10.3 tools

Description: PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation. Homepage: https://www.postgresql.org/ Keyword:tools
Prerequisites: gcc/7.3.0
Description:
postgresql/9.6.6 tools

Description: PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation. Homepage: https://www.postgresql.org/ Keyword:tools
Prerequisites: -
Description:
pplacer/1.1.alpha19 bio

Description: Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis. Homepage: http://matsen.fhcrc.org/pplacer/ Keyword:bio
Prerequisites: -
Description:
prank/140110 -

Description: PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. Homepage: http://code.google.com/p/prank-msa/
Prerequisites: gcc/5.4.0
Description:
prank/140603 -

Description: PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. Homepage: http://wasabiapp.org/software/prank/
Prerequisites: gcc/5.4.0
Description:
prank/170427 -

Description: PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. Homepage: http://wasabiapp.org/software/prank/
Prerequisites: gcc/7.3.0 or intel/2018.3
Description:
prinseq/0.20.4 bio

Description: A bioinformatics tool to PRe-process and show INformation of SEQuence data. Homepage: http://prinseq.sourceforge.net Extensions: Cairo-1.106, Contextual::Return-0.004008, Digest::MD5-2.54, ExtUtils::Depends-0.405, ExtUtils::PkgConfig-1.15, File::Spec-3.62, File::Temp-0.2304, Getopt::Long-2.48, JSON-2.90, Math::Cephes::Matrix-0.5304, Math::MatrixReal-2.12, MIME::Base64-3.15, Pod::Usage-1.68, Statistics::PCA-0.0.1, Text::SimpleTable-2.03, Want-0.26 Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
prodigal/2.6.3 bio

Description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Homepage: http://prodigal.ornl.gov/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
proj/4.9.3 geo

Description: Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates - Homepage: http://trac.osgeo.org/proj/ Keyword:geo
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1
Description:
proj/5.1.0 geo

Description: Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates Homepage: http://trac.osgeo.org/proj/ Keyword:geo
Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.0.2
Description:
proj/5.2.0 geo

Description: Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates Homepage: http://trac.osgeo.org/proj/ Keyword:geo
Prerequisites: intel/2018.3 and openmpi/3.1.2
Description:
proj4-fortran/1.0 -

Description: proj4-fortran is a f77 and f90 wrappers for proj4, a cartograohic projections library. Homepage: https://github.com/mhagdorn/proj4-fortran
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
proovread/2.14.1 -

Description: PacBio hybrid error correction through iterative short read consensus Homepage: https://github.com/BioInf-Wuerzburg/proovread
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
protobuf/3.3.0 tools

Description: Google Protocol Buffers Homepage: https://github.com/google/protobuf/ Keyword:tools
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
psi4/1.1 chem

Description: PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform computations with more than 2500 basis functions running serially or in parallel. Homepage: http://www.psicode.org/ Keyword:chem
Prerequisites: intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
psmc/0.6.5 bio

Description: This software package infers population size history from a diploid sequence using the Pairwise Sequentially Markovian Coalescent (PSMC) model. Homepage: https://github.com/lh3/psmc Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
pwrf/3.8.1 -

Description: Based on extensive experience with mesoscale modeling in the polar regions by the Polar Meteorology Group of the Byrd Polar and Climate Research Center at The Ohio State University, the Weather Research and Forecasting model (WRF) has been modified for use in the Polar Regions (referred to as the Polar WRF). Compiled with -DNO_LEAP_CALENDAR Homepage: http://polarmet.osu.edu/hines/PWRF/
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
pwrf/3.9.1 -

Description: Based on extensive experience with mesoscale modeling in the polar regions by the Polar Meteorology Group of the Byrd Polar and Climate Research Center at The Ohio State University, the Weather Research and Forecasting model (WRF) has been modified for use in the Polar Regions (referred to as the Polar WRF). Compiled with -DNO_LEAP_CALENDAR Homepage: http://polarmet.osu.edu/hines/PWRF/
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
pypy/5.8 tools

Description: PyPy is a fast, compliant alternative implementation of the Python language (2.7.13 and 3.5.3). Homepage: https://pypy.org/index.html Keyword:tools
Prerequisites: -
Description:
pyqt/4.12 -

Description: PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework. Homepage: http://www.riverbankcomputing.co.uk/software/pyqt
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
python/2.7.13 tools Python

Description: Python is a programming language that lets you work more quickly and integrate your systems more effectively. Homepage: http://python.org/ Keyword:tools CC-Wiki: Python
Prerequisites: -
Description:
python/2.7.14 tools Python

Description: Python is a programming language that lets you work more quickly and integrate your systems more effectively. Homepage: http://python.org/ Extensions: pip-9.0.1, pysqlite-2.8.3, readline-6.2.4.1, setuptools-37.0.0, virtualenv-15.1.0, wheel-0.30.0 Keyword:tools CC-Wiki: Python
Prerequisites: -
Description:
python/3.5.2 tools Python

Description: Python is a programming language that lets you work more quickly and integrate your systems more effectively. Homepage: http://python.org/ Keyword:tools CC-Wiki: Python
Prerequisites: -
Description:
python/3.5.4 tools Python

Description: Python is a programming language that lets you work more quickly and integrate your systems more effectively. Homepage: http://python.org/ Extensions: pip-9.0.1, readline-6.2.4.1, setuptools-37.0.0, virtualenv-15.1.0, wheel-0.30.0 Keyword:tools CC-Wiki: Python
Prerequisites: -
Description:
python/3.6.3 tools Python

Description: Python is a programming language that lets you work more quickly and integrate your systems more effectively. Homepage: http://python.org/ Extensions: pip-9.0.1, readline-6.2.4.1, setuptools-37.0.0, virtualenv-15.1.0, wheel-0.30.0 Keyword:tools CC-Wiki: Python
Prerequisites: -
Description:
python/3.7.0 tools Python

Description: Python is a programming language that lets you work more quickly and integrate your systems more effectively. Homepage: http://python.org/ Extensions: gnureadline-6.3.8, pip-18.0, setuptools-40.0.0, virtualenv-16.0.0, wheel-0.31.1 Keyword:tools CC-Wiki: Python
Prerequisites: -
Description:
python27-mpi4py/2.0.0 tools

Description: MPIMessage Passing Interface for Python (mpi4py) provides bindings of the Message Passing Interface (MPIMessage Passing Interface) standard for the Python programming language, allowing any Python program to exploit multiple processors. Homepage: https://bitbucket.org/mpi4py/mpi4py Keyword:tools
Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1
Description:
python27-scipy-stack/2017a math

Description: Bundle which contains the Scientific Python stack, including Cycler, mpmath, numpy, scipy, sympy, pandas, matplotlib, ipython_genutils, traitlets, ptyprocess, pathlib2, pickleshare, pexpect, simplegeneric, ipython, ipykernel, jupyter_client, jupyter_core, pyzmq, tornado, futures and ipyparallel. Homepage: http://python.org/ Extensions: arff-2.1.0, backports.shutil_get_terminal_size-1.0.0, backports_abc-0.4, bitstring-3.1.5, blist-1.3.6, certifi-2016.8.8, cryptography-1.7.1, Cycler-0.10.0, Cython-0.25.2, dateutil-2.6.0, deap-1.0.2, decorator-4.0.10, ecdsa-0.13, enum34-1.1.6, funcsigs-1.0.2, functools32-3.2.3-2, ipykernel-4.4.1, ipython-5.1.0, ipython_genutils-0.1.0, ipywidgets-5.2.2, Jinja2-2.8, jsonschema-2.5.1, jupyter_client-4.3.0, jupyter_core-4.1.1, lockfile-0.12.2, MarkupSafe-0.23, matplotlib-1.5.3, mistune-0.7.3, mock-2.0.0, mpmath-0.19, nbformat-4.1.0, netaddr-0.7.18, netifaces-0.10.5, nose-1.3.7, notebook-4.2.2, numpy-1.12.0, pandas-0.19.2, paramiko-2.1.1, path.py-10.0, pathlib2-2.1.0, paycheck-1.0.2, pbr-1.10.0, pexpect-4.2.0, pickleshare-0.7.4, prompt_toolkit-1.0.9, ptyprocess-0.5.1, pycrypto-2.6.1, Pygments-2.1.3, pyparsing-2.1.10, pysqlite-2.8.3, pytz-2016.10, PyZMQ-16.0.2, requests-2.11.0, scipy-0.18.1, setuptools-32.3.1, simplegeneric-0.8.1, singledispatch-3.4.0.3, six-1.10.0, sympy-1.0, terminado-0.6, tornado-4.4.1, traitlets-4.2.2, widgetsnbextension-1.2.6 Keyword:math
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description:
python35-mpi4py/2.0.0 tools

Description: MPIMessage Passing Interface for Python (mpi4py) provides bindings of the Message Passing Interface (MPIMessage Passing Interface) standard for the Python programming language, allowing any Python program to exploit multiple processors. Homepage: https://bitbucket.org/mpi4py/mpi4py Keyword:tools
Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1
Description:
python35-scipy-stack/2017a math

Description: Bundle which contains the Scientific Python stack, including Cycler, mpmath, numpy, scipy, sympy, pandas, matplotlib, ipython_genutils, traitlets, ptyprocess, pathlib2, pickleshare, pexpect, simplegeneric, ipython, ipykernel, jupyter_client, jupyter_core, pyzmq, tornado, futures and ipyparallel. Homepage: http://python.org/ Extensions: arff-2.1.0, backports.shutil_get_terminal_size-1.0.0, bitstring-3.1.5, blist-1.3.6, certifi-2016.8.8, cryptography-1.7.1, Cycler-0.10.0, Cython-0.25.2, dateutil-2.6.0, deap-1.0.2, decorator-4.0.10, ecdsa-0.13, enum34-1.1.6, funcsigs-1.0.2, ipykernel-4.4.1, ipython-5.1.0, ipython_genutils-0.1.0, ipywidgets-5.2.2, Jinja2-2.8, jsonschema-2.5.1, jupyter_client-4.3.0, jupyter_core-4.1.1, lockfile-0.12.2, MarkupSafe-0.23, matplotlib-1.5.3, mistune-0.7.3, mock-2.0.0, mpmath-0.19, nbformat-4.1.0, netaddr-0.7.18, netifaces-0.10.5, nose-1.3.7, notebook-4.2.2, numpy-1.12.0, pandas-0.19.2, paramiko-2.1.1, path.py-10.0, pathlib2-2.1.0, paycheck-1.0.2, pbr-1.10.0, pexpect-4.2.0, pickleshare-0.7.4, prompt_toolkit-1.0.9, ptyprocess-0.5.1, pycrypto-2.6.1, Pygments-2.1.3, pyparsing-2.1.10, pytz-2016.10, PyZMQ-16.0.2, requests-2.11.0, scipy-0.18.1, setuptools-32.3.1, simplegeneric-0.8.1, singledispatch-3.4.0.3, six-1.10.0, sympy-1.0, terminado-0.6, tornado-4.4.1, traitlets-4.2.2, widgetsnbextension-1.2.6 Keyword:math
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description:
qca/2.1.3 -

Description: Taking a hint from the similarly-named Java Cryptography Architecture, QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as Providers. The advantage of this model is to allow applications to avoid linking to or explicitly depending on any particular cryptographic library. This allows one to easily change or upgrade crypto implementations without even needing to recompile the application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX. Homepage: http://delta.affinix.com/qca/
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
qgis/2.18.24 -

Description: QGIS is a user friendly Open Source Geographic Information System (GIS) Homepage: http://www.qgis.org/
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
qhull/2015.2 math

Description: Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. - Homepage: http://www.qhull.org Keyword:math
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2018.3
Description:
qjson/0.9.0 -

Description: QJson is a Qt-based library that maps JSON data to QVariant objects and vice versa. Homepage: http://qjson.sourceforge.net/
Prerequisites: -
Description:
qrupdate/1.1.2 math

Description: qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions. - Homepage: https://sourceforge.net/projects/qrupdate/ Keyword:math
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2018.3
Description:
qscintilla/2.10.7 -

Description: QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control Homepage: https://www.riverbankcomputing.com/software/qscintilla
Prerequisites: -
Description:
qt/3.3.8 tools

Description: Qt is a comprehensive cross-platform C++ application framework. Homepage: http://qt.io/ Keyword:tools
Prerequisites: -
Description:
qt/4.8.7 tools

Description: Qt is a comprehensive cross-platform C++ application framework. Homepage: http://qt.io/ Keyword:tools
Prerequisites: -
Description:
qt/5.10.1 tools

Description: Qt is a comprehensive cross-platform C++ application framework. Homepage: http://qt.io/ Keyword:tools
Prerequisites: -
Description:
qt/5.6.1 tools

Description: Qt is a comprehensive cross-platform C++ application framework. Homepage: http://qt.io/ Keyword:tools
Prerequisites: -
Description:
qt/5.9.6 tools

Description: Qt is a comprehensive cross-platform C++ application framework. Homepage: http://qt.io/ Keyword:tools
Prerequisites: -
Description:
quantumespresso/6.0 chem Quantum ESPRESSO

Description: Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). - Homepage: http://www.pwscf.org/ Keyword:chem CC-Wiki: Quantum ESPRESSO
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description:
quantumespresso/6.1 chem Quantum ESPRESSO

Description: Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). Homepage: http://www.pwscf.org/ Keyword:chem CC-Wiki: Quantum ESPRESSO
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
quantumespresso/6.3 chem Quantum ESPRESSO

Description: Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). Homepage: http://www.pwscf.org/ Keyword:chem CC-Wiki: Quantum ESPRESSO
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
quorum/1.1.1 -

Description: QuorUM is an error corrector for Illumina reads Homepage: http://www.genome.umd.edu/quorum.html
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
qwt/6.1.3 -

Description: The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. Homepage: http://qwt.sourceforge.net/
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
qwtpolar/1.1.1 -

Description: The QwtPolar library contains classes for displaying values on a polar coordinate system. Homepage: http://qwtpolar.sourceforge.net/
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
r-bundle-bioconductor/3.4 bio

Description: R is a free software environment for statistical computing and graphics. Homepage: http://www.r-project.org/ Extensions: abind-1.4-5, acepack-1.4.1, ade4-1.7-6, affy-1.52.0, affycoretools-1.46.5, affyio-1.44.0, AgiMicroRna-2.24.0, ALDEx2-1.6.0, annaffy-1.46.0, annotate-1.52.1, AnnotationDbi-1.36.2, AnnotationForge-1.16.1, AnnotationHub-2.6.5, ape-4.1, assertthat-0.2.0, assertthat-0.2.0, backports-1.1.0, base64-2.0, base64enc-0.1-3, baySeq-2.8.0, beanplot-1.2, BH-1.62.0-1, BiasedUrn-1.07, bindr-0.1, bindrcpp-0.2, Biobase-2.34.0, BiocGenerics-0.20.0, BiocInstaller-1.24.0, BiocParallel-1.8.2, biomaRt-2.30.0, biomformat-1.2.0, Biostrings-2.42.1, biovizBase-1.22.0, bit-1.1-12, bit64-0.9-7, bitops-1.0-6, blob-1.1.0, BSgenome-1.42.0, BSgenome.Hsapiens.UCSC.hg19-1.4.0, bumphunter-1.14.0, Category-2.40.0, caTools-1.17.1, CGHbase-1.34.0, checkmate-1.8.2, clusterRepro-0.5-1.1, coin-1.2-0, colorspace-1.3-2, corpcor-1.6.9, cummeRbund-2.16.0, curl-2.7, dada2-1.2.2, data.table-1.10.4, DBI-0.7, DEGseq-1.28.0, DEoptimR-1.0-8, derfinder-1.8.5, derfinderHelper-1.8.1, DESeq2-1.14.1, dichromat-2.0-0, digest-0.6.12, digest-0.6.12, diptest-0.75-7, doParallel-1.0.10, doRNG-1.6.6, dplyr-0.7.1, DynDoc-1.52.0, edgeR-3.16.5, ellipse-0.3-8, ensembldb-1.6.2, evaluate-0.10.1, fastcluster-1.1.22, FDb.InfiniumMethylation.hg19-2.2.0, ff-2.2-13, flexmix-2.3-14, foreach-1.4.3, Formula-1.2-1, fpc-2.1-10, futile.logger-1.4.3, futile.logger-1.4.3, futile.logger-1.4.3, futile.options-1.0.0, futile.options-1.0.0, futile.options-1.0.0, gcrma-2.46.0, gdata-2.18.0, gdsfmt-1.10.1, genefilter-1.56.0, geneLenDataBase-1.10.0, geneplotter-1.52.0, GenomeGraphs-1.34.0, GenomeInfoDb-1.10.3, GenomicAlignments-1.10.1, GenomicFeatures-1.26.4, GenomicFiles-1.10.3, GenomicRanges-1.26.4, genoset-1.30.0, GEOquery-2.40.0, GGally-1.3.1, ggbio-1.22.4, ggplot2-2.2.1, glmnet-2.0-10, glue-1.1.1, GO.db-3.4.0, goseq-1.26.0, GOstats-2.40.0, gplots-3.0.1, graph-1.52.0, gridBase-0.4-7, gridExtra-2.2.1, GSEABase-1.36.0, gtable-0.2.0, gtools-3.5.0, Gviz-1.18.2, HCsnip-1.14.0, hgu133plus2.db-3.2.3, highr-0.6, Hmisc-4.0-3, Homo.sapiens-1.3.1, htmlTable-1.9, htmltools-0.3.6, htmlwidgets-0.8, httpuv-1.3.3, httr-1.2.1, hwriter-1.3.2, igraph-1.0.1, illuminaio-0.16.0, impute-1.48.0, interactiveDisplayBase-1.12.0, IRanges-2.8.2, irlba-2.2.1, iterators-1.0.8, jsonlite-1.5, KEGG.db-3.2.3, KEGGgraph-1.32.0, KEGGprofile-1.16.0, KEGGREST-1.14.1, kernlab-0.9-25, knitr-1.16, labeling-0.3, lambda.r-1.1.9, lambda.r-1.1.9, lambda.r-1.1.9, latticeExtra-0.6-28, lazyeval-0.2.0, limma-3.30.13, locfit-1.5-9.1, logspline-2.1.9, lumi-2.26.4, magrittr-1.5, markdown-0.8, marray-1.52.0, maSigPro-1.46.0, matrixStats-0.52.2, mclust-5.3, memoise-1.1.0, metagenomeSeq-1.16.0, methylumi-2.20.0, mime-0.5, minfi-1.20.2, mixOmics-6.1.1, mixOmics-6.1.3, modeltools-0.2-21, multcomp-1.4-6, multtest-2.30.0, munsell-0.4.3, mvtnorm-1.0-6, nleqslv-3.3, NMF-0.20.6, NOISeq-2.18.0, nor1mix-1.2-2, oligoClasses-1.36.0, openssl-0.9.6, org.Hs.eg.db-3.4.0, OrganismDbi-1.16.0, pcaMethods-1.66.0, penalized-0.9-50, perm-1.0-0.0, perm-1.0-0.0, permute-0.9-4, PFAM.db-3.4.0, phyloseq-1.19.1, pkgconfig-2.0.1, pkgmaker-0.22, plogr-0.1-1, plyr-1.8.4, png-0.1-7, polyester-1.10.1, prabclus-2.2-6, preprocessCore-1.36.0, prettyunits-1.0.2, progress-1.1.2, quadprog-1.5-5, qvalue-2.6.0, R.methodsS3-1.7.1, R.oo-1.21.0, R.utils-2.5.0, R6-2.2.2, randomForestSRC-2.4.2, RBGL-1.50.0, RColorBrewer-1.1-2, Rcpp-0.12.11, RcppArmadillo-0.7.900.2.0, RcppParallel-4.3.20, RCurl-1.95-4.5, registry-0.3, ReportingTools-2.14.0, reshape-0.8.6, reshape2-1.4.2, rgl-0.98.1, Rgraphviz-2.18.0, rhdf5-2.18.0, rlang-0.1.1, RNASeqPower-1.14.0, rngtools-1.2.4, robustbase-0.92-7, Rsamtools-1.26.2, RSQLite-2.0, Rsubread-1.24.2, rtracklayer-1.34.2, S4Vectors-0.12.2, samr-2.0, sandwich-2.3-4, scales-0.4.1, shiny-1.0.3, ShortRead-1.32.1, sigaR-1.22.0, siggenes-1.48.0, sm-2.2-5.4, snow-0.4-2, snowfall-1.84-6.1, SNPRelate-1.8.0, sourcetools-0.1.6, SPIA-2.26.0, stringi-1.1.5, stringr-1.2.0, SummarizedExperiment-1.4.0, TeachingDemos-2.10, TH.data-1.0-8, tibble-1.3.3, tidyr-0.6.3, trimcluster-0.1-2, TxDb.Hsapiens.UCSC.hg19.knownGene-3.2.2, VariantAnnotation-1.20.3, vegan-2.4-3, venn-1.2, viridis-0.4.0, viridisLite-0.2.0, XML-3.98-1.9, xtable-1.8-2, xtable-1.8-2, XVector-0.14.1, yaml-2.1.14, zlibbioc-1.20.0, zoo-1.8-0 Keyword:bio
Prerequisites: gcc/5.4.0
Description:
r/3.3.3 tools R

Description: R is a free software environment for statistical computing and graphics. - Homepage: http://www.r-project.org/ Keyword:tools CC-Wiki: R
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description:
r/3.4.0 tools R

Description: R is a free software environment for statistical computing and graphics. Homepage: http://www.r-project.org/ Keyword:tools CC-Wiki: R
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
r/3.4.3 tools R

Description: R is a free software environment for statistical computing and graphics. Homepage: http://www.r-project.org/ Keyword:tools CC-Wiki: R
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
r/3.5.0 tools R

Description: R is a free software environment for statistical computing and graphics. Homepage: http://www.r-project.org/ Keyword:tools CC-Wiki: R
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
r/3.5.1 tools R

Description: R is a free software environment for statistical computing and graphics. Homepage: http://www.r-project.org/ Keyword:tools CC-Wiki: R
Prerequisites: gcc/7.3.0
Description:
racon/20170719 bio

Description: Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. Homepage: https://github.com/isovic/racon/ Keyword:bio
Prerequisites: gcc/5.4.0
Description:
randfold/2.0.1 -

Description: Minimum free energy of folding randomization test software Homepage: http://bioinformatics.psb.ugent.be/software/details/Randfold
Prerequisites: gcc/7.3.0
Description:
raxml/8.2.11 -

Description: RAxML search algorithm for maximum likelihood based inference of phylogenetic trees. Homepage: https://github.com/stamatak/standard-RAxML
Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or gcc/7.3.0 and openmpi/3.1.2 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
ray/3.0.0 bio

Description: Ray -- Parallel genome assemblies for parallel DNA sequencing. Homepage: https://github.com/zorino/ray Keyword:bio
Prerequisites: gcc/5.4.0 and openmpi/1.8.8 or intel/2016.4 and openmpi/1.8.8 or intel/2018.3 and openmpi/3.1.2
Description:
rdkit/2018.03.3 -

Description: RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python. Homepage: http://www.rdkit.org/
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
reapr/1.0.18 -

Description: REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. Homepage: https://www.sanger.ac.uk/science/tools/reapr Extensions: File::Spec::Link-0.5, Getopt::Long-2.5, List::Util-1.50
Prerequisites: intel/2016.4
Description:
recon/1.08 -

Description: Proper identification of repetitive sequences is an essential step in genome analysis. The RECON package performs de novo identification and classification of repeat sequence families from genomic sequences. The underlying algorithm is based on extensions to the usual approach of single linkage clustering of local pairwise alignments between genomic sequences. Specifically, our extensions use multiple alignment information to define the boundaries of individual copies of the repeats and to distinguish homologous but distinct repeat element families. RECON should be useful for first-pass automatic classification of repeats in newly sequenced genomes. Homepage: http://eddylab.org/software/recon/
Prerequisites: -
Description:
relion/2.1.0 -

Description: RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). Homepage: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page
Prerequisites: intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2018.3 and cuda/10.0.130 and openmpi/3.1.2
Description:
remora/1.8.2 -

Description: REsource MOnitoring for Remote Applications Homepage: https://github.com/TACC/remora
Prerequisites: -
Description:
repasthpc/2.0 bio

Description: The Repast Suite is a family of advanced, free, and open source agent-based modeling and simulation platforms that have collectively been under continuous development for over 15 years: Repast for High Performance Computing 2.2.0, released on 30 September 2016, is a lean and expert-focused C++-based modeling system that is designed for use on large computing clusters and supercomputers. Homepage: https://repast.github.io/ Keyword:bio
Prerequisites: intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
repasthpc/2.2.0 bio

Description: The Repast Suite is a family of advanced, free, and open source agent-based modeling and simulation platforms that have collectively been under continuous development for over 15 years: Repast for High Performance Computing 2.2.0, released on 30 September 2016, is a lean and expert-focused C++-based modeling system that is designed for use on large computing clusters and supercomputers. - Homepage: https://repast.github.io/ Keyword:bio
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description:
repeatmasker/4-0-7 -

Description: RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. Homepage: http://www.repeatmasker.org/
Prerequisites: gcc/5.4.0
Description:
repeatmodeler/1.0.11 -

Description: RepeatModeler is a de-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats. Homepage: http://repeatmasker.org/RepeatModeler/
Prerequisites: gcc/5.4.0
Description:
repeatscout/1.0.5 -

Description: RepeatScout is a tool to discover repetitive substrings in DNA. Homepage: https://bix.ucsd.edu/repeatscout/
Prerequisites: -
Description:
rmblast/2.6.0 -

Description: RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' for use with RepeatMasker and RepeatModeler. Homepage: http://www.repeatmasker.org/RMBlast.html
Prerequisites: gcc/5.4.0
Description:
rnammer/1.2 bio

Description: RNAmmer 1.2 predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences. The method is described in detail in the following article: RNammer: consistent annotation of rRNA genes in genomic sequences. Lagesen K, Hallin PF, Roedland E, Staerfeldt HH, Rognes T Ussery DW. Nucleic Acids Res. Apr 22, 2007. Homepage: http://www.cbs.dtu.dk/cgi-bin/sw_request?rnammer Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
roary/3.12.0 -

Description: Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Homepage: https://sanger-pathogens.github.io/Roary/ Extensions: Array::Utils-0.5, B::Hooks::EndOfScope-0.24, CPAN::Meta::Check-0.014, Devel::OverloadInfo-0.005, Devel::StackTrace-2.03, Digest::MD5::File-0.08, Encode-2.98, Exception::Class-1.44, File::Grep-0.02, File::Path-2.16, File::pushd-1.016, File::Slurper-0.012, File::Spec-3.75, File::Temp-0.2308, File::Which-1.22, Getopt::Long-2.50, Graph::Writer::Dot-2.09, List::Util-1.50, Log::Log4perl-1.49, Module::Runtime::Conflicts-0.003, Moose-2.2011, namespace::autoclean-0.28, namespace::clean-0.27, Parse::Yapp::Driver-1.21, PerlIO::utf8_strict-0.007, Role::Tiny-2.000006, Sub::Identify-0.14, Sub::Name-0.21, Test::CleanNamespaces-0.23, Test::Needs-0.002005, Text::CSV-1.97, Text::CSV_XS-1.37, XML::Parser-2.44
Prerequisites: gcc/5.4.0 and openmpi/2.1.1
Description:
root/5.34.36 tools

Description: The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way. Homepage: http://root.cern.ch/drupal/ Keyword:tools
Prerequisites: gcc/4.8.5 or gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description:
root/6.08.02 tools

Description: The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way. Homepage: http://root.cern.ch/drupal/ Keyword:tools
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
root/6.14.04 tools

Description: The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way. Homepage: http://root.cern.ch/drupal/ Keyword:tools
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
rosetta/3.8 chem

Description: Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and nucleic acids. Homepage: https://www.rosettacommons.org Keyword:chem
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description:
rosetta/3.9 chem

Description: Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and nucleic acids. Homepage: https://www.rosettacommons.org Keyword:chem
Prerequisites: gcc/5.4.0 and openmpi/2.1.1 or gcc/7.3.0 and openmpi/3.1.2
Description:
rsem/1.3.0 bio

Description: RNA-Seq by Expectation-Maximization Homepage: http://deweylab.github.io/RSEM/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4
Description:
rstudio-server/1.1.206 tools

Description: RStudio Server enables you to provide a browser based interface to a version of R running on a remote Linux server, bringing the power and productivity of the RStudio IDE to server-based deployments of R. Homepage: https://www.rstudio.com/ Keyword:tools
Prerequisites: intel/2016.4
Description:
rstudio-server/1.1.447 tools

Description: RStudio Server enables you to provide a browser based interface to a version of R running on a remote Linux server, bringing the power and productivity of the RStudio IDE to server-based deployments of R. Homepage: https://www.rstudio.com/ Keyword:tools
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
rtk/1.4.0 -

Description: Insighteconstruction Toolkit (RTK) is an open-source and cross-platform software for fast circular cone-beam CT reconstruction based on the Insight Toolkit (ITK). RTK is developped by the RTK consortium. RTK provides or will provide Basic operators for reconstruction, e.g., filtering, forward, projection and backprojection Multithreaded CPU and GPU versions Tools for respiratory motion correction I/O for several scanners Preprocessing of raw data for scatter correction Homepage: https://itk.org
Prerequisites: intel/2016.4
Description:
ruby/2.3.1 tools

Description: Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write. - Homepage: https://www.ruby-lang.org Keyword:tools
Prerequisites: -
Description:
rubygems/2.3.1 tools

Description: Bundle which contains a collection of popular RubyGems, including ffi, childprocess, json, cabin, backports, arr-pm, clamp, multipart-post, faraday, faraday_middleware, highline, net-http-pipeline, net-http-persistent, multi_json, public_suffix, addressable, gh, launchy, ethon, typhoeus, websocket, pusher-client, diff-lcs, rspec-support, rspec-mocks, rspec-expections, rspec-core, rspec, rack, rack-protection, tilt, sinatra, rack-test, bundler. Homepage: https://rubygems.org Extensions: addressable-2.4.0, arr-pm-0.0.10, backports-3.6.8, bundler-1.15.4, cabin-0.9.0, childprocess-0.5.9, clamp-1.1.1, diff-lcs-1.2.5, ethon-0.10.1, faraday-0.10.0, faraday_middleware-0.10.1, ffi-1.9.14, gh-0.15.0, highline-1.7.8, json-2.0.2, launchy-2.4.3, multi_json-1.12.1, multipart-post-2.0.0, net-http-persistent-2.9.4, net-http-pipeline-1.0.1, public_suffix-2.0.4, pusher-client-0.6.2, rack-1.6.5, rack-protection-1.5.3, rack-test-0.6.3, rspec-3.5.0, rspec-core-3.5.4, rspec-expectations-3.5.0, rspec-mocks-3.5.0, rspec-support-3.5.0, sinatra-1.4.7, tilt-2.0.5, typhoeus-0.6.9, websocket-1.2.3 Keyword:tools
Prerequisites: -
Description:
rust/1.28.0 -

Description: Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. Homepage: https://www.rust-lang.org
Prerequisites: gcc/6.4.0
Description:
sabre/1.00 bio

Description: A barcode demultiplexing and trimming tool for FastQ files Homepage: https://github.com/najoshi/sabre Keyword:bio
Prerequisites: intel/2016.4
Description:
sagemath/8.1 tools

Description: SageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more. Access their combined power through a common, Python-based language or directly via interfaces or wrappers. Homepage: http://www.sagemath.org/ Keyword:tools
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
salmon/0.11.3 bio

Description: Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Homepage: https://github.com/COMBINE-lab/salmon Keyword:bio
Prerequisites: gcc/5.4.0 and openmpi/2.1.1
Description:
salmon/0.8.2 bio

Description: Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Homepage: https://github.com/COMBINE-lab/salmon Keyword:bio
Prerequisites: gcc/5.4.0 and openmpi/2.1.1
Description:
salmon/0.9.1 bio

Description: Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Homepage: https://github.com/COMBINE-lab/salmon Keyword:bio
Prerequisites: gcc/5.4.0 and openmpi/2.1.1
Description:
salmonbeta/0.6.0 -

Description: Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves is accuracy and speed via a number of different innovations, including the use of quasi-mapping (accurate but fast-to-compute proxies for traditional read alignments), and massively-parallel stochastic collapsed variational inference. The result is a versatile tool that fits nicely into many differnt pipelines. For example, you can choose to make use of our quasi-mapping algorithm by providing Salmon with raw sequencing reads, or, if it is more convenient, you can provide Salmon with regular alignments (e.g. an unsorted BAM file produced with your favorite aligner), and it will use the same wicked-fast, state-of-the-art inference algorithm to estimate transcript-level abundances for your experiment. Homepage: https://github.com/COMBINE-lab/salmon/
Prerequisites: -
Description:
sambamba/0.6.7 bio

Description: Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth Homepage: http://lomereiter.github.io/sambamba/ Keyword:bio
Prerequisites: -
Description:
samblaster/0.1.24 -

Description: samblaster: a tool to mark duplicates and extract discordant and split reads from sam files Homepage: https://github.com/GregoryFaust/samblaster
Prerequisites: -
Description:
samtools/0.1.17 bio

Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Homepage: http://www.htslib.org/ Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
samtools/0.1.18 bio

Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Homepage: http://www.htslib.org/ Keyword:bio
Prerequisites: intel/2016.4
Description:
samtools/0.1.20 bio

Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. - Homepage: http://www.htslib.org/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2018.3
Description:
samtools/1.3.1 bio

Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. - Homepage: http://www.htslib.org/ Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1 or intel/2018.3
Description:
samtools/1.5 bio

Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Homepage: http://www.htslib.org/ Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
samtools/1.9 bio

Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Homepage: http://www.htslib.org/ Keyword:bio
Prerequisites: gcc/4.8.5 or gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
sbt/1.1.1 tools

Description: sbt is a build tool for Scala, Java, and more. It requires Java 1.8 or later. sbt uses a small number of concepts to support flexible and powerful build definitions. There are not that many concepts, but sbt is not exactly like other build systems and there are details you will stumble on if you haven t read the documentation. The Getting Started Guide covers the concepts you need to know to create and maintain an sbt build definition. It is highly recommended to read the Getting Started Guide. Homepage: http://www.scala-sbt.org/ Keyword:tools
Prerequisites: -
Description:
scalapack/1.8.0 math

Description: The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. Homepage: http://www.netlib.org/scalapack/ Keyword:math
Prerequisites: gcc/5.4.0 and openmpi/1.8.8
Description:
scalapack/2.0.2 math

Description: The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. Homepage: http://www.netlib.org/scalapack/ Keyword:math
Prerequisites: gcc/6.4.0 and cuda/9.0.176 and openmpi/2.1.1 or gcc/6.4.0 and openmpi/2.1.1 or gcc/7.3.0 and cuda/10.0.130 and openmpi/3.1.2
Description:
scipy-stack/2017b math

Description: Bundle which contains the Scientific Python stack, including Cycler, mpmath, numpy, scipy, sympy, pandas, matplotlib, ipython_genutils, traitlets, ptyprocess, pathlib2, pickleshare, pexpect, simplegeneric, ipython, ipykernel, jupyter_client, jupyter_core, pyzmq, tornado, futures and ipyparallel. Homepage: http://python.org/ Keyword:math
Prerequisites: -
Description:
scipy-stack/2018b math

Description: Bundle which contains the Scientific Python stack, including Cycler, mpmath, numpy, scipy, sympy, pandas, matplotlib, ipython_genutils, traitlets, ptyprocess, pathlib2, pickleshare, pexpect, simplegeneric, ipython, ipykernel, jupyter_client, jupyter_core, pyzmq, tornado, futures and ipyparallel. Homepage: http://python.org/ Keyword:math
Prerequisites: -
Description:
scotch/6.0.4 math

Description: Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. - Homepage: http://gforge.inria.fr/projects/scotch/ Keyword:math
Prerequisites: gcc/4.8.5 and openmpi/2.1.1 or gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1 or intel/2017.5 and impi/2017.4.239
Description:
scotch/6.0.6 math

Description: Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. Homepage: http://gforge.inria.fr/projects/scotch/ Keyword:math
Prerequisites: gcc/7.3.0 and openmpi/3.1.2 or intel/2018.3 and openmpi/3.1.2
Description:
sdl/1.2.15 -

Description: SDL: Simple DirectMedia Layer, a cross-platform multimedia library Homepage: http://www.libsdl.org/
Prerequisites: gcc/7.3.0 or intel/2018.3
Description:
sdl2/2.0.7 -

Description: SDL: Simple DirectMedia Layer, a cross-platform multimedia library Homepage: http://www.libsdl.org/
Prerequisites: gcc/7.3.0 or intel/2018.3
Description:
sedifoam/0.1 -

Description: SediFoam is a hybrid CFD-DEM solver for particle-laden flows based on two open-source codes: OpenFOAM, an object-oriented CFD platform by OpenCFD, and LAMMPS, a highly efficient molecular dynamics solver by Sandia National Laboratories. The solver has ben rigorously and extensively validated [Gupta2015b]. A capability demonstration of the present solver in the context of sediment transport is published in Sun and Xiao [Sun2016]. Other application include sand dune migration [Sun2016b], cohesive particle setteling [Sun2017cohesive], sediment transport of irregular partilces [Sun2017irregular], particle plume in stratified flows [Wang2016]. Homepage: https://github.com/xiaoh/sediFoam
Prerequisites: gcc/5.4.0 and openmpi/2.1.1
Description:
seexpr/2.11 vis

Description: SeExpr is a simple expression language that we use to provide artistic control and customization to our core software. We use it for procedural geometry synthesis, image synthesis, simulation control, and much more. Homepage: https://www.disneyanimation.com/technology/seexpr.html Keyword:vis
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
selscan/1.2.0 bio

Description: selscan -- a program to calculate EHH-based scans for positive selection in genomes selscan currently implements EHH, iHS, XP-EHH, nSL, and iHH12 and requires phased data. It should be run separately for each chromosome and population (or population pair for XP-EHH). selscan is 'dumb' with respect ancestral/derived coding and simply expects haplotype data to be coded 0/1. Unstandardized iHS scores are thus reported as ln(iHH1/iHH0) based on the coding you have provided. Homepage: https://github.com/szpiech/selscan Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
seqan/2.4.0 bio

Description: SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data Homepage: https://www.seqan.de/ Keyword:bio
Prerequisites: gcc/5.4.0
Description:
seqmule/1.2.6 bio

Description: SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file. SeqMule also has some built-in functions, such as pooling consensus calls from various callers, plotting a Venn diagram showing intersection among different callers, and downloading databases. SeqMule can be used for both Mendelian disease study and cancer genome study. Homepage: http://seqmule.openbioinformatics.org/en/latest/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
seqtk/1.2 bio

Description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip. Homepage: https://github.com/lh3/seqtk/ Keyword:bio
Prerequisites: intel/2016.4 or intel/2018.3
Description:
seqtk/1.2-r101c bio

Description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip. Homepage: https://github.com/lh3/seqtk/ Keyword:bio
Prerequisites: intel/2016.4
Description:
sextractor/2.19.5 -

Description: SExtractor is a program that builds a catalogue of objects from an astronomical image. Although it is particularly oriented towards reduction of large scale galaxy-survey data, it can perform reasonably well on moderately crowded star fields. Homepage: ://www.astromatic.net/software/sextractor
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
sga/0.10.15 bio

Description: SGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads. For running examples see src/examples and the sga wiki https://github.com/jts/sga/wiki For questions or support contact jared.simpson --at-- oicr.on.ca Homepage: https://github.com/jts/sga/wiki Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
shengbte/1.1.1 phys

Description: ShengBTE is a software package for solving the Boltzmann Transport Equation for phonons. Also installed is the 'thirdorder' package of Python scripts. Homepage: http://www.shengbte.org/ Extensions: thirdorder-1.0.2 Keyword:phys
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2
Description:
shotmap/1.1 bio

Description: Shotmap is a software workflow that functionally annotates and compares shotgun metagenomes. Specifically, it will: 1. Compared unassembled or assembled metagenomic sequences to a protein family database 2. Calculate metagenome functional abundance and diversity 3. Compare metagenomes using a variety of statistical and ecological tools 4. Identify protein families that differentiate metagenomes using robust statistical tests Shotmap can be run on a multicore computer or can optionally interface with an SGE-configured computing cluste (i.e., a cloud). Shotmap can also optionally manage the information and data associated with this workflow in a relational database. Homepage: https://github.com/sharpton/shotmap Keyword:bio
Prerequisites: gcc/5.4.0
Description:
sickle/1.33 bio

Description: Windowed Adaptive Trimming for fastq files using quality Homepage: https://github.com/najoshi/sickle Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
siesta/4.0 chem

Description: SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. - Homepage: http://departments.icmab.es/leem/siesta Keyword:chem
Prerequisites: gcc/6.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description:
siesta/4.0.1 chem

Description: SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. Homepage: http://departments.icmab.es/leem/siesta Keyword:chem
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
siesta/4.1-b2 chem

Description: SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. Homepage: http://departments.icmab.es/leem/siesta Keyword:chem
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
siesta/4.1-b3 chem

Description: SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. This version was built with Lua support. Homepage: http://departments.icmab.es/leem/siesta Keyword:chem
Prerequisites: intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
sift4g/2.0.0 -

Description: SIFT predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. Homepage: http://sift.bii.a-star.edu.sg/
Prerequisites: gcc/5.4.0 or gcc/5.4.0 and cuda/9.0.176 or gcc/7.3.0
Description:
signalp/4.1f bio

Description: SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive bacteria, Gram-negative bacteria, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks. Homepage: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp Keyword:bio
Prerequisites: -
Description:
sip/4.19.2 tools

Description: SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries. Homepage: http://www.riverbankcomputing.com/software/sip/ Keyword:tools
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
snap/2013-11-29 bio

Description: SNAP: Semi-HMM-based Nucleic Acid Parser gene prediction tool - Version Releaseed on: 11/29/2013. Homepage: http://korflab.ucdavis.edu/software.html Keyword:bio
Prerequisites: gcc/5.4.0
Description:
snappy/1.1.3 tools

Description: Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression. Homepage: https://github.com/google/snappy Keyword:tools
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
snpeff/4.3t bio

Description: SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). Homepage: http://sourceforge.net/projects/snpeff/ Keyword:bio
Prerequisites: -
Description:
soapdenovo2/r240 bio

Description: SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the successor of SOAPdenovo. Homepage: http://soap.genomics.org.cn/index.html Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
sortmerna/2.1 bio

Description: SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads. Homepage: http://bioinfo.lifl.fr/RNA/sortmerna/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
spades/3.10.1 bio

Description: Genome assembler for single-cell and isolates data sets Homepage: http://cab.spbu.ru/software/spades/ Keyword:bio
Prerequisites: gcc/5.4.0
Description:
spades/3.11.1 bio

Description: Genome assembler for single-cell and isolates data sets Homepage: http://cab.spbu.ru/software/spades/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
spades/3.13.0 bio

Description: Genome assembler for single-cell and isolates data sets Homepage: http://cab.spbu.ru/software/spades/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
spark/2.1.0 tools Apache Spark

Description: Spark is Hadoop MapReduce done in memory - Homepage: http://spark.apache.org Keyword:tools CC-Wiki: Apache Spark
Prerequisites: -
Description:
spark/2.1.1 tools Apache Spark

Description: Spark is Hadoop MapReduce done in memory Homepage: http://spark.apache.org Keyword:tools CC-Wiki: Apache Spark
Prerequisites: -
Description:
spark/2.2.0 tools Apache Spark

Description: Spark is Hadoop MapReduce done in memory Homepage: http://spark.apache.org Keyword:tools CC-Wiki: Apache Spark
Prerequisites: -
Description:
spark/2.2.1 tools Apache Spark

Description: Spark is Hadoop MapReduce done in memory Homepage: http://spark.apache.org Keyword:tools CC-Wiki: Apache Spark
Prerequisites: -
Description:
spark/2.3.0 tools Apache Spark

Description: Spark is Hadoop MapReduce done in memory Homepage: http://spark.apache.org Keyword:tools CC-Wiki: Apache Spark
Prerequisites: -
Description:
speedseq/0.1.2 bio

Description: A flexible framework for rapid genome analysis and interpretation Homepage: https://github.com/hall-lab/speedseq Keyword:bio
Prerequisites: gcc/5.4.0
Description:
spglib/1.9.9 chem

Description: Spglib is a C library for finding and handling crystal symmetries. Homepage: https://github.com/atztogo/spglib Keyword:chem
Prerequisites: gcc/4.8.5 or gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2018.3
Description:
spherls/1.0.0 -

Description: SPHERLS simulates the interaction of radial pulsation and convection in stars. Homepage: https://github.com/cgeroux/SPHERLS/
Prerequisites: gcc/5.4.0 and openmpi/1.8.8
Description:
squid/1.9g -

Description: Author: Sean Eddy A C library that is bundled with much of the above software. C function library for sequence analysis. SQUID is my own personal library of C functions and utility programs for sequence analysis. I don't really suggest that you use it in your programs, as I change it at will. However, it does contains some small utility programs that some people have found useful in scripts that drive large HMMER tasks. Homepage: http://eddylab.org/software.html
Prerequisites: gcc/7.3.0 or intel/2018.3
Description:
sra-toolkit/2.8.2-1 bio

Description: The NCBI SRA Toolkit enables reading (dumping) of sequencing files from the SRA database and writing (loading) files into the .sra format Homepage: http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=std Keyword:bio
Prerequisites: -
Description:
sspace-longread/1-1 bio

Description: SSPACE-LongRead is a stand-alone program for scaffolding pre-assembled contigs using long reads (e.g. PacBio RS reads). Homepage: https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE-longread Keyword:bio
Prerequisites: intel/2016.4 or intel/2018.3
Description:
sspace_basic/2.1.1 bio

Description: SSPACE Basic, SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension Homepage: https://github.com/nsoranzo/sspace_basic Keyword:bio
Prerequisites: -
Description:
stacks/1.35 bio

Description: Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. Homepage: http://creskolab.uoregon.edu/stacks/ Keyword:bio
Prerequisites: intel/2016.4
Description:
stacks/1.44 bio

Description: Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. Homepage: http://creskolab.uoregon.edu/stacks/ Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
stacks/1.45 bio

Description: Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. - Homepage: http://creskolab.uoregon.edu/stacks/ Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description:
stacks/1.46 bio

Description: Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. Homepage: http://catchenlab.life.illinois.edu/stacks/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
stacks/2.0b bio

Description: Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. Homepage: http://creskolab.uoregon.edu/stacks/ Keyword:bio
Prerequisites: gcc/5.4.0
Description:
stacks/2.0Beta10a bio

Description: Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. Homepage: http://creskolab.uoregon.edu/stacks/ Keyword:bio
Prerequisites: gcc/5.4.0
Description:
star/2.5.2b bio

Description: STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. Homepage: https://github.com/alexdobin/STAR Keyword:bio
Prerequisites: intel/2016.4
Description:
star/2.5.3a bio

Description: STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. Homepage: https://github.com/alexdobin/STAR Keyword:bio
Prerequisites: intel/2016.4
Description:
star/2.6.0a bio

Description: STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. Homepage: https://github.com/alexdobin/STAR Keyword:bio
Prerequisites: intel/2016.4
Description:
star/2.6.0c bio

Description: STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. Homepage: https://github.com/alexdobin/STAR Keyword:bio
Prerequisites: intel/2016.4
Description:
star/2.6.1a bio

Description: STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. Homepage: https://github.com/alexdobin/STAR Keyword:bio
Prerequisites: intel/2016.4
Description:
star/2.6.1c bio

Description: STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. Homepage: https://github.com/alexdobin/STAR Keyword:bio
Prerequisites: intel/2018.3
Description:
starccm-mixed/11.06.011 phys StarCCM

Description: Predicting the real-world performance of a product requires simulation tools that span a variety of engineering disciplines. STAR-CCM+ is an all-in-one solution that delivers accurate and efficient multidisciplinary technologies in a single integrated user interface. This version uses mixed precision. Homepage: http://mdx.plm.automation.siemens.com/star-ccm-plus Keyword:phys CC-Wiki: StarCCM
Prerequisites: -
Description:
starccm-mixed/12.04.011 phys StarCCM

Description: Predicting the real-world performance of a product requires simulation tools that span a variety of engineering disciplines. STAR-CCM+ is an all-in-one solution that delivers accurate and efficient multidisciplinary technologies in a single integrated user interface. This version uses mixed precision. Homepage: http://mdx.plm.automation.siemens.com/star-ccm-plus Keyword:phys CC-Wiki: StarCCM
Prerequisites: -
Description:
starccm-mixed/12.06.011 phys StarCCM

Description: Predicting the real-world performance of a product requires simulation tools that span a variety of engineering disciplines. STAR-CCM+ is an all-in-one solution that delivers accurate and efficient multidisciplinary technologies in a single integrated user interface. This version uses mixed precision. Homepage: http://mdx.plm.automation.siemens.com/star-ccm-plus Keyword:phys CC-Wiki: StarCCM
Prerequisites: -
Description:
starccm-mixed/13.04.010 phys StarCCM

Description: Predicting the real-world performance of a product requires simulation tools that span a variety of engineering disciplines. STAR-CCM+ is an all-in-one solution that delivers accurate and efficient multidisciplinary technologies in a single integrated user interface. This version uses mixed precision. Homepage: http://mdx.plm.automation.siemens.com/star-ccm-plus Keyword:phys CC-Wiki: StarCCM
Prerequisites: -
Description:
starccm/11.06.011-R8 phys StarCCM

Description: Predicting the real-world performance of a product requires simulation tools that span a variety of engineering disciplines. STAR-CCM+ is an all-in-one solution that delivers accurate and efficient multidisciplinary technologies in a single integrated user interface. This verison uses double precision. Homepage: http://mdx.plm.automation.siemens.com/star-ccm-plus Keyword:phys CC-Wiki: StarCCM
Prerequisites: -
Description:
starccm/12.04.011-R8 phys StarCCM

Description: Predicting the real-world performance of a product requires simulation tools that span a variety of engineering disciplines. STAR-CCM+ is an all-in-one solution that delivers accurate and efficient multidisciplinary technologies in a single integrated user interface. This verison uses double precision. Homepage: http://mdx.plm.automation.siemens.com/star-ccm-plus Keyword:phys CC-Wiki: StarCCM
Prerequisites: -
Description:
starccm/12.06.011-R8 phys StarCCM

Description: Predicting the real-world performance of a product requires simulation tools that span a variety of engineering disciplines. STAR-CCM+ is an all-in-one solution that delivers accurate and efficient multidisciplinary technologies in a single integrated user interface. This verison uses double precision. Homepage: http://mdx.plm.automation.siemens.com/star-ccm-plus Keyword:phys CC-Wiki: StarCCM
Prerequisites: -
Description:
starccm/13.04.010-R8 phys StarCCM

Description: Predicting the real-world performance of a product requires simulation tools that span a variety of engineering disciplines. STAR-CCM+ is an all-in-one solution that delivers accurate and efficient multidisciplinary technologies in a single integrated user interface. This verison uses double precision. Homepage: http://mdx.plm.automation.siemens.com/star-ccm-plus Keyword:phys CC-Wiki: StarCCM
Prerequisites: -
Description:
stringtie/1.3.3b bio

Description: StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. Homepage: http://ccb.jhu.edu/software/stringtie/ Keyword:bio
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
stringtie/1.3.4d bio

Description: StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. Homepage: http://ccb.jhu.edu/software/stringtie/ Keyword:bio
Prerequisites: intel/2016.4 and openmpi/2.1.1 or intel/2018.3
Description:
structure/2.3.4 bio

Description: The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Homepage: http://web.stanford.edu/group/pritchardlab/software/ Keyword:bio
Prerequisites: intel/2016.4 or intel/2018.3
Description:
su2/5.0.0 math

Description: An open-source collection of software tools written in C++ for performing Partial Differential Equation (PDE) analysis and solving PDE-constrained optimization problems. The toolset is designed with computational fluid dynamics and aerodynamic shape optimization in mind. Homepage: http://su2.stanford.edu Keyword:math
Prerequisites: gcc/5.4.0 and openmpi/2.1.1 or gcc/7.3.0 and openmpi/3.1.2 or intel/2016.4 and openmpi/2.1.1
Description:
su2/6.0.1 math

Description: An open-source collection of software tools written in C++ for performing Partial Differential Equation (PDE) analysis and solving PDE-constrained optimization problems. The toolset is designed with computational fluid dynamics and aerodynamic shape optimization in mind. Homepage: http://su2.stanford.edu Keyword:math
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
su2/6.1.0 math

Description: An open-source collection of software tools written in C++ for performing Partial Differential Equation (PDE) analysis and solving PDE-constrained optimization problems. The toolset is designed with computational fluid dynamics and aerodynamic shape optimization in mind. Homepage: http://su2.stanford.edu Keyword:math
Prerequisites: intel/2018.3 and openmpi/3.1.2
Description:
subread/1.5.2 bio

Description: High performance read alignment, quantification and mutation discovery Homepage: http://subread.sourceforge.net/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
suitesparse/4.5.4 math

Description: SuiteSparse is a collection of libraries manipulate sparse matrices. - Homepage: http://faculty.cse.tamu.edu/davis/suitesparse.html Keyword:math
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2018.3
Description:
sumaclust/1.0.20 bio

Description: SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences. Homepage: http://metabarcoding.org/sumatra Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
superlu/5.1.1 math

Description: SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. - Homepage: http://crd-legacy.lbl.gov/~xiaoye/SuperLU/ Keyword:math
Prerequisites: intel/2016.4
Description:
superlu/5.2.1 math

Description: SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. Homepage: http://crd-legacy.lbl.gov/~xiaoye/SuperLU/ Keyword:math
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2018.3
Description:
supernova/2.0.0 bio

Description: Supernova is delivered as a single, self-contained tar file that can be unpacked anywhere on your system. It bundles all of its own required software dependencies, which are pre-compiled to run on a range of Linux distributions. Homepage: https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome Keyword:bio
Prerequisites: -
Description:
supernova/2.1.1 bio

Description: Supernova is delivered as a single, self-contained tar file that can be unpacked anywhere on your system. It bundles all of its own required software dependencies, which are pre-compiled to run on a range of Linux distributions. Homepage: https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome Keyword:bio
Prerequisites: -
Description:
tabix/0.2.6 bio

Description: Generic indexer for TAB-delimited genome position files Homepage: http://samtools.sourceforge.net Keyword:bio
Prerequisites: intel/2016.4 or intel/2018.3
Description:
tau/2.27.1 -

Description: The TAU Performance System is a portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, Java, Python. Homepage: http://tau.uoregon.edu
Prerequisites: gcc/7.3.0 and openmpi/3.1.2
Description:
tbb/2017.2.132 tools

Description: Intel Threading Building Blocks 2017 (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based parallel applications that scale to available processor cores, are compatible with multiple environments, and are easier to maintain. Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms. Homepage: http://software.intel.com/en-us/articles/intel-tbb/ Keyword:tools
Prerequisites: -
Description:
tcl/8.5.19 tools

Description: Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. Homepage: http://www.tcl.tk/ Keyword:tools
Prerequisites: -
Description:
tktable/2.10 -

Description: Tcl is a simple-to-learn yet very powerful language. Its syntax is described in just a dozen rules, but it has all the features needed to rapidly create useful programs in almost any field of application - on a wide variety of international platforms. Tk is a graphical toolkit for Tcl. It allows you to develop graphical applications that run on Windows, Linux, MacOS X and many other platforms. And not just from Tcl - Tk can be used from many languages including C, Ruby, Perl, Python and Lua. Homepage: http://wiki.tcl.tk/1877
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
tmhmm/2.0c bio

Description: TMHMM 2.0 predicts transmembrane helices in proteins. The method is described in: Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes. Anders Krogh and Bjorn Larsson, Gunnar von Heijne, and Erik L.L. Sonnhammer. J. Mol. Biol. 305:567-580, 2001. and: A hidden Markov model for predicting transmembrane helices in protein sequences. Erik L.L. Sonnhammer, Gunnar von Heijne, and Anders Krogh. In J. Glasgow et al., eds.: Proc. of ISMB6, pages 175-182. AAAI Press, 1998. Homepage: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm Keyword:bio
Prerequisites: -
Description:
tophat/2.1.1 bio

Description: TopHat is a fast splice junction mapper for RNA-Seq reads. - Homepage: http://ccb.jhu.edu/software/tophat/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2017.1 or intel/2018.3
Description:
torch/20170530 ai

Description: Torch is a scientific computing framework with wide support for machine learning algorithms that puts GPUs first. It is easy to use and efficient, thanks to an easy and fast scripting language, LuaJIT, and an underlying C/CUDA implementation. Homepage: http://torch.ch/ Keyword:ai
Prerequisites: gcc/5.4.0 and cuda/8.0.44 or intel/2016.4 and cuda/8.0.44
Description:
torch/20170731 ai

Description: Torch is a scientific computing framework with wide support for machine learning algorithms that puts GPUs first. It is easy to use and efficient, thanks to an easy and fast scripting language, LuaJIT, and an underlying C/CUDA implementation. Homepage: http://torch.ch/ Keyword:ai
Prerequisites: intel/2016.4 and cuda/8.0.44
Description:
torch/20171030 ai

Description: Torch is a scientific computing framework with wide support for machine learning algorithms that puts GPUs first. It is easy to use and efficient, thanks to an easy and fast scripting language, LuaJIT, and an underlying C/CUDA implementation. Homepage: http://torch.ch/ Keyword:ai
Prerequisites: intel/2016.4 and cuda/8.0.44
Description:
towhee/8.1.0 -

Description: Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling. The code has subsequently been extended to several ensembles, many different force fields, and solid (or at least porous) phases. Homepage: http://towhee.sourceforge.net/
Prerequisites: gcc/5.4.0 and openmpi/2.1.1 or gcc/7.3.0 and openmpi/3.1.2
Description:
trans-abyss/1.5.5 bio

Description: de novo assembly of RNA-Seq data using ABySS Homepage: http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/ Keyword:bio
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
trans-abyss/2.0.1 bio

Description: de novo assembly of RNA-Seq data using ABySS Homepage: http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/ Keyword:bio
Prerequisites: gcc/7.3.0 and openmpi/3.1.2
Description:
transdecoder/3.0.1 bio

Description: TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. - Homepage: https://transdecoder.github.io/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
transrate/1.0.3 bio

Description: Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly. Homepage: http://hibberdlab.com/transrate/ Keyword:bio
Prerequisites: -
Description:
trf/4.09 -

Description: Tandem repeats finder: a program to analyze DNA sequences. Legacy version. Homepage: https://tandem.bu.edu/trf/trf.html
Prerequisites: -
Description:
trilinos/12.10.1 tools

Description: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages. Homepage: http://trilinos.sandia.gov/ Keyword:tools
Prerequisites: gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
trimal/1.4 bio

Description: trimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment Homepage: http://trimal.cgenomics.org/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
trimmomatic/0.36 bio

Description: Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line. - Homepage: http://www.usadellab.org/cms/?page=trimmomatic Keyword:bio
Prerequisites: -
Description:
trinity/2.4.0 bio

Description: Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. Homepage: http://trinityrnaseq.github.io/ Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
trinity/2.5.0 bio

Description: Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. Homepage: http://trinityrnaseq.github.io/ Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
trinity/2.6.5 bio

Description: Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. Homepage: http://trinityrnaseq.github.io/ Keyword:bio
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
trinity/2.8.4 bio

Description: Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. Homepage: http://trinityrnaseq.github.io/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
trinotate/3.0.2 bio

Description: Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Homepage: https://trinotate.github.io/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
trnascan-se/2.0.0 -

Description: tRNAscan-SE: An improved tool for transfer RNA detection, Patricia Chan and Todd Lowe, School of Engineering, University of California, Santa Cruz, CA. tRNAscan-SE was written in the PERL (version 5.0) script language. Input consists of DNA or RNA sequences in FASTA format. tRNA predictions are output in standard tabular or ACeDB format. tRNAscan-SE does no tRNA detection itself, but instead combines the strengths of three independent tRNA prediction programs by negotiating the flow of information between them, performing a limited amount of post-processing, and outputting the results in one of several formats. Homepage: http://lowelab.ucsc.edu/
Prerequisites: gcc/5.4.0
Description:
udunits/2.2.24 tools

Description: UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement. Homepage: http://www.unidata.ucar.edu/software/udunits/ Keyword:tools
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
udunits/2.2.26 tools

Description: UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement. Homepage: http://www.unidata.ucar.edu/software/udunits/ Keyword:tools
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
valgrind-mpi/3.13.0 -

Description: Valgrind: Debugging and profiling tools Homepage: http://valgrind.org/downloads/
Prerequisites: gcc/5.4.0 and openmpi/2.1.1
Description:
valgrind-mpi/3.14.0 -

Description: Valgrind: Debugging and profiling tools Homepage: http://valgrind.org/downloads/
Prerequisites: gcc/7.3.0 and openmpi/3.1.2
Description:
vasp/4.6 chem VASP

Description: The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, based on Density Futional Theory (DFT). In this version Transition State Tools for VASP (http://theory.cm.utexas.edu/vtsttools/) as well as VASPsol (https://github.com/henniggroup/VASPsol) has been implemented to the original vasp . Homepage: http://www.vasp.at Keyword:chem CC-Wiki: VASP
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
vasp/5.4.1 chem VASP

Description: The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, based on Density Futional Theory (DFT). In this version Transition State Tools for VASP (http://theory.cm.utexas.edu/vtsttools/) as well as VASPsol (https://github.com/henniggroup/VASPsol) has been implemented to the original vasp . Homepage: http://www.vasp.at Keyword:chem CC-Wiki: VASP
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
vasp/5.4.4 chem VASP

Description: The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, based on Density Futional Theory (DFT). In this version VASPsol (https://github.com/henniggroup/VASPsol) has been implemented to the original version of vasp Homepage: http://www.vasp.at Keyword:chem CC-Wiki: VASP
Prerequisites: intel/2017.5 and impi/2017.4.239
Description:
vcftools/0.1.14 bio

Description: The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. - Homepage: https://vcftools.github.io Keyword:bio
Prerequisites: intel/2016.4 or intel/2018.3
Description:
velvet/1.2.10 bio

Description: Sequence assembler for very short reads Homepage: http://www.ebi.ac.uk/~zerbino/velvet/ Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
verifybamid/1.1.3 -

Description: verifyBamID is a software that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples. verifyBamID can detect sample contamination and swaps when external genotypes are available. When external genotypes are not available, verifyBamID still robustly detects sample swaps. Homepage: http://csg.sph.umich.edu/kang/verifyBamID/index.html
Prerequisites: -
Description:
viennacl/1.7.1 math

Description: ViennaCL is a free open-source linear algebra library for computations on many-core architectures (GPUs, MIC) and multi-core CPUs. The library is written in C++ and supports CUDA, OpenCL, and OpenMP (including switches at runtime). Homepage: http://viennacl.sourceforge.net/ Keyword:math
Prerequisites: gcc/5.4.0 and cuda/8.0.44 or gcc/7.3.0 and cuda/10.0.130 or intel/2016.4 and cuda/8.0.44
Description:
viennarna/2.4.10 -

Description: The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. Homepage: http://www.tbi.univie.ac.at/RNA/
Prerequisites: intel/2018.3
Description:
viennarna/2.4.9 -

Description: The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. Homepage: http://www.tbi.univie.ac.at/RNA/
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4
Description:
visit/2.12.3 vis

Description: VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool. Homepage: https://wci.llnl.gov/simulation/computer-codes/visit Keyword:vis
Prerequisites: gcc/5.4.0 and openmpi/2.1.1
Description:
visit/2.13.0 vis

Description: VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool. Homepage: https://wci.llnl.gov/simulation/computer-codes/visit Keyword:vis
Prerequisites: gcc/5.4.0 and openmpi/2.1.1
Description:
vmd/1.9.3 vis

Description: VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Homepage: http://www.ks.uiuc.edu/Research/vmd Keyword:vis
Prerequisites: intel/2016.4 or intel/2018.3
Description:
voro++/0.4.6 math

Description: Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles. Homepage: http://math.lbl.gov/voro++/ Keyword:math
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
vsearch/2.4.3 bio

Description: VSEARCH stands for vectorized search, as the tool takes advantage of parallelism in the form of SIMD vectorization as well as multiple threads to perform accurate alignments at high speed. VSEARCH uses an optimal global aligner (full dynamic programming Needleman-Wunsch), in contrast to USEARCH which by default uses a heuristic seed and extend aligner. This usually results in more accurate alignments and overall improved sensitivity (recall) with VSEARCH, especially for alignments with gaps. Homepage: https://github.com/torognes/vsearch Keyword:bio
Prerequisites: intel/2016.4
Description:
vsearch/2.5.0 bio

Description: VSEARCH stands for vectorized search, as the tool takes advantage of parallelism in the form of SIMD vectorization as well as multiple threads to perform accurate alignments at high speed. VSEARCH uses an optimal global aligner (full dynamic programming Needleman-Wunsch), in contrast to USEARCH which by default uses a heuristic seed and extend aligner. This usually results in more accurate alignments and overall improved sensitivity (recall) with VSEARCH, especially for alignments with gaps. Homepage: https://github.com/torognes/vsearch Keyword:bio
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4
Description:
vsearch/2.9.1 bio

Description: VSEARCH stands for vectorized search, as the tool takes advantage of parallelism in the form of SIMD vectorization as well as multiple threads to perform accurate alignments at high speed. VSEARCH uses an optimal global aligner (full dynamic programming Needleman-Wunsch), in contrast to USEARCH which by default uses a heuristic seed and extend aligner. This usually results in more accurate alignments and overall improved sensitivity (recall) with VSEARCH, especially for alignments with gaps. Homepage: https://github.com/torognes/vsearch Keyword:bio
Prerequisites: intel/2018.3
Description:
vtk-mpi/6.3.0 vis

Description: The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. Homepage: http://www.vtk.org Keyword:vis
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
vtk/6.3.0 vis

Description: The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. Homepage: http://www.vtk.org Keyword:vis
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2016.4 and openmpi/2.0.2 or intel/2018.3
Description:
vtk/8.0.0 vis

Description: The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. Homepage: http://www.vtk.org Keyword:vis
Prerequisites: gcc/5.4.0 and openmpi/2.1.1 or gcc/7.3.0 and openmpi/3.1.2 or intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
vtk/8.1.1 vis

Description: The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. Homepage: http://www.vtk.org Keyword:vis
Prerequisites: intel/2018.3 and openmpi/3.1.2
Description:
vtune/2018.3 -

Description: Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java. Homepage: http://software.intel.com/en-us/intel-vtune-amplifier-xe
Prerequisites: -
Description:
wgrib2/2.0.7 -

Description: A program to decode/manipulate GRIB-2 files. Homepage: http://www.cpc.noaa.gov/products/wesley/wgrib2/
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
wham/2.0.9.1 -

Description: fast, memory efficient implementation of the Weighted Histogram Analysis Method (WHAM). Homepage: http://membrane.urmc.rochester.edu/content/wham
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
wps/3.8.0 geo

Description: WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. - Homepage: http://www.wrf-model.org Keyword:geo
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description:
wps/3.8.1 geo

Description: WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. Compiled with -DNO_LEAP_CALENDAR - Homepage: http://www.wrf-model.org Keyword:geo
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description:
wps/3.9.1 geo

Description: WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. Compiled with -DNO_LEAP_CALENDAR. The WPS Geographical Input Data are included in the geog directory. Homepage: http://www.wrf-model.org Keyword:geo
Prerequisites: intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
wrf-fire/20170625 geo

Description: WRF-Fire combines the Weather Research and Forecasting model (WRF) with a fire code implementing a surface fire behavior model, called SFIRE, based on semi-empirical formulas calculate the rate of spread of the fire line (the interface between burning and unignited fuel) based on fuel properties, wind velocities from WRF, and terrain slope. The fire spread is implemented by the level set method. Homepage: http://www.openwfm.org/wiki/WRF-SFIRE Keyword:geo
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
wrf/3.8.0 geo

Description: The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. - Homepage: http://www.wrf-model.org Keyword:geo
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description:
wrf/3.8.1 geo

Description: The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. Compiled with -DNO_LEAP_CALENDAR Homepage: http://www.wrf-model.org Keyword:geo
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description:
wrf/3.9.1.1 geo

Description: The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. Compiled with -DNO_LEAP_CALENDAR Homepage: http://www.wrf-model.org Keyword:geo
Prerequisites: intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
wxwidgets/3.1.1 -

Description: wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux and other platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform's native API rather than emulating the GUI. It's also extensive, free, open-source and mature. Homepage: http://www.wxwidgets.org/
Prerequisites: gcc/5.4.0 or gcc/7.3.0
Description:
xcrysden/1.5.60 vis

Description: XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. Homepage: http://www.xcrysden.org/ Keyword:vis
Prerequisites: intel/2016.4 or intel/2018.3
Description:
xdrfile/1.1.4 -

Description: library for reading and writing xtc, edr and trr files Homepage: http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library
Prerequisites: intel/2016.4 or intel/2018.3
Description:
xerces-c++/3.1.1 tools

Description: Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs. Homepage: http://xerces.apache.org/xerces-c/ Keyword:tools
Prerequisites: - or intel/2016.4 or intel/2018.3
Description:
xgboost/0.7 math

Description: XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, flexible and portable. Homepage: https://github.com/dmlc/xgboost Keyword:math
Prerequisites: gcc/6.4.0
Description:
xmlf90/1.5.4 -

Description: xmlf90 is a suite of libraries to handle XML in Fortran. It has two major components: - A XML parsing library. The parser was designed to be a useful tool in the extraction and analysis of data in the context of scientific computing, and thus the priorities were efficiency and the ability to deal with very large XML files while maintaining a small memory footprint. The most complete programming interface is based on the very successful SAX (Simple API for XML) model, although a partial DOM interface and a very experimental XPATH interface are also present. - A library (xmlf90-wxml) that facilitates the writing of well-formed XML, including such features as automatic start-tag completion, attribute pretty-printing, and element indentation. There are also helper routines to handle the output of numerical arrays. Homepage: https://launchpad.net/xmlf90/
Prerequisites: gcc/5.4.0 or gcc/7.3.0 or intel/2016.4 or intel/2018.3
Description:
xmm-sas/16.1.0 phys

Description: The Science Analysis System (SAS) is a collection of tasks, scripts and libraries, specifically designed to reduce and analyze data collected by the XMM-Newton observatory. Homepage: https://www.cosmos.esa.int/web/xmm-newton/sas Extensions: Switch-2.17, XML::LibXML-2.0132 Keyword:phys
Prerequisites: gcc/5.4.0
Description:
yaehmop/3.0.3 chem

Description: "Yet Another extended Huckel Molecular Orbital Package (YAeHMOP) was developed by Greg Landrum whilest a graduate student in the research group of Professor Roald Hoffmann at Cornell University. YAeHMOP is intended to be an easy to use, transparent, extended Huckel calculation and visualization package which can perform calculations on both molecular and extended materials in 1,2, or 3 dimensions. Homepage: http://yaehmop.sourceforge.net/ Keyword:chem
Prerequisites: gcc/6.4.0 or intel/2016.4 and openmpi/2.0.2 or intel/2018.3 and openmpi/3.1.2
Description:
yaxt/0.5.1 tools

Description: Yet Another eXchange Tool Homepage: https://www.dkrz.de/redmine/projects/yaxt Keyword:tools
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2018.3 and openmpi/3.1.2
Description:
yaxt/0.6.0 tools

Description: Yet Another eXchange Tool Homepage: https://www.dkrz.de/redmine/projects/yaxt Keyword:tools
Prerequisites: intel/2018.3 and openmpi/3.1.2
Description:

Disponibles uniquement sur certaines grappe

Most application software is installed in CVMFSCernVM File System, a distributed file system which makes central management of the many packages easier. Certain packages, however, are not installed in CVMFSCernVM File System but are installed only at some sites, or are installed separately at each site. This is usually due to license restrictions on the package in question. Such packages are listed in the following table.

List of software installed locally
Module Type Documentation Machines Description
adf chem ADF graham Amsterdam Density Functional Modeling Suite, computational chemistry software
dirac/16.0 phys cedar The DIRAC program computes molecular properties using relativistic quantum chemical methods. Homepage: http://diracprogram.org
dirac/17.0
galaxy/17.09 bio cedar Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming or systems administration experience. Any group on Cedar can have one Galaxy instance. The Galaxy instance will be run under a shared account which will be created by admins. Please contact support@computecanada.ca to set up Galaxy for you. Homepage: https://usegalaxy.org/
gaussian/g03.d01 chem Gaussian cedar & graham Gaussian is a general purpose computational chemistry software package. Homepage: http://gaussian.com/
gaussian/g09.b01
gaussian/g09.e01
gaussian/g09.a03
gaussian/g09.b01
gbrowse/2.56 bio GBrowse cedar GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. Homepage: http://gmod.org/wiki/GBrowse
sas/9.4 math cedar SAS is a software suite developed by SAS Institute for advanced analytics, multivariate analyses, business intelligence, data management, and predictive analytics. SAS on cedar is licensed software and it belongs to users from the Alberta School of Business who are eligible to run SAS. Homepage: https://www.sas.com/en_ca/home.html
x2go/4.0.1.22 vis cedar X2Go is an open source remote desktop software for Linux that uses the NX technology protocol. On cedar we support only ICEVM window manager Homepage: https://wiki.x2go.org/doku.php

Logiciels sur les systèmes installés avant 2016

Voir la documentation de nos partenaires régionaux.