Available software

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A current list of the software available on Compute Canada national systems is below. This list changes frequently as new software is added. You can request the installation or updating of a particular program or library by writing to support@computecanada.ca.

Notes

Except for basic system programs, you access most software by loading a module. See Using modules for more on how to use the Lmod module system. Note that some prerequisite modules are loaded by default.

Here are a few things to know about the available software:

  • Most Python modules are not installed as (Lmod) modules. They are instead provided as binary wheels, stored on the Compute Canada systems under /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/. One such package is Tensorflow. For instructions on how to install Python packages, see the Python page.
  • Similarly, most R or Perl packages are not installed either. We recommend installing them in your personal or group file space. See the R and Perl pages for instructions on how to do so.
  • Note that Docker is not available on Compute Canada clusters but Singularity is available by loading the module singularity. Docker containers can be converted to Singularity as discussed here.
  • Some of the software packages listed below are not immediately usable because they require you to have a license. You may need to be granted access to them by us. Attempting to load the module for one of these will give you instructions on what to do to obtain access.
  • While the vast majority of the software packages below are accessible on all Compute Canada servers, a few are only available at one site or another due to licensing restrictions.
    • The chemistry programs ADF, AMBER, and Gaussian are only available at Graham and so do not appear on the list below.
  • Many packages related to the operating system, such as Autotools, Make, Git, and others, are not installed as modules but are part of the default environment. These are not listed below.

List of modules

Types are: ai (artificial intelligence), bio (biology, bioinformatics), chem (chemistry), geo (earth sciences), io (input/output), math (mathematics), mpi (MPI), phys (physics and engineering), tools (languages and libraries), vis (visualization).

Module Type Documentation Description
abaqus/6.14.1 -

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
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
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: 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:
allinea-cpu/7.1 tools

Description: Profiler and debugger, combining Allinea MAP and Allinea DDT. Homepage: http://www.allinea.com
Prerequisites: -
Description:
allinea-gpu/7.1 tools

Description: Profiler and debugger, combining Allinea MAP and Allinea DDT, with support for CUDA. Homepage: http://www.allinea.com
Prerequisites: -
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 intel/2016.4
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: gcc/5.4.0 or intel/2016.4
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:
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 intel/2016.4 or intel/2017.1
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:
ascp/3.5.4 -

Description: Aspera ASCP is a high speed file transfer software Homepage: http://downloads.asperasoft.com/
Prerequisites: -
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 intel/2016.4 or intel/2017.1
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:
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
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:
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 intel/2016.4 or intel/2017.1
Description:
beast/2.4.0 chem

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:chem
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:
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:
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:
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 intel/2016.4 or intel/2017.1
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:
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/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:
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 intel/2016.4 or intel/2017.1
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:
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:
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:
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
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
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:
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
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:
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:
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 intel/2016.4 or intel/2017.1
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 intel/2016.4 and openmpi/2.1.1
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 MPI. 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 MPI. Homepage: http://chapel.cray.com Keyword:tools
Prerequisites: gcc/5.4.0
Description:
chemps2/1.8 -

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
Prerequisites: intel/2016.4
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:
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
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 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:
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:
cst/2017 -

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/
Prerequisites: -
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
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: intel/2016.4
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 intel/2016.4 and cuda/8.0.44
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
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
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:
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
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:
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 -

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
Prerequisites: gcc/5.4.0 or intel/2016.4
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:
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
Description:
emboss/6.6.0 chem

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:chem
Prerequisites: intel/2016.4
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
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:
fast-gbs/2017-01-25 -

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
Prerequisites: -
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:
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 intel/2016.4
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/ Keyword:bio
Prerequisites: gcc/5.4.0
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 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
Description:
fftw/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/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 intel/2016.4 or intel/2017.1
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
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
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:
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/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:
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 intel/2016.4 or intel/2017.1
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
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 intel/2016.4
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 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 intel/2016.4 or intel/2017.1
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: intel/2016.4
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 intel/2016.4 or intel/2017.1
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:
gmt/5.4.2 -

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/
Prerequisites: intel/2016.4
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:
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/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/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. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. - 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. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. - 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:
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 intel/2016.4 or intel/2017.1
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 intel/2016.4 or intel/2017.1
Description:
guile/1.8.8 -

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
Prerequisites: 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:
harminv/1.4 -

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
Prerequisites: intel/2016.4
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 intel/2016.4 or intel/2017.1
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 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:
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/5.4.0 or intel/2016.4 or intel/2017.1
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
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 intel/2016.4
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 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/2.0.2 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:
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:
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 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:
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:
impi/2017.4.239 mpi

Description: Intel MPI Library, compatible with MPICH ABI Homepage: http://software.intel.com/en-us/intel-mpi-library/
Prerequisites: intel/2017.5
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:
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 MPI and Intel MKL - 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 MPI and Intel MKL - 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:
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 intel/2016.4
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: intel/2016.4 or intel/2017.1
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/1.8.0_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:
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 intel/2016.4 or intel/2017.1
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:
kim/1.8.2 -

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/
Prerequisites: intel/2016.4
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:
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:
libctl/3.2.2 -

Description: libctl is a free Guile-based library implementing flexible control files for scientific simulations. Homepage: http://ab-initio.mit.edu/libctl
Prerequisites: intel/2016.4
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:
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: -
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
Description:
libplinkio/0.9.5 -

Description: A small C and Python library for reading PLINK genotype files. Homepage: https://github.com/mfranberg/libplinkio
Prerequisites: gcc/5.4.0 or intel/2016.4
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: intel/2016.4
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 intel/2016.4 or intel/2017.1
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:
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 intel/2016.4 and openmpi/2.1.1
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 intel/2016.4
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:
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: intel/2016.4
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:
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:
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:
meep/1.3 -

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
Prerequisites: intel/2016.4 and openmpi/2.1.1
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:
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 intel/2016.4
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
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 intel/2016.4
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 intel/2016.4 or intel/2017.1
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 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
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:
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
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
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:
mpfi/1.5.1 -

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
Prerequisites: gcc/5.4.0 or intel/2016.4
Description:
mpi.net/13-08-2017 mpi

Description: MPI.NET is a high-performance, easy-to-use implementation of the Message Passing Interface (MPI) 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:
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
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
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:
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: intel/2016.4
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
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 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:
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 intel/2016.4 or intel/2017.1
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 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:
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 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:
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 intel/2016.4 or intel/2017.1
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: 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 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/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:
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
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:
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
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
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
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:
open3dqsar/2.3 -

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
Prerequisites: intel/2016.4
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: intel/2016.4
Description:
openblas/0.2.20 -

Description: OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. Homepage: http://xianyi.github.com/OpenBLAS/
Prerequisites: gcc/6.4.0
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:
openfoam/2.3.1 phys

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
Prerequisites: gcc/4.8.5 and openmpi/2.1.1
Description:
openfoam/3.0.1 phys

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
Prerequisites: gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1
Description:
openfoam/4.1 phys

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
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:
openfoam/5.0 phys

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
Prerequisites: gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1
Description:
openmm/7.1.1 chem

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

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

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

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

Description: The Open MPI Project is an open source MPI-2 implementation. Homepage: http://www.open-mpi.org/ Keyword:mpi CC-Wiki: MPI
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 MPI Project is an open source MPI-2 implementation. Homepage: http://www.open-mpi.org/ Keyword:mpi CC-Wiki: MPI
Prerequisites: gcc/4.8.5 or gcc/5.4.0 or gcc/6.4.0 or intel/2014.6 or intel/2016.4 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 pgi/17.3
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: intel/2016.4 and openmpi/2.0.2
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 intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
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/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/5.3.0 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:
parmetis/4.0.3 math

Description: ParMETIS is an MPI-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: intel/2016.4 and openmpi/2.0.2
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 -

Description: An API for the Polarizable Continuum Model. Homepage: https://pcmsolver.readthedocs.org
Prerequisites: gcc/5.4.0 or intel/2016.4
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
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:
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/3.7.5 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/3.7.5 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:
pgi/17.3 tools

Description: C, C++ and Fortran compilers from The Portland Group - PGI - Homepage: http://www.pgroup.com/
Prerequisites: -
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:
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:
platypus/0.8.1 -

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
Prerequisites: gcc/5.4.0
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
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:
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 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:
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:
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:
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:
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
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
Description:
protobuf/3.3.0 tools

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

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/
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/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/3.6.3 tools Python

Description: Python is a programming language that lets you work more quickly and integrate your systems more effectively. Homepage: http://python.org/ Keyword:tools CC-Wiki: Python
Prerequisites: -
Description:
python27-mpi4py/2.0.0 tools

Description: MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) 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: MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) 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:
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 intel/2016.4 or intel/2017.1
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 intel/2016.4 or intel/2017.1
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/5.6.1 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:
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:
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:
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
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:
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: intel/2016.4
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
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:
rsem/1.3.0 -

Description: RNA-Seq by Expectation-Maximization Homepage: http://deweylab.github.io/RSEM/
Prerequisites: gcc/5.4.0 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:
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:
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/0.1.20 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 intel/2016.4 or intel/2017.1
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
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:
scalapack/2.0.2 -

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/
Prerequisites: gcc/6.4.0 and openmpi/2.1.1
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
Description:
selscan/1.2.0 -

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
Prerequisites: gcc/5.4.0 or intel/2016.4
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
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:
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:
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: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
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 -

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/
Prerequisites: gcc/5.4.0 or intel/2016.4
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
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 intel/2016.4
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 intel/2016.4
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
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:
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 intel/2016.4 or intel/2017.1
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
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 intel/2016.4
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:
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/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:
stringtie/1.3.3b -

Description: StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. Homepage: http://ccb.jhu.edu/software/stringtie/
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description:
structure/2.3.4 -

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/
Prerequisites: intel/2016.4
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 intel/2016.4 and openmpi/2.1.1
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
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 intel/2016.4 or intel/2017.1
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 intel/2016.4
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:
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
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:
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 intel/2016.4 or intel/2017.1
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:
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:
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
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
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 intel/2016.4
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:
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
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: intel/2016.4
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:
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
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 intel/2016.4 and cuda/8.0.44
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
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: intel/2016.4
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: intel/2016.4
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: intel/2016.4
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: intel/2016.4 and openmpi/2.1.1
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:
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:
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
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
Description:


Software on legacy systems

Software installed on legacy regional systems is listed on these pages: