Available software

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A current list of the software available on Compute Canada national systems is below. Note that this list changes frequently as new software is added and that users can request the installation or updating of a particular program or library by writing to support@computecanada.ca. A list of software installed on legacy regional systems can be found here,

Note that some prerequisites are loaded by default. See Using modules for details on how to use the module system.

Module Name Version Description
abinit/8.2.2 abinit 8.2.2 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

Prerequisites: intel/2016.4 and openmpi/2.0.2
Description: Homepage: http://www.abinit.org/
abyss/1.9.0 abyss 1.9.0 Assembly By Short Sequences

Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.0.2
Description: a de novo, parallel, paired-end sequence assembler - Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss
bamtools/2.4.1 bamtools 2.4.1 BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files

Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: Homepage: https://github.com/pezmaster31/bamtools
bcftools/1.4 bcftools 1.4 Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools

Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants - Homepage: http://www.htslib.org/
beagle-lib/2.1.2 beagle-lib 2.1.2 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

Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: -
beast/2.4.0 beast 2.4.0 BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences

Prerequisites: intel/2016.4
Description: 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/
bedtools/2.26.0 bedtools 2.26.0 The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage

Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. - Homepage: https://github.com/arq5x/bedtools2
bioperl/1.7.1 bioperl 1.7.1 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

Prerequisites: -
Description: Homepage: http://www.bioperl.org/
blast+/2.6.0 blast+ 2.6.0 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

Prerequisites: gcc/5.4.0
Description: Homepage: http://blast.ncbi.nlm.nih.gov/
blat/3.5 blat 3.5 BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more

Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: Homepage: http://genome.ucsc.edu/FAQ/FAQblat.html
boost-mpi/1.60.0 boost-mpi 1.60.0 Boost provides free peer-reviewed portable C++ source libraries

Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.0.2
Description: Homepage: http://www.boost.org/
boost/1.60.0 boost 1.60.0 Boost provides free peer-reviewed portable C++ source libraries

Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: Homepage: http://www.boost.org/
bowtie/1.1.2 bowtie 1.1.2 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

Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: -
bowtie2/2.3.0 bowtie2 2.3.0 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences

Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: 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
bwa/0.7.15 bwa 0.7.15 Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome

Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: Homepage: http://bio-bwa.sourceforge.net/
clhep/2.3.1.1 clhep 2.3.1.1 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

Prerequisites: intel/2016.4
Description: Homepage: http://proj-clhep.web.cern.ch/proj-clhep/
cufflinks/2.2.1 cufflinks 2.2.1 Transcript assembly, differential expression, and differential regulation for RNA-Seq

Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: Homepage: http://cole-trapnell-lab.github.io/cufflinks/
eigen/3.3.2 eigen 3.3.2 Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms

Prerequisites: -
Description: Homepage: http://eigen.tuxfamily.org/index.php?title=Main_Page
fastqc/0.11.5 fastqc 0.11.5 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

Prerequisites: -
Description: Homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
fftw/3.3.5 fftw 3.3.5 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

Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.0.2
Description: Homepage: http://www.fftw.org
gcc/4.8.5 gcc 4.8.5 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,...)

Prerequisites: -
Description: Homepage: http://gcc.gnu.org/
gcc/5.4.0 gcc 5.4.0 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,...)

Prerequisites: -
Description: Homepage: http://gcc.gnu.org/
gdal/2.1.3 gdal 2.1.3 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

Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: 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/
geant4/10.02.p03 geant4 10.02.p03 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

Prerequisites: intel/2016.4
Description: Homepage: http://geant4.cern.ch/
geos/3.6.1 geos 3.6.1 GEOS (Geometry Engine

Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: Open Source) is a C++ port of the Java Topology Suite (JTS) - Homepage: http://trac.osgeo.org/geos
gromacs/5.0.7 gromacs 5.0.7 GROMACS is a versatile package to perform molecular dynamics, i.e

Prerequisites: intel/2016.4 and openmpi/2.0.2
Description: simulate the Newtonian equations of motion for systems with hundreds to millions of particles. - Homepage: http://www.gromacs.org
gromacs/5.1.4 gromacs 5.1.4 GROMACS is a versatile package to perform molecular dynamics, i.e

Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.0.2
Description: simulate the Newtonian equations of motion for systems with hundreds to millions of particles. - Homepage: http://www.gromacs.org
gsl/2.2.1 gsl 2.2.1 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

Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: Homepage: http://www.gnu.org/software/gsl/
hdf5-mpi/1.8.18 hdf5-mpi 1.8.18 HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections

Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.0.2
Description: Homepage: http://www.hdfgroup.org/HDF5/
hdf5/1.8.18 hdf5 1.8.18 HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections

Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: Homepage: http://www.hdfgroup.org/HDF5/
hmmer/3.1b2 hmmer 3.1b2 HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments

Prerequisites: intel/2016.4
Description: 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/
hpl/2.2 hpl 2.2 HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers

Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.0.2
Description: 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/
htslib/1.4 htslib 1.4 A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix

Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: Homepage: http://www.htslib.org/
igraph/0.7.1 igraph 0.7.1 igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use

Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.0.2
Description: igraph is open source and free. igraph can be programmed in R, Python and C/C++. - Homepage: http://igraph.org
imkl/11.3.4.258 imkl 11.3.4.258 Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance

Prerequisites: -
Description: 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/
imkl/2017.1.132 imkl 2017.1.132 Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance

Prerequisites: -
Description: 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/
intel/2016.4 intel 2016.4 Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL
intel/2017.1 intel 2017.1 Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL
jags/4.2.0 jags 4.2.0 JAGS is Just Another Gibbs Sampler

Prerequisites: intel/2016.4 or intel/2017.1
Description: It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation - Homepage: http://mcmc-jags.sourceforge.net/
jasper/1.900.1 jasper 1.900.1 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

Prerequisites: -
Description: Homepage: http://www.ece.uvic.ca/~frodo/jasper/
java/1.8.0_121 java 1.8.0_121 Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers

Prerequisites: -
Description: Homepage: http://java.com/
jellyfish/2.2.6 jellyfish 2.2.6 Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA

Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: Homepage: http://www.genome.umd.edu/jellyfish.html
julia/0.5.1 julia 0.5.1 A high-level, high-performance dynamic language for technical computing

Prerequisites: intel/2016.4
Description: Homepage: http://julialang.org
libxc/3.0.0 libxc 3.0.0 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

Prerequisites: intel/2016.4
Description: Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Libxc
mcr/R2013a mcr R2013a 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

Prerequisites: -
Description: Homepage: http://www.mathworks.com/products/compiler/mcr/
mcr/R2014a mcr R2014a 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

Prerequisites: -
Description: Homepage: http://www.mathworks.com/products/compiler/mcr/
mcr/R2014b mcr R2014b 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

Prerequisites: -
Description: Homepage: http://www.mathworks.com/products/compiler/mcr/
mcr/R2015a mcr R2015a 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

Prerequisites: -
Description: Homepage: http://www.mathworks.com/products/compiler/mcr/
mcr/R2015b mcr R2015b 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

Prerequisites: -
Description: Homepage: http://www.mathworks.com/products/compiler/mcr/
mcr/R2016a mcr R2016a 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

Prerequisites: -
Description: Homepage: http://www.mathworks.com/products/compiler/mcr/
mcr/R2016b mcr R2016b 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

Prerequisites: -
Description: Homepage: http://www.mathworks.com/products/compiler/mcr/
metis/4.0.3 metis 4.0.3 METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices

Prerequisites: gcc/5.4.0 or intel/2016.4
Description: 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
metis/5.1.0 metis 5.1.0 METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices

Prerequisites: intel/2016.4
Description: 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
mothur/1.39.4 mothur 1.39.4 Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community

Prerequisites: gcc/5.4.0 or intel/2016.4
Description: Homepage: http://www.mothur.org/
mrbayes/3.2.6 mrbayes 3.2.6 MrBayes is a program for the Bayesian estimation of phylogeny

Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.0.2
Description: Homepage: http://mrbayes.csit.fsu.edu
netcdf-c++-mpi/4.2 netcdf-c++-mpi 4.2 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

Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.0.2
Description: Homepage: http://www.unidata.ucar.edu/software/netcdf/
netcdf-c++/4.2 netcdf-c++ 4.2 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

Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: Homepage: http://www.unidata.ucar.edu/software/netcdf/
netcdf-c++4-mpi/4.3.0 netcdf-c++4-mpi 4.3.0 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

Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.0.2
Description: Homepage: http://www.unidata.ucar.edu/software/netcdf/
netcdf-fortran-mpi/4.4.4 netcdf-fortran-mpi 4.4.4 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

Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.0.2
Description: Homepage: http://www.unidata.ucar.edu/software/netcdf/
netcdf-mpi/4.4.1.1 netcdf-mpi 4.4.1.1 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

Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.0.2
Description: Homepage: http://www.unidata.ucar.edu/software/netcdf/
netcdf/4.4.1.1 netcdf 4.4.1.1 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

Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: Homepage: http://www.unidata.ucar.edu/software/netcdf/
openmpi/2.0.2 openmpi 2.0.2 The Open MPI Project is an open source MPI-2 implementation

Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: Homepage: http://www.open-mpi.org/
perl/5.22.2 perl 5.22.2 Perl 5 is a highly capable, feature-rich programming language with over 29 years of development

Prerequisites: -
Description: Homepage: https://www.perl.org/
petsc-64bits/3.7.5 petsc-64bits 3.7.5 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

Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.0.2
Description: Homepage: http://www.mcs.anl.gov/petsc
petsc/3.7.5 petsc 3.7.5 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

Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.0.2
Description: Homepage: http://www.mcs.anl.gov/petsc
python/2.7.13 python 2.7.13 Python is a programming language that lets you work more quickly and integrate your systems more effectively

Prerequisites: -
Description: Homepage: http://python.org/
python/3.5.2 python 3.5.2 Python is a programming language that lets you work more quickly and integrate your systems more effectively

Prerequisites: -
Description: Homepage: http://python.org/
python27-scipy-stack/2017a python27-scipy-stack 2017a 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

Prerequisites: intel/2017.1
Description: Homepage: http://python.org/
quantumespresso/6.0 quantumespresso 6.0 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)

Prerequisites: intel/2016.4 and openmpi/2.0.2
Description: Homepage: http://www.pwscf.org/
r/3.3.3 r 3.3.3 R is a free software environment for statistical computing and graphics

Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: Homepage: http://www.r-project.org/
ray/2.3.1 ray 2.3.1 Ray -- Parallel genome assemblies for parallel DNA sequencing

Prerequisites: gcc/5.4.0 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.0.2
Description: Homepage: http://sourceforge.net/projects/denovoassembler/
repasthpc/2.2.0 repasthpc 2.2.0 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

Prerequisites: intel/2016.4 and openmpi/2.0.2
Description: Homepage: https://repast.github.io/
samtools/0.1.20 samtools 0.1.20 SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format

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

Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: Homepage: http://www.htslib.org/
spark/2.1.0 spark 2.1.0 Spark is Hadoop MapReduce done in memory

Prerequisites: -
Description: Homepage: http://spark.apache.org
stacks/1.45 stacks 1.45 Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform

Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: 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/
tbb/2017.2.132 tbb 2017.2.132 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

Prerequisites: -
Description: Homepage: http://software.intel.com/en-us/articles/intel-tbb/
tophat/2.1.1 tophat 2.1.1 TopHat is a fast splice junction mapper for RNA-Seq reads

Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: Homepage: http://ccb.jhu.edu/software/tophat/
transdecoder/3.0.1 transdecoder 3.0.1 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

Prerequisites: gcc/5.4.0
Description: Homepage: https://transdecoder.github.io/
trimmomatic/0.36 trimmomatic 0.36 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

Prerequisites: -
Description: Homepage: http://www.usadellab.org/cms/?page=trimmomatic
trinity/2.4.0 trinity 2.4.0 Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data

Prerequisites: intel/2016.4
Description: 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/
wps/3.8.0 wps 3.8.0 WRF Preprocessing System (WPS) for WRF

Prerequisites: intel/2016.4 and openmpi/2.0.2
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
wrf/3.8.0 wrf 3.8.0 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

Prerequisites: intel/2016.4 and openmpi/2.0.2
Description: Homepage: http://www.wrf-model.org