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
arpack-ng/3.4.0 arpack-ng 3.4.0

ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: Homepage: http://forge.scilab.org/index.php/p/arpack-ng/
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/
boost/1.63.0 boost 1.63.0

Boost provides free peer-reviewed portable C++ source libraries
Prerequisites: intel/2016.4
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/
dl_poly4/4.08 dl_poly4 4.08

DL_POLY is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory by I.T
Prerequisites: intel/2016.4 and openmpi/2.0.2
Description: Todorov and W. Smith.
eclipse/4.6.0 eclipse 4.6.0

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
Prerequisites: -
Description: 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/
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/3.3.6 fftw 3.3.6

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: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: Homepage: http://www.fftw.org
gatk/3.7 gatk 3.7

The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data
Prerequisites: -
Description: 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.
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
glpk/4.61 glpk 4.61

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
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: Homepage: https://www.gnu.org/software/glpk/
gmap-gsnap/2017-04-13 gmap-gsnap 2017-04-13

GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program
Prerequisites: gcc/5.4.0 or intel/2016.4
Description: Homepage: http://research-pub.gene.com/gmap/
gromacs/2016.3 gromacs 2016.3

GROMACS is a versatile package to perform molecular dynamics. i.e
Prerequisites: intel/2016.4 and openmpi/2.0.2
Description: simulating the Newtonian equations of motion for systems with hundreds to millions of particles. - CC-Wiki: GROMACS - Homepage: http://www.gromacs.org
gromacs/4.6.7 gromacs 4.6.7

GROMACS is a versatile package to perform molecular dynamics. i.e
Prerequisites: intel/2016.4 and openmpi/2.0.2
Description: simulating the Newtonian equations of motion for systems with hundreds to millions of particles. - CC-Wiki: GROMACS - Homepage: http://www.gromacs.org
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/2.3.2 hmmer 2.3.2

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.
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 or pgi/17.3 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/
impute2/2.3.2 impute2 2.3.2

IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al
Prerequisites: -
Description: 2009 - Homepage: http://mathgen.stats.ox.ac.uk/impute/impute_v2.html
intel/2016.4 intel 2016.4

Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL
Prerequisites: -
Description: Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/
intel/2017.1 intel 2017.1

Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL
Prerequisites: -
Description: Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/
interproscan/5.23-62.0 interproscan 5.23-62.0

InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource
Prerequisites: gcc/5.4.0 or intel/2016.4
Description: Homepage: http://www.ebi.ac.uk/interpro/
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
mach/1.0.18 mach 1.0.18

MACH 1.0 is a Markov Chain based haplotyper that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals
Prerequisites: -
Description: Homepage: http://csg.sph.umich.edu/abecasis/MACH/
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: gcc/5.4.0 or intel/2016.4 or intel/2017.1
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
minia/2.0.7 minia 2.0.7

Minia is a short-read assembler based on a de Bruijn graph
Prerequisites: gcc/5.4.0 or intel/2016.4
Description: Homepage: http://minia.genouest.org/
minimac2/2014.9.15 minimac2 2014.9.15

minimac2 is an improved version of Minimac
Prerequisites: -
Description: 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
minimac3/2.0.1 minimac3 2.0.1

Minimac3 is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac and minimac2
Prerequisites: intel/2016.4
Description: 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
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
namd-multicore/2.12 namd-multicore 2.12

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
Prerequisites: intel/2016.4
Description: -
namd-verbs/2.12 namd-verbs 2.12

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
Prerequisites: intel/2016.4
Description: -
nco/4.6.6 nco 4.6.6

manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5
Prerequisites: intel/2016.4
Description: -
ncview/2.1.7 ncview 2.1.7

Ncview is a visual browser for netCDF format files
Prerequisites: intel/2016.4 and openmpi/2.0.2
Description: 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.
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/
octave/4.2.1 octave 4.2.1

GNU Octave is a high-level interpreted language, primarily intended for numerical computations
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: Homepage: http://www.gnu.org/software/octave/
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 or pgi/17.3
Description: -
openmpi/2.1.1 openmpi 2.1.1

The Open MPI Project is an open source MPI-2 implementation.
Prerequisites: intel/2016.4
Description: -
paraview-offscreen/5.3.0 paraview-offscreen 5.3.0

ParaView is a scientific parallel visualizer
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.paraview.org
paraview/5.3.0 paraview 5.3.0

ParaView is a scientific parallel visualizer
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.paraview.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
pgi/17.3 pgi 17.3

C, C++ and Fortran compilers from The Portland Group
Prerequisites: -
Description: PGI - Homepage: http://www.pgroup.com/
picard/2.1.1 picard 2.1.1

A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format
Prerequisites: -
Description: Homepage: http://broadinstitute.github.io/picard/
plink/1.07 plink 1.07

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
Prerequisites: intel/2016.4
Description: 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.
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/
qhull/2015.2 qhull 2015.2

Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: 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
qrupdate/1.1.2 qrupdate 1.1.2

qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: Homepage: https://sourceforge.net/projects/qrupdate/
qt/4.8.7 qt 4.8.7

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

Qt is a comprehensive cross-platform C++ application framework
Prerequisites: -
Description: Homepage: http://qt.io/
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/
rnammer/1.2 rnammer 1.2

RNAmmer 1.2 predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences
Prerequisites: intel/2016.4
Description: 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.
rstudio-server/1.1.206 rstudio-server 1.1.206

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
Prerequisites: intel/2016.4
Description: Homepage: https://www.rstudio.com/
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/
siesta/4.0 siesta 4.0

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
Prerequisites: intel/2016.4 and openmpi/2.0.2
Description: Homepage: http://departments.icmab.es/leem/siesta
signalp/4.1f signalp 4.1f

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
Prerequisites: -
Description: 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.
spark/2.1.0 spark 2.1.0

Spark is Hadoop MapReduce done in memory
Prerequisites: -
Description: Homepage: http://spark.apache.org
spark/2.1.1 spark 2.1.1

Spark is Hadoop MapReduce done in memory
Prerequisites: -
Description: -
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/
suitesparse/4.5.4 suitesparse 4.5.4

SuiteSparse is a collection of libraries manipulate sparse matrices
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: Homepage: http://faculty.cse.tamu.edu/davis/suitesparse.html
superlu/5.1.1 superlu 5.1.1

SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines
Prerequisites: intel/2016.4
Description: Homepage: http://crd-legacy.lbl.gov/~xiaoye/SuperLU/
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/
tmhmm/2.0c tmhmm 2.0c

TMHMM 2.0 predicts transmembrane helices in proteins
Prerequisites: -
Description: 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.
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/
udunits/2.2.24 udunits 2.2.24

UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.
Prerequisites: intel/2016.4
Description: -
vmd/1.9.3 vmd 1.9.3

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
Prerequisites: intel/2016.4
Description: -
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
wps/3.8.1 wps 3.8.1

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. Compiled with -DNO_LEAP_CALENDAR - 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
wrf/3.8.1 wrf 3.8.1

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: Compiled with -DNO_LEAP_CALENDAR - Homepage: http://www.wrf-model.org