Available software

From CC Doc
Jump to: navigation, search
Other languages:
English • ‎français

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 in the directory /opt/software. 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.
  • 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

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 or intel/2016.4 and openmpi/2.1.1
Description: -
abyss/1.9.0 abyss 1.9.0

Assembly By Short Sequences
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: -
armadillo/7.950.1 armadillo 7.950.1

Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: -
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: -
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: -
bamutil/1.0.13 bamutil 1.0.13

BamUtil is a repository that contains several programs that perform operations on SAM/BAM files
Prerequisites: intel/2016.4
Description: All of these programs are built into a single executable, bam.
bazel/0.5.2 bazel 0.5.2

Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software.
Prerequisites: -
Description: -
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: -
bcftools/1.5 bcftools 1.5

Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools
Prerequisites: gcc/5.4.0 or intel/2016.4
Description: -
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: -
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: -
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 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 boost 1.60.0

Boost provides free peer-reviewed portable C++ source libraries.
Prerequisites: gcc/4.8.5 or gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: -
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: -
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: -
canu/1.5 canu 1.5

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
Prerequisites: gcc/5.4.0
Description: -
cdo/1.7.2 cdo 1.7.2

CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description: -
cgal/4.9 cgal 4.9

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.
Prerequisites: gcc/4.8.5 or gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: -
chapel-single/1.15.0 chapel-single 1.15.0

Chapel is an emerging parallel programming language whose design and development is being led by Cray Inc
Prerequisites: gcc/5.4.0
Description: 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.
chapel-slurm-gasnetrun_ibv/1.15.0 chapel-slurm-gasnetrun_ibv 1.15.0

Chapel is an emerging parallel programming language whose design and development is being led by Cray Inc
Prerequisites: gcc/5.4.0
Description: 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.
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/
cnvnator/0.3.3 cnvnator 0.3.3

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
Prerequisites: gcc/5.4.0 or intel/2016.4
Description: -
cp2k/4.1 cp2k 4.1

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
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 cpmd 3.17.1

The CPMD code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description: -
cuda/8.0.44 cuda 8.0.44

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
Prerequisites: gcc/5.4.0 or intel/2016.4
Description: -
cudnn/5.1 cudnn 5.1

The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.
Prerequisites: gcc/5.4.0 and cuda/8.0.44 or intel/2016.4 and cuda/8.0.44
Description: -
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: -
dealii/8.5.0 dealii 8.5.0

A C++ software library supporting the creation of finite element codes and an open community of users and developers.
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description: -
diamond/0.9.8 diamond 0.9.8

Accelerated BLAST compatible local sequence aligner
Prerequisites: gcc/5.4.0
Description: -
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 or intel/2016.4 and openmpi/2.1.1
Description: -
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
esmf/7.0.1 esmf 7.0.1

The Earth System Modeling Framework (ESMF) is software for building and coupling weather, climate, and related models.
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description: -
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/
fastx-toolkit/0.0.14 fastx-toolkit 0.0.14

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
Prerequisites: gcc/5.4.0
Description: -
fftw-mpi/2.1.5 fftw-mpi 2.1.5

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/2.1.1
Description: -
fftw-mpi/3.3.6 fftw-mpi 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 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: -
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: -
g2clib/1.6.0 g2clib 1.6.0

Library contains GRIB2 encoder/decoder ('C' version).
Prerequisites: -
Description: -
g2lib/1.4.0 g2lib 1.4.0

Library contains GRIB2 encoder/decoder and search/indexing routines.
Prerequisites: -
Description: -
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: -
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: -
glm/0.9.7.2 glm 0.9.7.2

OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications.
Prerequisites: intel/2016.4
Description: -
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: -
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: -
grackle/2.1 grackle 2.1

Grackle is a chemistry and radiative cooling library for astrophysical simulations and models.
Prerequisites: intel/2016.4
Description: -
gromacs-plumed/2016.3 gromacs-plumed 2016.3

GROMACS is a versatile package to perform molecular dynamics. This version contains the PLUMED patches in order to run metadynamics. - 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 gromacs 2016.3

GROMACS is a versatile package to perform molecular dynamics. i.e
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/4.6.7 gromacs 4.6.7

GROMACS is a versatile package to perform molecular dynamics. i.e
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 gromacs 5.0.7

GROMACS is a versatile package to perform molecular dynamics, i.e
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 gromacs 5.1.4

GROMACS is a versatile package to perform molecular dynamics, i.e
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/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: -
hdf/4.2.12 hdf 4.2.12

HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.
Prerequisites: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: -
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 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: -
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: -
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: gcc/5.4.0 or intel/2016.4
Description: -
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: gcc/5.4.0 or intel/2016.4
Description: -
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: 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 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: -
htslib/1.5 htslib 1.5

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
Description: -
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 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/11.3.4.258 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: -
jags/4.2.0 jags 4.2.0

JAGS is Just Another Gibbs Sampler
Prerequisites: intel/2016.4 or intel/2017.1
Description: -
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: -
julia/0.5.1 julia 0.5.1

A high-level, high-performance dynamic language for technical computing.
Prerequisites: intel/2016.4
Description: -
julia/0.6.0 julia 0.6.0

A high-level, high-performance dynamic language for technical computing.
Prerequisites: intel/2016.4
Description: -
kraken/0.10.5-beta kraken 0.10.5-beta

Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies
Prerequisites: gcc/5.4.0 or intel/2016.4
Description: -
lammps/20170331 lammps 20170331

LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics simulation
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description: -
libgtextutils/0.7 libgtextutils 0.7

ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream
Prerequisites: -
Description: -
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/
magma/2.2.0 magma 2.2.0

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.
Prerequisites: gcc/5.4.0 and cuda/8.0.44 or intel/2016.4 and cuda/8.0.44
Description: -
matio/1.5.2 matio 1.5.2

matio is an C library for reading and writing Matlab MAT files.
Prerequisites: intel/2016.4
Description: -
matlab/2017a matlab 2017a

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.
Prerequisites: -
Description: -
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: -
mcr/R2013b mcr R2013b

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: -
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: -
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: -
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: -
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: -
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: -
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: -
megahit/1.1.1 megahit 1.1.1

MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil
Prerequisites: gcc/5.4.0 and cuda/8.0.44
Description: It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly.
metaphlan/2.2.0 metaphlan 2.2.0

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.
Prerequisites: intel/2016.4
Description: -
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: -
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/4.8.5 or gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: -
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: -
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
mono/4.6.2.7 mono 4.6.2.7

An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET
Prerequisites: gcc/5.4.0 or intel/2016.4
Description: -
mono/5.4.0.56 mono 5.4.0.56

An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET.
Prerequisites: gcc/5.4.0
Description: -
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: -
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 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/3.23 mummer 3.23

MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form
Prerequisites: gcc/5.4.0
Description: AMOS makes use of it.
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 or intel/2016.4 and cuda/8.0.44
Description: -
namd-verbs-smp/2.12 namd-verbs-smp 2.12

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
Prerequisites: intel/2016.4 and cuda/8.0.44
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: -
ncl/6.4.0 ncl 6.4.0

NCL is an interpreted language designed specifically for scientific data analysis and visualization.
Prerequisites: intel/2016.4 and openmpi/2.1.1
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 or intel/2016.4 and openmpi/2.1.1
Description: -
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 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 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: -
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 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 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 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 netcdf-fortran 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 or intel/2016.4 or intel/2017.1
Description: -
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 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/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: -
nlopt/2.4.2 nlopt 2.4.2

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.
Prerequisites: intel/2016.4
Description: -
nwchem/6.6.revision27746 nwchem 6.6.revision27746

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.
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description: -
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: -
openbabel/2.4.1 openbabel 2.4.1

Open Babel is a chemical toolbox designed to speak the many languages of chemical data
Prerequisites: intel/2016.4
Description: 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.
openfoam/4.1 openfoam 4.1

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.
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: -
openmpi/1.8.8 openmpi 1.8.8

The Open MPI Project is an open source MPI-2 implementation.
Prerequisites: intel/2016.4
Description: -
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/2016.4 and cuda/8.0.44 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: gcc/4.8.5 or 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: -
orca/4.0.0.2 orca 4.0.0.2

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.
Prerequisites: intel/2016.4 and openmpi/2.0.2
Description: -
p4est/1.1 p4est 1.1

The p4est software library enables the dynamic management of a collection of adaptive octrees, conveniently called a forest of octrees
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description: -
parallel/20170622 parallel 20170622

parallel: Build and execute shell commands in parallel
Prerequisites: gcc/5.4.0 or 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 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 paraview 5.3.0

ParaView is a scientific parallel visualizer.
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 parmetis 4.0.3

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
Prerequisites: intel/2016.4 and openmpi/2.0.2
Description: 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.
pear/0.9.10 pear 0.9.10

PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger
Prerequisites: intel/2016.4
Description: It is fully parallelized and can run with as low as just a few kilobytes of memory.
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/
perl4-corelibs/0.003 perl4-corelibs 0.003

Libraries historically supplied with Perl 4
Prerequisites: intel/2016.4
Description: -
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/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 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/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 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/
pilon/1.22 pilon 1.22

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 ...
Prerequisites: -
Description: -
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.
plumed/2.3.0 plumed 2.3.0

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
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 plumed 2.3.2

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
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 pnetcdf 1.8.1

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
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description: -
prinseq/0.20.4 prinseq 0.20.4

A bioinformatics tool to PRe-process and show INformation of SEQuence data.
Prerequisites: gcc/5.4.0
Description: -
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: -
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: -
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/2016.4 or intel/2017.1
Description: -
python35-scipy-stack/2017a python35-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: gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: -
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: -
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: -
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 or intel/2016.4 and openmpi/2.1.1
Description: -
r-bundle-bioconductor/3.4 r-bundle-bioconductor 3.4

R is a free software environment for statistical computing and graphics.
Prerequisites: gcc/5.4.0
Description: -
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: -
r/3.4.0 r 3.4.0

R is a free software environment for statistical computing and graphics.
Prerequisites: intel/2016.4
Description: -
racon/20170719 racon 20170719

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.
Prerequisites: gcc/5.4.0
Description: -
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 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: -
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 or intel/2016.4 and openmpi/2.1.1
Description: -
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.
root/6.08.02 root 6.08.02

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.
Prerequisites: gcc/5.4.0
Description: -
rosetta/3.8 rosetta 3.8

Rosetta is the premier software suite for modeling macromolecular structures
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description: -
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: -
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: -
samtools/1.5 samtools 1.5

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
Description: -
scotch/6.0.4 scotch 6.0.4

Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.
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: -
shengbte/1.1.1 shengbte 1.1.1

ShengBTE is a software package for solving the Boltzmann Transport Equation for phonons
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.0.2
Description: -
shotmap/1.1 shotmap 1.1

Shotmap is a software workflow that functionally annotates and compares shotgun metagenomes
Prerequisites: gcc/5.4.0
Description: 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.
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 or intel/2016.4 and openmpi/2.1.1
Description: -
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.
spades/3.10.1 spades 3.10.1

Genome assembler for single-cell and isolates data sets
Prerequisites: gcc/5.4.0
Description: -
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: -
spglib/1.9.9 spglib 1.9.9

Spglib is a C library for finding and handling crystal symmetries.
Prerequisites: gcc/4.8.5 or gcc/5.4.0 or intel/2016.4 or intel/2017.1
Description: -
sspace-longread/1-1 sspace-longread 1-1

SSPACE-LongRead is a stand-alone program for scaffolding pre-assembled contigs using long reads (e.g
Prerequisites: intel/2016.4
Description: PacBio RS reads).
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/1.46 stacks 1.46

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
Description: -
subread/1.5.2 subread 1.5.2

High performance read alignment, quantification and mutation discovery
Prerequisites: gcc/5.4.0
Description: -
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: -
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/
tabix/0.2.6 tabix 0.2.6

Generic indexer for TAB-delimited genome position files
Prerequisites: intel/2016.4
Description: -
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: -
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: -
torch/20170530 torch 20170530

Torch is a scientific computing framework with wide support for machine learning algorithms that puts GPUs first
Prerequisites: gcc/5.4.0 and cuda/8.0.44 or intel/2016.4 and cuda/8.0.44
Description: -
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/
trilinos/12.10.1 trilinos 12.10.1

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
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description: A unique design feature of Trilinos is its focus on packages.
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: gcc/5.4.0 or intel/2016.4
Description: -
trinotate/3.0.2 trinotate 3.0.2

Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.
Prerequisites: gcc/5.4.0
Description: -
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: -
vasp/4.6 vasp 4.6

The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description: 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 .
vasp/5.4.1 vasp 5.4.1

The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description: 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 .
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: -
voro++/0.4.6 voro++ 0.4.6

Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation
Prerequisites: intel/2016.4
Description: 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.
vtk/8.0.0 vtk 8.0.0

The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description: 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.
wps/3.8.0 wps 3.8.0

WRF Preprocessing System (WPS) for WRF
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description: -
wps/3.8.1 wps 3.8.1

WRF Preprocessing System (WPS) for WRF
Prerequisites: intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1
Description: -
wrf-fire/20170625 wrf-fire 20170625

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
Prerequisites: intel/2016.4 and openmpi/2.1.1
Description: The fire spread is implemented by the level set method.
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 or intel/2016.4 and openmpi/2.1.1
Description: -
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 or intel/2016.4 and openmpi/2.1.1
Description: -
xcrysden/1.5.60 xcrysden 1.5.60

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.
Prerequisites: intel/2016.4
Description: -
yaxt/0.5.1 yaxt 0.5.1

Yet Another eXchange Tool
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: