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We provide a range of pre-installed scientific software. Most of our software is made available through software modules (see our guide for instructions on loading and using modules).

Some of our software is also provided by other means, including the use of Singularity containers.

Where software requires special usage instructions or considerations, these are noted below.

Quick Links:

Software available as modules

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Anaconda3

Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.

https://www.anaconda.com

  • Anaconda3 v5.1.0: system
  • Anaconda3 v5.3.0: system
  • Anaconda3 v2019.10: system

Usage Guidance

By default, conda will store your environments and downloaded packages in your home directory under ~/.conda - this will quickly cause your home directory to run out of space. To prevent this from happening we recommend the following:

  1. Create a dedicated conda folder in your group home folder with subdirectories for packages and environments e.g.
    cd /well/<group>/users/<username>
    mkdir -p conda/pkgs conda/envs
  2. Create the file ~/.condarc containing the following configuration (NB indented lines are indented two spaces):
    pkgs_dirs:
      - /well/<group>/users/<username>/conda/pkgs
    envs_dirs:
      - /well/<group>/users/<username>/conda/envs

ANTs

ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data.

http://stnava.github.io/ANTs/

  • ANTs v2.3.1 (versionsuffix: '-Python-3.6.6'): foss/2018b

arpack-ng

ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.

http://forge.scilab.org/index.php/p/arpack-ng/

  • arpack-ng v3.5.0: foss/2018b

Autoconf

Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.

http://www.gnu.org/software/autoconf/

  • Autoconf v2.69: GCC/4.9.3-2.25, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.2.0, system

Automake

Automake: GNU Standards-compliant Makefile generator

https://www.gnu.org/software/automake/automake.html

  • Automake v1.15: GCC/4.9.3-2.25, system
  • Automake v1.15.1: GCCcore/6.4.0
  • Automake v1.16.1: GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.2.0

Autotools

This bundle collect the standard GNU build tools: Autoconf, Automake and libtool

http://autotools.io

  • Autotools v20150215: GCC/4.9.3-2.25, system
  • Autotools v20170619: GCCcore/6.4.0
  • Autotools v20180311: GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.2.0

BamTools

BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.

https://github.com/pezmaster31/bamtools

  • BamTools v2.5.1: foss/2018b

Bazel

Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software.

http://bazel.io/

  • Bazel v0.20.0: GCCcore/7.3.0, GCCcore/8.2.0

BBMap

BBMap short read aligner, and other bioinformatic tools.

https://sourceforge.net/projects/bbmap/

  • BBMap v38.50b: GCC/8.2.0-2.31.1

BEDOPS

BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.

http://bedops.readthedocs.io/en/latest/index.html

  • BEDOPS v2.4.35: foss/2018b

BEDTools

The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.

https://github.com/arq5x/bedtools2

  • BEDTools v2.27.1: foss/2018b

binutils

binutils: GNU binary utilities

https://directory.fsf.org/project/binutils/

  • binutils v2.25: GCCcore/4.9.3, system
  • binutils v2.28: GCCcore/6.4.0, system
  • binutils v2.30: GCCcore/7.3.0, system
  • binutils v2.31.1: GCCcore/8.2.0, system
  • binutils v2.32: GCCcore/8.3.0, GCCcore/9.2.0, system

Bio-DB-HTS

Read files using HTSlib including BAM/CRAM, Tabix and BCF database files

https://metacpan.org/release/Bio-DB-HTS

  • Bio-DB-HTS v2.11 (versionsuffix: '-Perl-5.28.0'): foss/2018b

BioPerl

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.

http://www.bioperl.org/

  • BioPerl v1.7.2 (versionsuffix: '-Perl-5.28.0'): foss/2018b

Bison

Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.

http://www.gnu.org/software/bison

  • Bison v3.0.4: GCCcore/4.9.3, GCCcore/6.4.0, GCCcore/7.3.0, system
  • Bison v3.0.5: GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, system
  • Bison v3.3.2: GCCcore/8.3.0, GCCcore/9.2.0, system

Boost

Boost provides free peer-reviewed portable C++ source libraries.

http://www.boost.org/

  • Boost v1.67.0: foss/2018b

BWA

Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.

http://bio-bwa.sourceforge.net/

  • BWA v0.7.17: foss/2018b, intel/2018a

bx-python

The bx-python project is a Python library and associated set of scripts to allow for rapid implementation of genome scale analyses.

https://github.com/bxlab/bx-python

  • bx-python v0.8.2 (versionsuffix: '-Python-3.6.6'): foss/2018b

bzip2

bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.

https://sourceware.org/bzip2

  • bzip2 v1.0.6: GCCcore/7.3.0, GCCcore/8.2.0
  • bzip2 v1.0.8: GCCcore/8.3.0

cairo

Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB

https://cairographics.org

  • cairo v1.14.12: GCCcore/7.3.0
  • cairo v1.16.0: GCCcore/8.2.0, GCCcore/8.3.0

CellRanger

Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.

https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger

  • CellRanger v3.1.0: system

CMake

CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.

https://www.cmake.org

  • CMake v3.11.4: GCCcore/7.3.0
  • CMake v3.12.1: GCCcore/7.3.0
  • CMake v3.13.3: GCCcore/8.2.0
  • CMake v3.15.3: GCCcore/8.3.0

Coreutils

The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system.

http://www.gnu.org/software/coreutils/

  • Coreutils v8.29: GCCcore/6.4.0

CUDA

CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.

https://developer.nvidia.com/cuda-toolkit

  • CUDA v9.2.88: GCC/7.3.0-2.30
  • CUDA v10.1.105: GCC/8.2.0-2.31.1
  • CUDA v10.1.243: GCC/8.3.0

cuDNN

The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.

https://developer.nvidia.com/cudnn

  • cuDNN v7.6.4.38: gcccuda/2019a, gcccuda/2019b

cURL

libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more.

https://curl.haxx.se

  • cURL v7.60.0: GCCcore/7.3.0
  • cURL v7.63.0: GCCcore/8.2.0
  • cURL v7.66.0: GCCcore/8.3.0

cutadapt

Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

https://opensource.scilifelab.se/projects/cutadapt/

  • cutadapt v1.18: GCCcore/8.2.0
  • cutadapt v1.18 (versionsuffix: '-Python-3.6.6'): foss/2018b

dask

Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling.

http://github.com/dask/dask/

  • dask v0.19.4 (versionsuffix: '-Python-3.6.6'): foss/2018b

DBD-mysql

Perl binding for MySQL

http://search.cpan.org/dist/DBD-mysql/lib/DBD/mysql.pm

  • DBD-mysql v4.048 (versionsuffix: '-Perl-5.28.0'): foss/2018b

DBus

D-Bus is a message bus system, a simple way for applications to talk to one another. In addition to interprocess communication, D-Bus helps coordinate process lifecycle; it makes it simple and reliable to code a "single instance" application or daemon, and to launch applications and daemons on demand when their services are needed.

http://dbus.freedesktop.org/

  • DBus v1.13.6: GCCcore/7.3.0

deepTools

deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.

https://deeptools.readthedocs.io/

  • deepTools v3.3.1 (versionsuffix: '-Python-3.6.6'): foss/2018b

NB Please ensure that you load plotly before using this version of deeptools e.g. module load plotly.py/4.4.1-foss-2018b-Python-3.6.6 . This is due to a bug in the deeptools module which should be fixed in a future release.

Doxygen

Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.

https://www.doxygen.org

  • Doxygen v1.8.14: GCCcore/7.3.0
  • Doxygen v1.8.15: GCCcore/8.2.0
  • Doxygen v1.8.16: GCCcore/8.3.0

EasyBuild

EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.

https://easybuilders.github.io/easybuild

  • EasyBuild v3.8.1: system
  • EasyBuild v3.9.2: system
  • EasyBuild v3.9.3: system
  • EasyBuild v3.9.4: system
  • EasyBuild v4.0.0: system
  • EasyBuild v4.0.1: system
  • EasyBuild v4.1.0: system

Emacs

GNU Emacs is an extensible, customizable text editor--and more. At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming language with extensions to support text editing.

http://www.gnu.org/software/emacs/

  • Emacs v25.3: GCCcore/7.3.0

expat

Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags)

https://libexpat.github.io

  • expat v2.2.5: GCCcore/6.4.0, GCCcore/7.3.0
  • expat v2.2.6: GCCcore/8.2.0
  • expat v2.2.7: GCCcore/8.3.0

FastQC

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.

https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

  • FastQC v0.11.8 (versionsuffix: '-Java-11'): system

FFmpeg

A complete, cross-platform solution to record, convert and stream audio and video.

https://www.ffmpeg.org/

  • FFmpeg v4.2.1: GCCcore/8.3.0

FFTW

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.

http://www.fftw.org

  • FFTW v3.3.4: gompi/2016a
  • FFTW v3.3.7: gompi/2018a
  • FFTW v3.3.8: gompi/2018b, gompi/2019a, gompi/2019b, gompic/2018b, gompic/2019a, gompic/2019b

file

The file command is 'a file type guesser', that is, a command-line tool that tells you in words what kind of data a file contains.

http://www.darwinsys.com/file/

  • file v5.35: GCCcore/7.3.0

flex

Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.

http://flex.sourceforge.net/

  • flex v2.5.39: GCCcore/4.9.3, system
  • flex v2.6.3: system
  • flex v2.6.4: GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.2.0, system

FLTK

FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.

https://www.fltk.org

  • FLTK v1.3.4: foss/2018b
  • FLTK v1.3.5: GCC/8.2.0-2.31.1, GCC/8.3.0

fontconfig

Fontconfig is a library designed to provide system-wide font configuration, customization and application access.

https://www.freedesktop.org/wiki/Software/fontconfig/

  • fontconfig v2.13.0: GCCcore/7.3.0
  • fontconfig v2.13.1: GCCcore/8.2.0, GCCcore/8.3.0

foss

GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.

https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain

  • foss v2016a: system
  • foss v2018a: system
  • foss v2018b: system
  • foss v2019a: system
  • foss v2019b: system

fosscuda

GCC based compiler toolchain with CUDA support, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.

(none)

  • fosscuda v2018b: system
  • fosscuda v2019a: system
  • fosscuda v2019b: system

freeglut

freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library.

http://freeglut.sourceforge.net/

  • freeglut v3.0.0: foss/2018b

freetype

FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well.

http://freetype.org

  • freetype v2.9.1: GCCcore/7.3.0, GCCcore/8.2.0
  • freetype v2.10.1: GCCcore/8.3.0

FriBidi

The Free Implementation of the Unicode Bidirectional Algorithm.

https://github.com/fribidi/fribidi

  • FriBidi v1.0.5: GCCcore/7.3.0, GCCcore/8.3.0

FSL

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.

http://www.fmrib.ox.ac.uk/fsl/

  • FSL v5.0.11 (versionsuffix: '-Python-3.6.6'): foss/2018b

GC3Pie

GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution environments.

https://gc3pie.readthedocs.org

  • GC3Pie v2.6.4 (versionsuffix: '-Python-3.6.6'): system

GCC

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,...).

http://gcc.gnu.org/

  • GCC v4.9.3 (versionsuffix: '-2.25'): system
  • GCC v6.4.0 (versionsuffix: '-2.28'): system
  • GCC v7.3.0 (versionsuffix: '-2.30'): system
  • GCC v8.2.0 (versionsuffix: '-2.31.1'): system
  • GCC v8.3.0: system

GCCcore

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,...).

https://gcc.gnu.org/

  • GCCcore v4.9.3: system
  • GCCcore v6.4.0: system
  • GCCcore v7.3.0: system
  • GCCcore v8.2.0: system
  • GCCcore v8.3.0: system
  • GCCcore v9.2.0: system

gcccuda

GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.

(none)

  • gcccuda v2018b: system
  • gcccuda v2019a: system
  • gcccuda v2019b: system

GDAL

GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.

https://www.gdal.org/

  • GDAL v2.2.3 (versionsuffix: '-Python-3.6.6'): foss/2018b
  • GDAL v3.0.0 (versionsuffix: '-Python-3.7.2'): foss/2019a

Gdk-Pixbuf

The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3.

https://developer.gnome.org/gdk-pixbuf/stable/

  • Gdk-Pixbuf v2.36.12: foss/2018b

GEOS

GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)

http://trac.osgeo.org/geos

  • GEOS v3.6.2 (versionsuffix: '-Python-3.6.6'): foss/2018b
  • GEOS v3.7.2 (versionsuffix: '-Python-3.7.2'): foss/2019a

gettext

GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation

https://www.gnu.org/software/gettext/

  • gettext v0.19.8.1: GCCcore/7.3.0, GCCcore/8.2.0, system
  • gettext v0.20.1: GCCcore/8.3.0, system

gflags

The gflags package contains a C++ library that implements commandline flags processing. It includes built-in support for standard types such as string and the ability to define flags in the source file in which they are used.

https://github.com/gflags/gflags

  • gflags v2.2.2: GCCcore/8.3.0

Ghostscript

Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that.

https://ghostscript.com

  • Ghostscript v9.23: GCCcore/7.3.0
  • Ghostscript v9.27: GCCcore/8.2.0
  • Ghostscript v9.50: GCCcore/8.3.0

git

Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.

http://git-scm.com/

  • git v2.19.1: GCCcore/7.3.0

GitPython

GitPython is a python library used to interact with Git repositories

https://github.com/gitpython-developers/GitPython

  • GitPython v2.1.11 (versionsuffix: '-Python-3.6.6'): foss/2018b
  • GitPython v3.0.3 (versionsuffix: '-Python-3.7.2'): GCCcore/8.2.0

GL2PS

GL2PS: an OpenGL to PostScript printing library

http://www.geuz.org/gl2ps/

  • GL2PS v1.4.0: foss/2018b

GLib

GLib is one of the base libraries of the GTK+ project

https://www.gtk.org/

  • GLib v2.54.3: GCCcore/7.3.0
  • GLib v2.60.1: GCCcore/8.2.0
  • GLib v2.62.0: GCCcore/8.3.0

glog

A C++ implementation of the Google logging module.

https://github.com/google/glog

  • glog v0.4.0: GCCcore/8.3.0

GLPK

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.

https://www.gnu.org/software/glpk/

  • GLPK v4.65: GCCcore/7.3.0

GMP

GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.

https://gmplib.org/

  • GMP v6.1.2: GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0

gnuplot

Portable interactive, function plotting utility

http://gnuplot.sourceforge.net/

  • gnuplot v5.2.5: foss/2018b

GObject-Introspection

GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library.

https://wiki.gnome.org/GObjectIntrospection/

  • GObject-Introspection v1.54.1 (versionsuffix: '-Python-2.7.15'): foss/2018b

gompi

GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.

(none)

  • gompi v2016a: system
  • gompi v2018a: system
  • gompi v2018b: system
  • gompi v2019a: system
  • gompi v2019b: system

gompic

GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled.

(none)

  • gompic v2018b: system
  • gompic v2019a: system
  • gompic v2019b: system

gperf

GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.

https://www.gnu.org/software/gperf/

  • gperf v3.1: GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0

GraphicsMagick

GraphicsMagick is the swiss army knife of image processing.

http://www.graphicsmagick.org/

  • GraphicsMagick v1.3.31: foss/2018b

GROMACS

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a CPU only build, containing both MPI and threadMPI builds.

http://www.gromacs.org

  • GROMACS v2019: foss/2018b

GSL

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.

https://www.gnu.org/software/gsl/

  • GSL v2.5: GCC/7.3.0-2.30, GCC/8.2.0-2.31.1
  • GSL v2.6: GCC/8.3.0

h5py

HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.

http://www.h5py.org/

  • h5py v2.8.0 (versionsuffix: '-Python-3.6.6'): foss/2018b
  • h5py v2.9.0: fosscuda/2019a

HarfBuzz

HarfBuzz is an OpenType text shaping engine.

https://www.freedesktop.org/wiki/Software/HarfBuzz

  • HarfBuzz v2.2.0: foss/2018b

Harmony

Scalable integration of single cell RNAseq data for batch correction and meta analysis

https://portals.broadinstitute.org/harmony/

  • Harmony v1.0.0 (versionsuffix: '-R-3.5.1'): foss/2018b

HDF5

HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.

https://portal.hdfgroup.org/display/support

  • HDF5 v1.10.2: foss/2018b
  • HDF5 v1.10.5: gompi/2019a, gompi/2019b, gompic/2019a

help2man

help2man produces simple manual pages from the '--help' and '--version' output of other commands.

https://www.gnu.org/software/help2man/

  • help2man v1.47.4: GCCcore/6.4.0, GCCcore/7.3.0, system
  • help2man v1.47.7: GCCcore/8.2.0
  • help2man v1.47.8: GCCcore/8.3.0
  • help2man v1.47.10: GCCcore/9.2.0

HISAT2

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome).

https://ccb.jhu.edu/software/hisat2/index.shtml

  • HISAT2 v2.1.0: foss/2018b

HMMER

HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.

http://hmmer.org/

  • HMMER v3.2.1: foss/2018b

HTSlib

A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix

http://www.htslib.org/

  • HTSlib v1.9: foss/2018b

hwloc

The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.

https://www.open-mpi.org/projects/hwloc/

  • hwloc v1.11.2: GCC/4.9.3-2.25
  • hwloc v1.11.8: GCCcore/6.4.0
  • hwloc v1.11.10: GCCcore/7.3.0
  • hwloc v1.11.11: GCCcore/8.2.0
  • hwloc v1.11.12: GCCcore/8.3.0
  • hwloc v2.1.0: GCCcore/9.2.0

hypothesis

Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets you find more bugs in your code with less work.

https://github.com/HypothesisWorks/hypothesis

  • hypothesis v4.44.2 (versionsuffix: '-Python-3.7.4'): GCCcore/8.3.0

icc

Intel C and C++ compilers

https://software.intel.com/en-us/intel-compilers/

  • icc v2018.1.163 (versionsuffix: '-GCC-6.4.0-2.28'): system
  • icc v2019.1.144 (versionsuffix: '-GCC-8.2.0-2.31.1'): system

iccifort

Intel C, C++ & Fortran compilers

https://software.intel.com/en-us/intel-compilers/

  • iccifort v2018.1.163 (versionsuffix: '-GCC-6.4.0-2.28'): system
  • iccifort v2019.1.144 (versionsuffix: '-GCC-8.2.0-2.31.1'): system
  • iccifort v2019.5.281: system

ICU

ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications.

http://site.icu-project.org/home

  • ICU v61.1: GCCcore/7.3.0
  • ICU v64.2: GCCcore/8.2.0, GCCcore/8.3.0

ifort

Intel Fortran compiler

https://software.intel.com/en-us/intel-compilers/

  • ifort v2018.1.163 (versionsuffix: '-GCC-6.4.0-2.28'): system
  • ifort v2019.1.144 (versionsuffix: '-GCC-8.2.0-2.31.1'): system

IGV

This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files.

http://www.broadinstitute.org/software/igv/

  • IGV v2.5.0 (versionsuffix: '-Java-11'): system

IGVTools

This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files. See also http://www.broadinstitute.org/software/igv/igvtools_commandline.

https://software.broadinstitute.org/software/igv/igvtools

  • IGVTools v2.4.18 (versionsuffix: '-Java-1.8'): system

iimpi

Intel C/C++ and Fortran compilers, alongside Intel MPI.

http://software.intel.com/en-us/intel-cluster-toolkit-compiler/

  • iimpi v2018a: system
  • iimpi v2019a: system

ImageMagick

ImageMagick is a software suite to create, edit, compose, or convert bitmap images

https://www.imagemagick.org/

  • ImageMagick v7.0.8-11: GCCcore/7.3.0
  • ImageMagick v7.0.8-46: GCCcore/8.2.0
  • ImageMagick v7.0.9-5: GCCcore/8.3.0

imkl

Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.

https://software.intel.com/en-us/intel-mkl/

  • imkl v2018.1.163: iimpi/2018a
  • imkl v2019.1.144: iimpi/2019a

impi

Intel MPI Library, compatible with MPICH ABI

https://software.intel.com/en-us/intel-mpi-library/

  • impi v2018.1.163: iccifort/2018.1.163-GCC-6.4.0-2.28
  • impi v2018.4.274: iccifort/2019.1.144-GCC-8.2.0-2.31.1

intel

Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL).

https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain

  • intel v2018a: system
  • intel v2019a: system

intltool

intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.

http://freedesktop.org/wiki/Software/intltool/

  • intltool v0.51.0: GCCcore/8.2.0, GCCcore/8.3.0
  • intltool v0.51.0 (versionsuffix: '-Perl-5.28.0'): GCCcore/7.3.0

ITK

Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data.

https://itk.org

  • ITK v4.13.1 (versionsuffix: '-Python-3.6.6'): foss/2018b

JasPer

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.

https://www.ece.uvic.ca/~frodo/jasper/

  • JasPer v2.0.14: GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0

Java

Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.

http://openjdk.java.net

  • Java v1.8.0_31: system
  • Java v1.8.0_192: system
  • Java v11.0.2: system

jemalloc

jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.

http://www.canonware.com/jemalloc

  • jemalloc v5.1.0: GCCcore/7.3.0

Keras

Keras is a minimalist, highly modular neural networks library, written in Python and capable of running on top of either TensorFlow or Theano.

https://keras.io/

  • Keras v2.2.4 (versionsuffix: '-Python-3.7.2'): fosscuda/2019a

LAME

LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.

http://lame.sourceforge.net/

  • LAME v3.100: GCCcore/8.3.0

libcerf

libcerf is a self-contained numeric library that provides an efficient and accurate implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions.

http://apps.jcns.fz-juelich.de/doku/sc/libcerf

  • libcerf v1.7: GCCcore/7.3.0

libdrm

Direct Rendering Manager runtime library.

http://dri.freedesktop.org

  • libdrm v2.4.92: GCCcore/7.3.0
  • libdrm v2.4.97: GCCcore/8.2.0
  • libdrm v2.4.99: GCCcore/8.3.0

libffi

The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time.

http://sourceware.org/libffi/

  • libffi v3.2.1: GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, system

libgd

GD is an open source code library for the dynamic creation of images by programmers.

https://libgd.github.io/

  • libgd v2.2.5: GCCcore/7.3.0

libgeotiff

Library for reading and writing coordinate system information from/to GeoTIFF files

https://directory.fsf.org/wiki/Libgeotiff

  • libgeotiff v1.4.2: foss/2018b
  • libgeotiff v1.5.1: GCCcore/8.2.0, GCCcore/8.3.0

libGLU

The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.

ftp://ftp.freedesktop.org/pub/mesa/glu/

  • libGLU v9.0.0: GCCcore/8.2.0, foss/2018b
  • libGLU v9.0.1: GCCcore/8.3.0

libgpuarray

Library to manipulate tensors on the GPU.

http://deeplearning.net/software/libgpuarray/

  • libgpuarray v0.7.6: fosscuda/2019a

libjpeg-turbo

libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.

https://sourceforge.net/projects/libjpeg-turbo/

  • libjpeg-turbo v2.0.0: GCCcore/7.3.0
  • libjpeg-turbo v2.0.2: GCCcore/7.3.0, GCCcore/8.2.0
  • libjpeg-turbo v2.0.3: GCCcore/8.3.0

libpciaccess

Generic PCI access library.

https://cgit.freedesktop.org/xorg/lib/libpciaccess/

  • libpciaccess v0.14: GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0
  • libpciaccess v0.16: GCCcore/9.2.0

libpng

libpng is the official PNG reference library

http://www.libpng.org/pub/png/libpng.html

  • libpng v1.6.34: GCCcore/7.3.0
  • libpng v1.6.36: GCCcore/8.2.0
  • libpng v1.6.37: GCCcore/8.3.0

libreadline

The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.

https://tiswww.case.edu/php/chet/readline/rltop.html

  • libreadline v7.0: GCCcore/7.3.0
  • libreadline v8.0: GCCcore/8.2.0, GCCcore/8.3.0

libsndfile

Libsndfile is a C library for reading and writing files containing sampled sound (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.

http://www.mega-nerd.com/libsndfile

  • libsndfile v1.0.28: GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0

LibTIFF

tiff: Library and tools for reading and writing TIFF data files

https://www.remotesensing.org/libtiff/

  • LibTIFF v4.0.9: GCCcore/7.3.0
  • LibTIFF v4.0.10: GCCcore/8.2.0, GCCcore/8.3.0

libtool

GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.

http://www.gnu.org/software/libtool

  • libtool v2.4.6: GCC/4.9.3-2.25, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.2.0, system

libunwind

The primary goal of libunwind is to define a portable and efficient C programming interface (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain (non-local goto). The API supports both local (same-process) and remote (across-process) operation. As such, the API is useful in a number of applications

https://www.nongnu.org/libunwind/

  • libunwind v1.3.1: GCCcore/8.2.0, GCCcore/8.3.0

libxml2

Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).

http://xmlsoft.org/

  • libxml2 v2.9.7: GCCcore/6.4.0
  • libxml2 v2.9.8: GCCcore/7.3.0, GCCcore/8.2.0
  • libxml2 v2.9.9: GCCcore/8.3.0
  • libxml2 v2.9.10: GCCcore/9.2.0

libxslt

Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform).

http://xmlsoft.org/

  • libxslt v1.1.32: GCCcore/7.3.0

libyaml

LibYAML is a YAML parser and emitter written in C.

https://pyyaml.org/wiki/LibYAML

  • libyaml v0.2.1: GCCcore/7.3.0, system
  • libyaml v0.2.2: GCCcore/8.2.0, GCCcore/8.3.0

LittleCMS

Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance.

http://www.littlecms.com/

  • LittleCMS v2.9: GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0

LLVM

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

http://llvm.org/

  • LLVM v6.0.0: GCCcore/7.3.0
  • LLVM v7.0.1: GCCcore/8.2.0
  • LLVM v9.0.0: GCCcore/8.3.0

lxml

The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.

http://lxml.de/

  • lxml v4.2.5 (versionsuffix: '-Python-3.6.6'): foss/2018b

LZO

Portable lossless data compression library

http://www.oberhumer.com/opensource/lzo/

  • LZO v2.10: foss/2018b

M4

GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.

http://www.gnu.org/software/m4/m4.html

  • M4 v1.4.17: GCC/4.9.3-2.25, GCCcore/4.9.3, system
  • M4 v1.4.18: GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.2.0, system

Mageck

Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.

https://sourceforge.net/projects/mageck/

  • Mageck v0.5.9.2 (versionsuffix: '-Python-3.6.6'): foss/2018b

magma

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.

https://icl.cs.utk.edu/magma/

  • magma v2.5.1: fosscuda/2019b

Mako

A super-fast templating language that borrows the best ideas from the existing templating languages

http://www.makotemplates.org

  • Mako v1.0.7 (versionsuffix: '-Python-2.7.15'): foss/2018b
  • Mako v1.0.8: GCCcore/8.2.0
  • Mako v1.1.0: GCCcore/8.3.0

MariaDB

MariaDB An enhanced, drop-in replacement for MySQL.

https://mariadb.org/

  • MariaDB v10.3.10: foss/2018b

MariaDB-connector-c

MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases.

https://downloads.mariadb.org/connector-c/

  • MariaDB-connector-c v2.3.7: GCCcore/8.2.0, foss/2018b

matplotlib

matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.

https://matplotlib.org

  • matplotlib v3.0.0 (versionsuffix: '-Python-3.6.6'): foss/2018b
  • matplotlib v3.0.2 (versionsuffix: '-Python-3.6.6'): foss/2018b
  • matplotlib v3.1.1 (versionsuffix: '-Python-3.7.4'): foss/2019b

MCR

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.

http://www.mathworks.com/products/compiler/mcr/

  • MCR vR2015a: system

Mesa

Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.

https://www.mesa3d.org/

  • Mesa v18.1.1: foss/2018b
  • Mesa v19.0.1: GCCcore/8.2.0
  • Mesa v19.1.7: GCCcore/8.3.0

Meson

Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.

https://mesonbuild.com

  • Meson v0.50.0 (versionsuffix: '-Python-3.7.2'): GCCcore/8.2.0
  • Meson v0.51.2 (versionsuffix: '-Python-3.7.4'): GCCcore/8.3.0

METIS

METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.

http://glaros.dtc.umn.edu/gkhome/metis/metis/overview

  • METIS v5.1.0: foss/2018b

motif

Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix.

http://motif.ics.com/

  • motif v2.3.8: foss/2018b

MPFR

The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.

https://www.mpfr.org

  • MPFR v4.0.1: GCCcore/7.3.0
  • MPFR v4.0.2: GCCcore/8.3.0

MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report. MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.

http://multiqc.info

  • MultiQC v1.7 (versionsuffix: '-Python-3.6.6'): foss/2018b

NASM

NASM: General-purpose x86 assembler

https://www.nasm.us/

  • NASM v2.13.03: GCCcore/7.3.0
  • NASM v2.14.02: GCCcore/8.2.0, GCCcore/8.3.0

ncbi-vdb

The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.

https://github.com/ncbi/ncbi-vdb

  • ncbi-vdb v2.9.3: foss/2018b

NCCL

The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs.

https://developer.nvidia.com/nccl

  • NCCL v2.4.2: gcccuda/2019a
  • NCCL v2.4.8: gcccuda/2019b

ncdf4

ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files

https://cran.r-project.org/web/packages/ncdf4

  • ncdf4 v1.16.1 (versionsuffix: '-R-3.6.0'): foss/2019a

ncurses

The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.

http://www.gnu.org/software/ncurses/

  • ncurses v6.0: system
  • ncurses v6.1: GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, system

netCDF

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.

https://www.unidata.ucar.edu/software/netcdf/

  • netCDF v4.6.1: foss/2018b
  • netCDF v4.6.2: gompi/2019a
  • netCDF v4.7.1: gompi/2019b

nettle

Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space.

http://www.lysator.liu.se/~nisse/nettle/

  • nettle v3.4: foss/2018b
  • nettle v3.4.1: GCCcore/8.2.0
  • nettle v3.5.1: GCCcore/8.3.0

NGS

NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing.

https://github.com/ncbi/ngs

  • NGS v2.9.3 (versionsuffix: '-Java-1.8'): foss/2018b

NiBabel

NiBabel provides read/write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.

https://nipy.github.io/nibabel

  • NiBabel v2.3.0 (versionsuffix: '-Python-3.6.6'): foss/2018b
  • NiBabel v2.5.1 (versionsuffix: '-Python-3.6.6'): foss/2018b

Ninja

Ninja is a small build system with a focus on speed.

https://ninja-build.org/

  • Ninja v1.9.0: GCCcore/8.2.0, GCCcore/8.3.0

Nipype

Nipype is a Python project that provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow.

http://nipy.org/nipype

  • Nipype v1.1.3 (versionsuffix: '-Python-3.6.6'): foss/2018b

NLopt

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.

http://ab-initio.mit.edu/wiki/index.php/NLopt

  • NLopt v2.4.2: GCCcore/7.3.0
  • NLopt v2.6.1: GCCcore/8.2.0, GCCcore/8.3.0

nodejs

Node.js is a platform built on Chrome's JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices.

http://nodejs.org

  • nodejs v10.15.1: foss/2018b

novoalign

Map short reads onto a reference genome from Illumina, Ion Torrent, and 454 next generation sequencing platforms

http://www.novocraft.com/products/novoalign/

  • novoalign v3.09.00: system

NSPR

Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions.

https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR

  • NSPR v4.20: GCCcore/7.3.0

NSS

Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications.

https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS

  • NSS v3.39: GCCcore/7.3.0

numactl

The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.

http://oss.sgi.com/projects/libnuma/

  • numactl v2.0.11: GCC/4.9.3-2.25, GCCcore/6.4.0, GCCcore/7.3.0
  • numactl v2.0.12: GCCcore/8.2.0, GCCcore/8.3.0
  • numactl v2.0.13: GCCcore/9.2.0

numba

Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.

https://numba.pydata.org/

  • numba v0.46.0: foss/2019a

Octave

GNU Octave is a high-level interpreted language, primarily intended for numerical computations.

http://www.gnu.org/software/octave/

  • Octave v4.4.1: foss/2018b

OpenBLAS

OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.

http://xianyi.github.com/OpenBLAS/

  • OpenBLAS v0.2.15 (versionsuffix: '-LAPACK-3.6.0'): GCC/4.9.3-2.25
  • OpenBLAS v0.2.20: GCC/6.4.0-2.28
  • OpenBLAS v0.3.1: GCC/7.3.0-2.30
  • OpenBLAS v0.3.5: GCC/8.2.0-2.31.1
  • OpenBLAS v0.3.7: GCC/8.3.0

OpenJPEG

OpenJPEG is an open-source JPEG 2000 codec written in C language. It has been developed in order to promote the use of JPEG 2000, a still-image compression standard from the Joint Photographic Experts Group (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as a JPEG 2000 Reference Software.

http://www.openjpeg.org/

  • OpenJPEG v2.3.0: GCCcore/7.3.0

OpenMPI

The Open MPI Project is an open source MPI-3 implementation.

https://www.open-mpi.org/

  • OpenMPI v1.10.2: GCC/4.9.3-2.25
  • OpenMPI v2.1.2: GCC/6.4.0-2.28
  • OpenMPI v3.1.1: GCC/7.3.0-2.30, gcccuda/2018b
  • OpenMPI v3.1.3: GCC/8.2.0-2.31.1, gcccuda/2019a
  • OpenMPI v3.1.4: GCC/8.3.0, gcccuda/2019b

OpenSSL

The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library.

http://www.openssl.org/

  • OpenSSL v1.1.0h: GCCcore/7.3.0

Pango

Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.

https://www.pango.org/

  • Pango v1.42.4: foss/2018b

PCRE

The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.

https://www.pcre.org/

  • PCRE v8.41: GCCcore/7.3.0
  • PCRE v8.43: GCCcore/8.2.0, GCCcore/8.3.0

Perl

Larry Wall's Practical Extraction and Report Language

https://www.perl.org/

  • Perl v5.22.1: foss/2016a
  • Perl v5.26.1: foss/2018a
  • Perl v5.28.0: GCCcore/7.3.0
  • Perl v5.28.1: GCCcore/8.2.0
  • Perl v5.30.0: GCCcore/8.3.0

pigz

pigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries.

https://zlib.net/pigz/

  • pigz v2.4: GCCcore/8.2.0

Pillow

Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.

https://pillow.readthedocs.org/

  • Pillow v5.3.0 (versionsuffix: '-Python-3.6.6'): foss/2018b
  • Pillow v6.2.1: GCCcore/8.3.0

pixman

Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.

http://www.pixman.org/

  • pixman v0.34.0: GCCcore/7.3.0
  • pixman v0.38.0: GCCcore/8.2.0
  • pixman v0.38.4: GCCcore/8.3.0

pkg-config

pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c pkg-config --libs --cflags glib-2.0 for instance, rather than hard-coding values on where to find glib (or other libraries).

http://www.freedesktop.org/wiki/Software/pkg-config/

  • pkg-config v0.29.2: GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, system

pkgconfig

pkgconfig is a Python module to interface with the pkg-config command line tool

http://github.com/matze/pkgconfig

  • pkgconfig v1.3.1 (versionsuffix: '-Python-3.6.6'): foss/2018b
  • pkgconfig v1.5.1 (versionsuffix: '-python'): GCCcore/8.2.0

PLINK

Whole-genome association analysis toolset

https://www.cog-genomics.org/plink/2.0/

  • PLINK v2.00-alpha2-x86_64: system

PROJ

Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates

https://proj.org

  • PROJ v5.0.0: foss/2018b
  • PROJ v6.0.0: GCCcore/8.2.0
  • PROJ v6.2.1: GCCcore/8.3.0

protobuf

Google Protocol Buffers

https://github.com/google/protobuf/

  • protobuf v3.6.1: GCCcore/7.3.0
  • protobuf v3.6.1.2: GCCcore/8.2.0

pybedtools

pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python.

https://daler.github.io/pybedtools

  • pybedtools v0.7.10 (versionsuffix: '-Python-3.6.6'): foss/2018b

pyBigWig

A python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files.

https://github.com/deeptools/pyBigWig

  • pyBigWig v0.3.13 (versionsuffix: '-Python-3.6.6'): foss/2018b

PyQt5

PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company.

http://www.riverbankcomputing.co.uk/software/pyqt

  • PyQt5 v5.11.3 (versionsuffix: '-Python-3.6.6'): foss/2018b

Pysam

Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.

https://github.com/pysam-developers/pysam

  • Pysam v0.15.1 (versionsuffix: '-Python-3.6.6'): foss/2018b

Python

Python is a programming language that lets you work more quickly and integrate your systems more effectively.

https://python.org/

  • Python v2.7.15: GCCcore/8.2.0, foss/2018b
  • Python v2.7.15 (versionsuffix: '-bare'): GCCcore/7.3.0
  • Python v2.7.16: GCCcore/8.3.0
  • Python v3.6.6: foss/2018b
  • Python v3.7.0: foss/2018b
  • Python v3.7.2: GCCcore/8.2.0
  • Python v3.7.4: GCCcore/8.3.0

For details or managing virtual environments and installing your own python packages, and to get the most out of Python on the BMRC cluster, please see our dedicated guide to Python on the BMRC cluster.

PyTorch

Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first.

https://pytorch.org/

  • PyTorch v1.3.1 (versionsuffix: '-Python-3.7.4'): foss/2019b, fosscuda/2019b

PyYAML

PyYAML is a YAML parser and emitter for the Python programming language.

https://github.com/yaml/pyyaml

  • PyYAML v3.13: system
  • PyYAML v3.13 (versionsuffix: '-Python-3.6.6'): foss/2018b
  • PyYAML v5.1: GCCcore/8.2.0
  • PyYAML v5.1.2: GCCcore/8.3.0

Qhull

Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull.

http://www.qhull.org

  • Qhull v2015.2: GCCcore/7.3.0

qrupdate

qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.

https://sourceforge.net/projects/qrupdate/

  • qrupdate v1.1.2: foss/2018b

Qt5

Qt is a comprehensive cross-platform C++ application framework.

http://qt.io/

  • Qt5 v5.10.1: foss/2018b
  • Qt5 v5.11.2: foss/2018b

R

R is a free software environment for statistical computing and graphics.

https://www.r-project.org/

  • R v3.5.1: foss/2018b
  • R v3.6.0: foss/2019a
  • R v3.6.2: foss/2019b

For details of how to install your own R packages, use RStudio for remote R interaction, or for recommended settings to generate plots, please see our dedicated page for Using R and RStudio.

 

R-bundle-Bioconductor

Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data.

https://bioconductor.org

  • R-bundle-Bioconductor v3.7 (versionsuffix: '-R-3.5.1'): foss/2018b
  • R-bundle-Bioconductor v3.8 (versionsuffix: '-R-3.5.1'): foss/2018b
  • R-bundle-Bioconductor v3.9 (versionsuffix: '-R-3.6.0'): foss/2019a

RAxML

RAxML search algorithm for maximum likelihood based inference of phylogenetic trees.

https://github.com/stamatak/standard-RAxML

  • RAxML v8.2.12 (versionsuffix: '-hybrid-avx2'): intel/2019a

RELION

RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM).

http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page

  • RELION v3.1-beta.2020.02.26: foss/2019a

rgdal

Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4 and <= 2.5.0) and access to projection/transformation operations from the 'PROJ.4' library.

http://rgdal.r-forge.r-project.org/

  • rgdal v1.4-4 (versionsuffix: '-R-3.6.0'): foss/2019a

RSEM

RNA-Seq by Expectation-Maximization

http://deweylab.github.io/RSEM/

  • RSEM v1.3.2: foss/2018b

RSeQC

RSeQC provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.

http://rseqc.sourceforge.net/

  • RSeQC v3.0.0 (versionsuffix: '-Python-3.6.6'): foss/2018b

ScaLAPACK

The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.

https://www.netlib.org/scalapack/

  • ScaLAPACK v2.0.2: gompi/2019b, gompic/2019b
  • ScaLAPACK v2.0.2 (versionsuffix: '-OpenBLAS-0.2.15-LAPACK-3.6.0'): gompi/2016a
  • ScaLAPACK v2.0.2 (versionsuffix: '-OpenBLAS-0.2.20'): gompi/2018a
  • ScaLAPACK v2.0.2 (versionsuffix: '-OpenBLAS-0.3.1'): gompi/2018b, gompic/2018b
  • ScaLAPACK v2.0.2 (versionsuffix: '-OpenBLAS-0.3.5'): gompi/2019a, gompic/2019a

scikit-image

scikit-image is a collection of algorithms for image processing.

https://scikit-image.org

  • scikit-image v0.14.1 (versionsuffix: '-Python-3.6.6'): foss/2018b

scikit-learn

Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.

https://scikit-learn.org/stable/index.html

  • scikit-learn v0.20.0 (versionsuffix: '-Python-3.6.6'): foss/2018b
  • scikit-learn v0.20.2 (versionsuffix: '-Python-3.6.6'): foss/2018b
  • scikit-learn v0.20.3: foss/2019a
  • scikit-learn v0.21.3 (versionsuffix: '-Python-3.7.4'): foss/2019b

SciPy-bundle

Bundle of Python packages for scientific software

https://python.org/

  • SciPy-bundle v2019.03: foss/2019a, fosscuda/2019a
  • SciPy-bundle v2019.10 (versionsuffix: '-Python-3.7.4'): foss/2019b, fosscuda/2019b

Seurat

Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data.

http://satijalab.org/seurat

  • Seurat v2.3.4 (versionsuffix: '-R-3.5.1'): foss/2018b

snakemake

The Snakemake python workflow management system is a tool to create reproducible and scalable data analyses.

https://snakemake.readthedocs.io

  • snakemake v5.2.4 (versionsuffix: '-Python-3.6.6'): foss/2018b
  • snakemake v5.7.1 (versionsuffix: '-Python-3.7.2'): foss/2019a

Users of snakemake should note that the default settings of snakemake will cause a catastrophic incident because by default snakemake runs the monitoring commands ten times per second. In order to use snakemake safely, you MUST therefore set --max-status-checks-per-second 0.01 in order to ensure that these commands are run 100 seconds apart.

SPAdes

Genome assembler for single-cell and isolates data sets

http://cab.spbu.ru/software/spades/

  • SPAdes v3.13.0: foss/2018b

SQLite

SQLite: SQL Database Engine in a C Library

https://www.sqlite.org/

  • SQLite v3.24.0: GCCcore/7.3.0
  • SQLite v3.27.2: GCCcore/8.2.0
  • SQLite v3.29.0: GCCcore/8.3.0

STAR

STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.

https://github.com/alexdobin/STAR

  • STAR v2.6.1c: foss/2018b
  • STAR v2.7.1a: foss/2018b

Subread

High performance read alignment, quantification and mutation discovery

http://subread.sourceforge.net/

  • Subread v1.6.4: foss/2018b

SuiteSparse

SuiteSparse is a collection of libraries manipulate sparse matrices.

http://faculty.cse.tamu.edu/davis/suitesparse.html

  • SuiteSparse v5.1.2 (versionsuffix: '-METIS-5.1.0'): foss/2018b

SWIG

SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.

http://www.swig.org/

  • SWIG v3.0.12 (versionsuffix: '-Python-3.6.6'): foss/2018b
  • SWIG v3.0.12 (versionsuffix: '-Python-3.7.2'): GCCcore/8.2.0
  • SWIG v4.0.1: GCCcore/8.3.0

sympy

SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries.

http://sympy.org/

  • sympy v1.3 (versionsuffix: '-Python-3.6.6'): foss/2018b

Szip

Szip compression software, providing lossless compression of scientific data

https://www.hdfgroup.org/doc_resource/SZIP/

  • Szip v2.1.1: GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0

tbb

Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable, composable and have future-proof scalability.

https://01.org/tbb/

  • tbb v2019_U4: GCCcore/8.2.0
  • tbb v2019_U9: GCCcore/8.3.0

Tcl

Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.

https://www.tcl.tk/

  • Tcl v8.6.8: GCCcore/7.3.0
  • Tcl v8.6.9: GCCcore/8.2.0, GCCcore/8.3.0

tcsh

Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax.

http://www.tcsh.org

  • tcsh v6.20.00: GCCcore/7.3.0

TensorFlow

An open-source software library for Machine Intelligence

https://www.tensorflow.org/

  • TensorFlow v1.13.1 (versionsuffix: '-Python-3.6.6'): foss/2018b
  • TensorFlow v1.13.1 (versionsuffix: '-Python-3.7.2'): fosscuda/2019a

texinfo

Texinfo is the official documentation format of the GNU project.

https://www.gnu.org/software/texinfo/

  • texinfo v6.5: GCCcore/7.3.0

Theano

Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.

https://deeplearning.net/software/theano

  • Theano v1.0.4: fosscuda/2019a

Tk

Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages.

https://www.tcl.tk/

  • Tk v8.6.8: GCCcore/7.3.0
  • Tk v8.6.9: GCCcore/8.2.0, GCCcore/8.3.0

Tkinter

Tkinter module, built with the Python buildsystem

https://python.org/

  • Tkinter v3.6.6 (versionsuffix: '-Python-3.6.6'): foss/2018b
  • Tkinter v3.7.4: GCCcore/8.3.0

Trim_Galore

Trim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data.

https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

  • Trim_Galore v0.6.2 (versionsuffix: '-Java-11'): GCCcore/8.2.0

UDUNITS

UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.

http://www.unidata.ucar.edu/software/udunits/

  • UDUNITS v2.2.26: GCCcore/8.2.0, GCCcore/8.3.0, foss/2018b

util-linux

Set of Linux utilities

https://www.kernel.org/pub/linux/utils/util-linux

  • util-linux v2.32: GCCcore/7.3.0
  • util-linux v2.33: GCCcore/8.2.0
  • util-linux v2.34: GCCcore/8.3.0

VEP

Variant Effect Predictor (VEP) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.

https://www.ensembl.org/info/docs/tools/vep

  • VEP v95.0 (versionsuffix: '-Perl-5.28.0'): foss/2018b

VTK

The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.

http://www.vtk.org

  • VTK v8.1.1 (versionsuffix: '-Python-3.6.6'): foss/2018b

wheel

A built-package format for Python.

https://pypi.python.org/pypi/wheel

  • wheel v0.31.1 (versionsuffix: '-Python-3.6.6'): foss/2018b

X11

The X Window System (X11) is a windowing system for bitmap displays

https://www.x.org

  • X11 v20180604: GCCcore/7.3.0
  • X11 v20190311: GCCcore/8.2.0
  • X11 v20190717: GCCcore/8.3.0

x264

x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL.

https://www.videolan.org/developers/x264.html

  • x264 v20190925: GCCcore/8.3.0

x265

x265 is a free software library and application for encoding video streams into the H.265 AVC compression format, and is released under the terms of the GNU GPL.

https://x265.org/

  • x265 v3.2: GCCcore/8.3.0

XML-LibXML

Perl binding for libxml2

http://search.cpan.org/src/SHLOMIF/XML-LibXML-2.0018/

  • XML-LibXML v2.0132 (versionsuffix: '-Perl-5.28.0'): GCCcore/7.3.0

XML-Parser

This is a Perl extension interface to James Clark's XML parser, expat.

http://search.cpan.org/~toddr/XML-Parser-2.41/

  • XML-Parser v2.44_01 (versionsuffix: '-Perl-5.28.0'): GCCcore/7.3.0

xorg-macros

X.org macros utilities.

https://cgit.freedesktop.org/xorg/util/macros

  • xorg-macros v1.19.1: GCCcore/6.4.0
  • xorg-macros v1.19.2: GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.2.0

xprop

The xprop utility is for displaying window and font properties in an X server. One window or font is selected using the command line arguments or possibly in the case of a window, by clicking on the desired window. A list of properties is then given, possibly with formatting information.

https://www.x.org/wiki/

  • xprop v1.2.3: GCCcore/7.3.0
  • xprop v1.2.4: GCCcore/8.2.0, GCCcore/8.3.0

XZ

xz: XZ utilities

https://tukaani.org/xz/

  • XZ v5.2.3: GCCcore/6.4.0
  • XZ v5.2.4: GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.2.0

Yasm

Yasm: Complete rewrite of the NASM assembler with BSD license

https://www.tortall.net/projects/yasm/

  • Yasm v1.3.0: GCCcore/8.3.0

zlib

zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.

http://www.zlib.net/

  • zlib v1.2.8: GCCcore/4.9.3, system
  • zlib v1.2.11: GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, GCCcore/9.2.0, system

Software available as singularity containers

SAIGE

SAIGE is an R-package for testing for associations between genetic variants and binary phenotypes with adjusting for sample relatedness and case-control imbalance. It can analyze very large sample data (ex. ~400,000 samples in UKBiobank) and produce accurate p-values by using saddlepoint approximation. 

  • SAIGE 0.36.4.2

Usage Guidance

The SAIGE software is provided as an executable singularity container located at /apps/singularity/saige_0.36.4.2.sif.

You can use it like a single application that encompasses SAIGE i.e.

$ /apps/singularity/saige_0.36.4.2.sif <SAIGE command goes here>

By default, singularity apps can see data only in the current working directory and in your home directory. If you need SAIGE to be able to see data in other directories then you will need to mount them using the -B parameter and running SAIGE like this:

singularity run -B /path/on/host:/path/inside/container /apps/singularity/saige_0.36.4.2.sif <SAIGE command goes here>

Although Singularity does not require it, it is often helpful to use the same paths both outside and inside the container e.g. use something like -B /well/<group>/users/<username>/data:/well/<group>/users/<username>/data . Mounting directories like this makes the process appear transparent and allows you to run commands on files in your data directory by referring to them with their full normal path.

When submitting SAIGE jobs to the cluster, it is vital that you restrict the number of threads that SAIGE will use by including this instruction in your submission script before running your SAIGE commands:

export OMP_NUM_THREADS=${NSLOTS:-1}

If you explicitly set a number of threads in your SAIGE command using --nThreads=X, it is also vital that this does not exceed the number of slots. You can ensure this by specifying --nThreads=${NSLOTS:-1}.

Without these additions, SAIGE will cause serious problems for other users and your job may need to be
terminated without warning.

Please note that by default, the BMRC Rprofile file will be de-activated when running inside a SAIGE container and you will see a warning message to this effect. This is normally the correct configuration.