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HPC Software - Virtualisation and Containers

Singularity

Singularity is a container platform. It allows you to create and run containers that package up pieces of software in a way that is portable and reproducible. You can build a container using Singularity on your laptop, and then run it on many of the largest HPC clusters in the world, local university or company clusters, a single server, in the cloud, or on a workstation down the hall. Your container is a single file, and you don’t have to worry about how to install all the software you need on each different operating system and system.

[https://sylabs.io/guides/3.5/user-guide/introduction.html - March 2020]

Available versions and module name

2.3 (singularity-2.3)

2.5.1 (singularity-2.5.1)

3.2.1 (singularity-3.2.1)

3.5.3 (singularity-3.5.3 or singularity)

Default version available

3.5.3

Website

https://sylabs.io/docs/

If, for whatever reason, you would like to use the older versions of the compilers, or other available software, you can simply "unload" the current module and load the older version. See Software Module Information webpage.

Software list

Bioinformatics
  • AmpliconNoise
  • ARB
  • BLAST (Legacy BLAST- Not BLAST+)
  • BLAST+
  • Bowtie2
  • CD-HIT
  • cdbtools
  • ChimeraSlayer
  • clearcut
  • Cufflinks
  • Cytoscape
  • FastQC
  • FastTree
  • Fastx-Toolkit
  • Gepard
  • HMMER
  • IGV
  • infernal
  • Kraken
  • metavelvet
  • mothur
  • MUSCLE
  • Ngopt
  • ParsInsert
  • Pear
  • Pplacer
  • QIIME
  • RAxML
  • rRNASelector
  • RSEM
  • RTAX
  • SAM Tools
  • SAMStat
  • SourceTracker
  • TopHat
  • Trimmomatic
  • Trinityrnaseq
  • UCLUST
  • UProC
  • USEARCH
  • Velvet
  • Velvet Optmiser
Compilers
  • Glasgow Haskell Compiler
  • GNU Bison
  • GNU Compiler
  • GNU Fortran Compiler
  • Go Compiler
  • Intel C and C++ Compiler
  • Intel Fortran Compiler
  • Mono C# Compiler and associated libraries
Data Mining and Analysis Applications
  • NCL (NCAR Command Language)
  • Ncview
  • NetCDF
  • NetCDF-Fortran
  • RapidMiner
  • STIR (Tomographic Imaging)
  • Weka
Development tools
  • Apache Maven
  • GNU Emacs
  • IntelliJ IDEA
  • RStudio
Documentation Tools
  • Tex Live
  • Tex Info
Engineering Applications
  • ANSYS (Fluent and Mechanical)
  • ABAQUS
  • AVL Fire
  • Comsol Multiphysics
Geospatial Tools
  • GDAL
  • GEOS
  • Panoply
Graphics Applications
  • Circos
  • ImageJ
  • ImageMagick
  • PLPlot
  • Xfig
Interpreters
  • Perl
  • Python (with many Modules Installed)
Mathematics and Statics
  • Mathematica
  • Grid Mathematica
  • Matlab
  • Matlab-Simulink
  • Octave
  • OpenBUGS
  • R
  • SPSS (by IBM)
Run Time Environments
  • Java
Simulation Software
  • APSIM
Software Libraries
  • Boost C++ Libraries
  • Expat XML Parser
  • FFTW
  • GMP (GNU Multiple Precision Arithmetic Library)
  • GNU Scientific Library (GSL)
  • HDF5
  • HDF-EOS5
  • Intel Math Kernel Libraries (Intel® MKL)
  • libbz2
  • libcurl
  • libjpeg
  • libpng
  • MPI
  • OpenBLAS
  • PCRE (Perl Compatible Regular Expressions)
  • szip
  • tcl
  • tk
  • UDUNITS
Text Tools and Software
  • Flex