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List of Installed Software

This is a list of some of the software installed on the cluster. Ask us if there is something that you need. It may already be on the cluster or we may be able to install it for you. You can also compile, build and install code under your home directory.

Software Installed by Downloading and/or Compiling

These are have been downloaded from their home pages and installed under /shared/opt/. Many of these required compiling from source.

Package & Version Description
bcl2fastq2-2.20.0 Genomics conversion software from Illumina
fastqc-0.10.1 A quality control analysis tool to spot potential problems in high throughput sequencing datasets.
fastqc-0.11.9 A quality control analysis tool to spot potential problems in high throughput sequencing datasets.
gromacs-2018.8 GROMACS 2018.8 compiled with PBS MPI
gromacs-2019.6 GROMACS 2019.6 compiled with PBS MPI
gromacs-2020.4 GROMACS 2020.4 compiled with PBS MPI
gromacs-2021.4 GROMACS 2021.4 compiled with PBS MPI
intel Intel compiler 2018
julia-1.0.0 High performance language for scientific applications.
julia-1.6.2 High performance language for scientific applications.
mmseqs2-v12 Many-against-Many searching to search and cluster huge sequence sets. See https://github.com/soedinglab/MMseqs2
ncbi-blast-2.13.0+ Basic Local Alignment Search Tool, see https://blast.ncbi.nlm.nih.gov/Blast.cgi
ncbi-blast-2.15.0+ Basic Local Alignment Search Tool, see https://blast.ncbi.nlm.nih.gov/Blast.cgi
ncbi-blast-2.2.22+ Basic Local Alignment Search Tool, see https://blast.ncbi.nlm.nih.gov/Blast.cgi
ncbi-blast-2.2.22_legacy BLAST using the Legacy C toolkit. No support or fixes.
ncbi-blast-2.2.26_legacy BLAST using the Legacy C toolkit. No support or fixes.
openmpi-4.0.4 OpenMPI for writing parallel and/or distributed computing software. See https://www.open-mpi.org
openmpi-4.1.2 OpenMPI for writing parallel and/or distributed computing software. See https://www.open-mpi.org
openmpi-4.1.5 OpenMPI for writing parallel and/or distributed computing software. See https://www.open-mpi.org
pblat-cluster-1.1 pblat is like BLAST but with parallel computing support.
qiime-2023.5 A microbiome bioinformatics platform. See https://qiime2.org
singularity-3.10.3 Older version of singularity for legacy applications.

Software Installed from Linux Software Repositories

These were installed from the standard Linux software repositories.

Editors

Package & Version Description Homepage URL
emacs-nox   26.1 GNU Emacs text editor without X support emacs-nox
nano   2.9.8 A small text editor nano
vim-enhanced   8.0.1763 A version of the VIM editor which includes recent enhancements vim-enhanced

Version Control

Package & Version Description Homepage URL
git   2.39.3 Fast Version Control System git

Misc

Package & Version Description Homepage URL
apptainer   1.2.5 Application and environment virtualization formerly known as Singularity apptainer
bzip2   1.0.6 A file compression utility bzip2
dmtcp   2.6.1~rc1 Checkpoint/Restart functionality for Linux processes dmtcp
dos2unix   7.4.0 Text file format converters dos2unix
environment-modules   4.5.2 Provides dynamic modification of a user’s environment environment-modules
facter   3.14.24 Command and ruby library for gathering system information facter
flex   2.6.1 A tool for creating scanners (text pattern recognizers) flex
gzip   1.9 The GNU data compression program gzip
htop   3.2.1 Interactive process viewer htop
leveldb   1.22 A fast and lightweight key/value database library by Google leveldb
lynx   2.8.9 A text-based Web browser lynx
mc   4.8.19 User-friendly text console file manager and visual shell mc
ncdu   1.19 Text-based disk usage viewer ncdu
pandoc   2.0.6 Conversion between markup formats pandoc
parallel   20190922 Shell tool for executing jobs in parallel parallel
pigz   2.4 Parallel implementation of gzip pigz
p7zip   16.02 Very high compression ratio file archiver p7zip
rsync   3.1.3 A program for synchronizing files over a network rsync
screen   4.6.2 A screen manager that supports multiple logins on one terminal screen
sqlite   3.26.0 Library that implements an embeddable SQL database engine sqlite
s3cmd   2.4.0 Tool for accessing Amazon Simple Storage Service s3cmd
tmux   2.7 A terminal multiplexer tmux
wget   1.19.5 A utility for retrieving files using the HTTP or FTP protocols wget
xz   5.2.4 LZMA compression utilities xz
zstd   1.4.4 Zstd compression library zstd

Science

Package & Version Description Homepage URL
arpack   3.7.0 Fortran 77 subroutines for solving large scale eigenvalue problems arpack
bowtie   1.2.3 An ultrafast, memory-efficient short read aligner bowtie
bowtie2   2.4.1 An ultra fast and memory-efficient read aligner bowtie2
bwa   0.7.17 Burrows-Wheeler Alignment tool bwa
fftw   3.3.5 A Fast Fourier Transform library fftw
gdal   3.0.4 GIS file format library gdal
geos   3.7.2 GEOS is a C++ port of the Java Topology Suite geos
gpsbabel   1.6.0 A tool to convert between various formats used by GPS devices gpsbabel
gsl   2.5 The GNU Scientific Library for numerical analysis gsl
hdf   4.2.14 A general purpose library and file format for storing scientific data hdf
hdf5   1.10.5 A general purpose library and file format for storing scientific data hdf5
htslib   1.9 C library for high-throughput sequencing data formats htslib
lapack   3.8.0 Numerical linear algebra package libraries lapack
nco   4.8.1 Suite of programs for manipulating NetCDF/HDF4 files nco
netcdf   4.7.0 Libraries for the Unidata network Common Data Form netcdf
netcdf-fortran   4.5.2 Fortran libraries for NetCDF-4 netcdf-fortran
proj   6.3.2 Cartographic projection software (PROJ) proj
qhull-devel   2015.2 Development files for qhull qhull-devel
samtools   1.9 Tools for nucleotide sequence alignments in the SAM format samtools

Languages and Debugging Tools

Package & Version Description Homepage URL
golang   1.20.10 The Go Programming Language golang
guile   2.0.14 A GNU implementation of Scheme for application extensibility guile
java-1.8.0-openjdk-headless   1.8.0.392.b08 OpenJDK 8 Headless Runtime Environment java-1.8.0-openjdk-headless
java-17-openjdk-headless   17.0.9.0.9 OpenJDK 17 Headless Runtime Environment java-17-openjdk-headless
java-latest-openjdk-headless   21.0.1.0.12 OpenJDK 21 Headless Runtime Environment java-latest-openjdk-headless
nodejs   10.24.0 JavaScript runtime nodejs
perl   5.26.3 Practical Extraction and Report Language perl
python2   2.7.18 An interpreted, interactive, object-oriented programming language python2
python36   3.6.8 Interpreter of the Python programming language python36
python38   3.8.17 Interpreter of the Python programming language python38
python3-numpy   1.14.3 A fast multidimensional array facility for Python python3-numpy
ruby   2.5.9 An interpreter of object-oriented scripting language ruby
R-core   4.3.2 The minimal R components necessary for a functional runtime R-core
strace   5.18 Tracks and displays system calls associated with a running process strace
tbb   2018.2 The Threading Building Blocks library abstracts low-level threading details tbb
valgrind   3.21.0 Dynamic analysis tools to detect memory or thread bugs and profile valgrind

Compilers and Libraries

Package & Version Description Homepage URL
armadillo   12.6.6 Fast C++ matrix library with syntax similar to MATLAB and Octave armadillo
armadillo-devel   12.6.6 Development headers and documentation for the Armadillo C++ library armadillo-devel
arpack   3.7.0 Fortran 77 subroutines for solving large scale eigenvalue problems arpack
atlas   3.10.3 Automatically Tuned Linear Algebra Software atlas
blas   3.8.0 The Basic Linear Algebra Subprograms library blas
cmake   3.26.5 Cross-platform make system cmake
fftw   3.3.5 A Fast Fourier Transform library fftw
fpc   3.2.0 Free Pascal Compiler fpc
gcc   8.5.0 Various compilers (C, C++, Objective-C, …) gcc
gcc-c++   8.5.0 C++ support for GCC gcc-c++
gcc-gfortran   8.5.0 Fortran support gcc-gfortran
ghc   8.2.2 Glasgow Haskell Compiler ghc
lapack   3.8.0 Numerical linear algebra package libraries lapack
mpfr   3.1.6 A C library for multiple-precision floating-point computations mpfr
openblas   0.3.15 An optimized BLAS library based on GotoBLAS2 openblas
qrupdate   1.1.2 A Fortran library for fast updates of QR and Cholesky decompositions qrupdate
snappy   1.1.8 Fast compression and decompression library snappy
suitesparse   4.4.6 A collection of sparse matrix libraries suitesparse

Created from git/hpc_software_list/software_list.py
This list updated: Friday, 19 January 2024