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. |
| fragpipe_21.1 | A proteomics pipeline with the MSFragger search engine. |
| 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-2.2.22_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. |
| ncbi-blast-2.2.22+ | Basic Local Alignment Search Tool, see https://blast.ncbi.nlm.nih.gov/Blast.cgi |
| ncbi-blast-2.7.1+ | Basic Local Alignment Search Tool, see https://blast.ncbi.nlm.nih.gov/Blast.cgi |
| 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 |
| 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 2.43.5 | Fast Version Control System | git |
Misc
| Package & Version | Description | Homepage URL |
|---|---|---|
| apptainer 1.3.5 | 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 |
| 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 1.21 | 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 1.22.7 | The Go Programming Language | golang |
| guile 2.0.14 | A GNU implementation of Scheme for application extensibility | guile |
| java-1.8.0-openjdk-headless 1.8.0.432.b06 | OpenJDK 8 Headless Runtime Environment | java-1.8.0-openjdk-headless |
| java-17-openjdk-headless 17.0.13.0.11 | OpenJDK 17 Headless Runtime Environment | java-17-openjdk-headless |
| java-latest-openjdk-headless 23.0.1.0.11 | OpenJDK 23 Headless Runtime Environment | java-latest-openjdk-headless |
| nodejs 10.24.0 | JavaScript runtime | nodejs |
| perl 5.26.3 | Practical Extraction and Report Language | perl |
| 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 4.4.2 | 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 3.22.0 | 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 |
| 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: Wednesday, 11 December 2024