Available Software
In the table below is a list of all software that is currently installed on the cluster. You can also directly see a real-time list of all available modules using the command below.
How To Use
Once you identify the software and version you want to run by looking at the table below, you will need to enable it by using our module system. Once loaded, you'll be able to run the software using the commands you typically use for your calculations.
If you don't have a need for a specific version, then you can just load the software by only its name instead.
Once you are done using a module, you can use "module unload software" to disable it.
Examples
Installed Software
| Software | BGSC | BOSE | Description |
|---|---|---|---|
| ADMIXTURE [ User Guide ] |
admixture/1.3.0 | admixture/1.3.0 | Used to estimate individual ancestry from single nucleotide polymorphism (SNP) data sets. |
| Adaptive Poisson-Boltzmann Solver (APBS) [ User Guide ] |
apbs/3.0.0 apbs/3.1.4 |
apbs/3.1.3 apbs/3.4.1 |
Solves the equations of continuum electrostatics for large biomolecular assemblages. |
| Apptainer [ User Guide ] |
apptainer/latest (1.2.5) apptainer/1.2.5 |
Popular HPC software for running scientific programs inside portable containers. | |
| Autoconf [ User Guide ] |
2.69* | 2.69* autoconf/2.72 |
Tool used for generating configure scripts for building software from source code. |
| Bayesian Analysis of Macroevolutionary Mixtures (BAMM) [ User Guide ] |
bamm/2.5.0 | Program for modeling complex dynamics of speciation, extinction, and trait evolution on phylogenetic trees. | |
| BLAST+ [ User Guide ] |
blast/2.15.0 | Basic Local Alignment Search Tool used to compare nucleotide or protein sequences to databases. | |
| CFOUR [ User Guide ] |
cfour-parallel/2.1 cfour/2.1 cfour/2.1.2 |
cfour-parallel/2.1 cfour-parallel/2.1-par-1 cfour/2.1 |
Used to perform high-level quantum chemical calculations on atoms and molecules. |
| Chemprop [ User Guide ] |
chemprop/2.2.1 | Train and evaluate message-passing neural networks for molecular property prediction. | |
| CUDA Toolkit [ User Guide ] |
cuda/10.2 cuda/11.4 |
cuda/10.0 cuda/11.4 cuda/12.6 |
Development environment used to support GPU-acceleration in software. |
| DMTCP [ User Guide ] |
dmtcp/2.6.0 | Distributed MultiThreaded Checkpointing | |
| DSuite [ User Guide ] |
DSuite/0.4 | DSuite/0.4 | Fast D‐statistics and related admixture evidence from VCF files |
| fpocket [ User Guide ] |
fpocket/4.2.2 | Ultra fast protein pocket detection | |
| Gaussian [ User Guide ] |
gaussian/09 gaussian/16 |
gaussian/16 | General purpose computational chemistry software |
| gcc [ User Guide ] |
gcc/9.3.0 | 8.3.1* gcc/9.3.0 gcc/10.3.0 gcc/11.1.0 |
General purpose compiler |
| git [ User Guide ] |
2.43.5/* git/2.28.0 |
2.27.0* git/2.51.0 |
Universally-used version control |
| Globus [ User Guide ] |
File transferring service for organizations and their users | ||
| Globus CLI [ User Guide ] |
globus-cli/3.24.0 | globus-cli/3.24.0 | File transferring service for organizations and their users; adapted to command line |
| GNU Octave [ User Guide ] |
octave/7.3.0 | Mathematics oriented scientific programming language largely compatibile with Matlab | |
| GNU Parallel [ User Guide ] |
parallel/20220622 | parallel/20220622 | Executes commands in parallel |
| gnuplot [ User Guide ] |
gnuplot/5.4.1 | Graphing program for 2D and 3D plotted graphs | |
| go [ User Guide ] |
go/1.16.4 | Go programming language | |
| GTDB-Tk [ User Guide ] |
GTDB-Tk/2.4.1 |
Program for objective taxonomic classifications for bacterial and archael genomes by assigning them to the Genome Taxonomy Database (GTDB) | |
| Gurobi Optimizer [ User Guide ] |
gurobi/12.0.3 gurobi/11.0.0 |
Solver for mathematical models | |
| Gurobi Optimizer Python API [ User Guide ] |
gurobipy/12.0.3 | Solver for mathematical models - Python API Version | |
| IBM ILOG CPLEX Optimization Studio [ User Guide ] |
cplex-studio/22.1.1 | Decision optimization software | |
| ifort [ User Guide ] |
ifort/2013splu2 | Fortran compiler | |
| ImageMagick [ User Guide ] |
imagemagick/7.1.0 | Image processing + conversions | |
| ImageJ / Fiji [ User Guide ] |
imagej/1.53 imagej-fiji/2.15.0 |
GUI-based program used to process and analyze scientific images and videos. | |
| Intel oneAPI Base + HPC Toolkit [ User Guide ] |
oneapi, oneapi-* | Intel oneAPI is a collection of tools (compilers, MPI, mkl, etc) from Intel in a single package. By loading the 'oneapi' module, you'll be given access to all the oneapi modules when you type 'module avail'. Every module started with 'oneapi-XX' | |
| Just Another Gibbs Sampler (JAGS) [ User Guide ] |
jags/4.3.2 | Used for analyzing Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) | |
| jre [ User Guide ] |
jre/1.8.0_291 | Java runtime environment | |
| julia [ User Guide ] |
julia/1.11.6 | High performance language | |
| Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) [ User Guide ] |
lammps-parallel/2020-03-03 lammps/2020-03-03 |
lammps/2Aug2023 | Molecular dynamics simulator |
| llama.cpp [ User Guide ] |
llama.cpp/b7126 | Tool used to perform inference on locally-hosted large language models | |
| Maple [ User Guide ] |
maple/2017 | Symbolic/numeric computing environment and programming language | |
| MedeA | 3.10.0* | Software package to hook into VASP, LAMMPS, and Gaussian. Note: License required for use. |
|
| MESA [ User Guide ] |
mesa/r15140 | mesa/r24.08.1 mesa/r24.03.1 mesa/r23051 mesa/r15140 |
Stellar evolution simulator |
| MRCC [ User Guide ] |
test-mrcc/20230828 | Quantum chemistry program suite for high-accuracy electronic structure calculations | |
| MUSCLE [ User Guide ] |
muscle/5.3 | Program used for multiple sequence alignment of protein and nucleotide sequences | |
| Music21 [ Website ] |
music21/8.1.0 | music21/8.1.0 | Python-based music analysis software |
| Nbia Data Retriever [ User Guide ] |
nbia-data-retriever/4.4.3-1 |
Program for downloading medical imaging data from the National Biomedical Imaging Archive (NBIA) | |
| Nanoscale Molecular Dynamics (NAMD) [ User Guide ] |
namd/2.13 namd/2.13-cuda |
namd/2.14 namd/2.14-cuda test-namd/3.0 test-namd/3.0-cuda namd/3.0.1 namd/3.0.1-cuda |
Molecular dynamics simulator |
| Network Simulator (NS) [ User Guide ] |
netsim/2.35 | Network traffic simulator | |
| Ollama [ User Guide ] |
ollama/0.11.4 ollama/0.12.0 ollama/0.12.10 |
Tool for hosting large language models from an api or on the command line | |
| OneDrive Client for Linux | onedrive/2.4.15 onedrive/2.4.23 |
onedrive/2.4.23 | Command-line tool for used for syncing files with a Microsoft OneDrive account. |
| openBabel | openbabel/3.1.1 | openbabel/3.1.1 | A chemical toolbox project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. |
| openJDK | openjdk/11 openjdk/16 |
Open-source implimentation of the java platform | |
| Open MPI | openmpi/1.10.0_ifort openmpi/4.0.3 openmpi/4.0.3_ifort |
openmpi/1.10.7 openmpi/2.1.6 openmpi/4.1.1 cray-openmpi/4.1.1 openmpi/5.0.3 |
Open-source message passing interface |
| PhyML | phyml/3.3.20200621 | Analyzes allignments of nucleotide or amino acid sequences using statistical approach | |
| Prokka [ User Guide ] |
prokka/1.14.5 | Rapid prokaryotic genome annotation | |
| Psi4 [ User Guide ] |
psi4/1.9.1 | Open-Source Quantum Chemistry – an electronic structure package | |
| Python [ User Guide ] |
python/2.7.18 python/3.9.2 |
python/3.9.2 | General-purpose high-level programming language This module not is recommended for use, see "Python Libraries (Conda)" below. |
| Python Libraries (Conda) [ User Guide ] |
python-libs | python-libs | Conda is the primary package system used for installing Python, its libraries, and creating shared environments for research groups. |
| p7zip | p7zip/16.02 | For compressing and extracting .7z files | |
| Q-Chem [ User Guide ] |
qchem-mpi/5.2-MPI qchem/5.2 |
qchem/5.2 | General-purpose electronic structure package |
| QGIS [ User Guide ] |
test-qgis/latest (3.22.16) test-qgis/3.22.16 Also Via OnDemand |
Free and open-source geographic information systems (GIS) application | |
| QIIME 2 [ User Guide ] |
qiime2/2024.5 | Microbiome multi-omics bioinformatics and data science platform | |
| R [ User Guide ] |
R/3.4.4 R/3.6.3 R/4.0.2 R/4.4.0 |
R/4.0.4 R/4.0.5 R/4.2.1 R/4.3.1 R/4.4.0 |
Programming language for statistical computing |
| RAxML Next Generation [ User Guide ] |
raxml-ng/0.9.0 | raxml-ng/1.1.0 | Phylogenetic tree inference tool |
| Rclone | rclone/1.62.2 | rclone/1.62.2 | Command-line tool allowing files to be synced between cloud providers, such as OneDrive, Google Drive, and Dropbox. |
| redmd/redmdstream [ User Guide ] |
redmd/2.3 redmdstream/1.0 |
Tools for modeling biomolecular systems. Stream is for model development, and redmd is a simulation engine. | |
| Roary [ User Guide ] |
roary/3.13.0 | High speed pan-genome pipeline | |
| RStudio [ User Guide ] |
2023.09.1 - Via OnDemand | A Integrated Development Environment (IDE) for the R programming language. | |
| Ruby | ruby/2.7.1 | ruby/2.7.1 ruby/3.4.2 |
General-purpose high-level programming language |
| SLEAP [ User Guide ] |
sleap/1.4.1 | Deep learning module for animal pose tracking. | |
| Stacks [ User Guide ] |
stacks/2.57 | software pipeline for building loci from short-read sequences | |
| Structure/Faststructure [ User Guide ] |
structure/2.3.3 faststructure/1.0.4 |
Variational framework for inferring population structure from SNP genotype data | |
| Subversion (SVN) | svn/1.10.6 svn/1.14.0 |
Version and revision control software | |
| Trinity [ User Guide ] |
trinity/2.15.2 |
Program for reconstructing transcript sequences from RNA-Seq data | |
| VCFTools | vcftools/0.1.16 | Program package for working with .vcf files. Also included in this module: Tabix, BCFtools, BGZip, Fixref plugin for VCFtools |
|
| VMD [ User Guide ] |
vmd/1.9.3 vmd/1.9.4 |
Program used to visualize molecules and analyze molectular structure |
* These are installed by default and do not need a module to use them.
Need Something Installed?
We have an eForm for you to fill out the detail of a requested software, whether it is unavailable in the cluster, or a specific version.
Please note that software requests are subject to approval and if your software requires a license, you must already have access to the license for your group.