This page documents the list of centrally provisioned software on Comet.
We will generally refer to software on our HPC facilities as being from one of the following categories. The level of support we offer may vary depending on the category of the package in question.
| Software Type | Category | Location | Example | Support Description |
|---|---|---|---|---|
| Your code | Your home or project directory | A custom Python script | The Research Software Engineering team can offer basic support and troubleshooting with your own HPC code to get it working or provide advice on potential compatibility issues. If the complexity of the support is deemed to be beyond standard, or the software is of sufficient complexity, you may be advised to engage dedicated RSE software developers at a chargeable day rate. Please contact us via team email hpc.researchcomputing@ncl.ac.uk, or use the IT Service ticket system to request assistance. | |
| 3rd Party code | Your home or project directory | A Python library downloaded from Github | The Research Software Engineering team can offer basic support and troubleshooting in the download, compilation and configuration of software included in this category. Support is accessible via direct team email hpc.researchcomputing@ncl.ac.uk, or the normal IT Service ticket system. If the complexity of the support is deemed to be beyond standard, or the software is of sufficient complexity, you may be advised to engage dedicated RSE software developers at a chargeable day rate. | |
| Loaded via Linux module | vendor | Centrally installed | GCC, Matlab or Conda | Software which is loaded from a module load command is packaged and has basic testing by our HPC support vendor. Help in the operation of the software is not covered by our vendor. RSE may be able to provide basic guidance via email hpc.researchcomputing@ncl.ac.uk, or the normal IT Service ticket system, but may not be able to assist with every possible application. Requests for additional/updated software titles in this category will be collated and submitted to our vendor for prioritization and estimate of implementation timescales. |
| Loaded via a container image | RSE | Centrally installed | CASTEP, Bioapps | Software which we have built and provided in the form of a container environment in the /nobackup containers folder. We will build and provide updates to these containers but cannot necessarily advise on the use of the software itself.We can provide some level of assistance for building containers, but depending on the level of complexity or size of user base, this may fall outside of our ability to deliver via our basic support provision and may require engagement of paid RSE services to help develop a solution. |
This software table describes the packages which are (or are intended to be) available on Comet.
| Title | Category | License | Interface | Help |
|---|---|---|---|---|
| | not installed | Commercial | Command Line | COMSOL |
| | not installed | Commercial | Desktop GUI | COMSOL |
| | not installed | Commercial | Command Line | Intel Compiler Suite |
| | not installed | Commercial | Command Line | Intel Compiler Suite |
| | not installed | Commercial | Command Line | Intel Compiler Suite |
| Abaqus | vendor | Command Line | Abaqus | |
| AFNI | vendor | Command Line | AFNI | |
| ALE | vendor | Command Line | ALE | |
| Amber MD | RSE | Command Line and Desktop GUI | Please see Amber MD | |
| Ambertools | RSE | Command Line and Desktop GUI | Please see Amber MD | |
| AMD Optimizing Compiler | vendor | Command Line | AOCC | |
| AMD Optimizing Compiler Libraries | vendor | Command Line | AOCC | |
| Ansys | RSE | Commercial | Command Line and Desktop GUI | ANSYS 2025 R2 and above are now provided by the ANSYS container environment |
| ANTS | vendor | Command Line | Please see ANTS | |
| APBS | RSE | Command Line | Please see Amber MD | |
| Apptainer | vendor | Command Line | Apptainer is our recommended container tool for Comet. Also consider browsing our Containers guide. | |
| ARP/wARP | RSE | Command Line | Please see CCP-EM Suite container | |
| ARPACK | vendor | Command Line | Please see ARPACK-NG | |
| Avogadro 2 | vendor | Desktop GUI | Please see Avogadro 2 | |
| BamUtil | vendor | Command Line | Please see Bioapps | |
| BCFTools | vendor | Command Line | Please see Bioapps | |
| bcl2fastq | vendor | Command Line | Obsolete. Replaced by BCL_convert - see BCL_convert |
|
| BEDTools | vendor | Command Line | Please see Bioapps | |
| BGEN | vendor | Command Line | Please see BGEN | |
| bgenix | vendor | Command Line | Please see bgenix | |
| Bioconda | vendor | Command Line | See the alternative Miniforge | |
| Bioconductor | vendor | Command Line | Most of Bioconductor is installed as part of the Bioapps container image. See that page for more details and a list of all installed libraries. | |
| Biopython | vendor | Command Line | Please see Biopython | |
| BLAS | vendor | Command Line | Please see OpenBLAS or LAPACK | |
| BLAST | vendor | Command Line | Please see BLAST | |
| BLAST+ | vendor | Command Line | Please see BLAST+ | |
| BOLT-LMM | vendor | Command Line | BOLT-LMM Help, BOLT-LMM compile issues | |
| Boost | vendor | Command Line | Please see boost | |
| Bowtie2 | vendor | Command Line | Please see Bioapps | |
| BUGS | vendor | Command Line | Please see BUGS | |
| BWA | vendor | Command Line | Please see Bioapps | |
| canu assemblers | vendor | Command Line | Please see canu assemblersx | |
| CASTEP | RSE | Command Line | Please see CASTEP | |
| CCP-EM Suite | RSE | Command Line | See CCP-EM Suite. | |
| CCP-EM v1 | RSE | Non-commercial, academic use | Command Line | Please see CCP-EM Suite container |
| CCP-EM v2 | RSE | Non-commercial, academic use | Command Line | Please see CCP-EM Suite container |
| CCP4 | RSE | Command Line + Desktop GUI | Please see CCP-EM Suite container | |
| CDO | vendor | Command Line | Please see CDO | |
| CellBender | vendor | Command Line | Please see CellBender | |
| CheckMySequence, DoubleHelix, FindMySequence | RSE | Command Line | Please see CCP-EM Suite container | |
| ChimeraX | vendor | Desktop GUI | Please see ChimeraX | |
| cmake | vendor | Command Line | cmake | |
| CNVKit | vendor | Command Line | Please see CNVKit | |
| Code_Saturne | vendor | Command Line | Please see Code Saturne | |
| Conda | vendor | Command Line | See the alternative Miniforge | |
| Convert3D | vendor | Command Line | Please see Bioapps | |
| CP2K | vendor | Command Line | Please see CP2K | |
| CryoDRGN | RSE | Command Line | Please see CCP-EM Suite container | |
| CryoSparc | vendor | Desktop GUI | ||
| CTFFind 4 | RSE | Command Line | Please see CCP-EM Suite container | |
| Cufflinks | vendor | Command Line | Please see Cufflinks | |
| cutadapt | vendor | Command Line | Please see Cutadapt | |
| DBD-csv | vendor | Command Line | Please see DBD-CSV | |
| DBD-mysql | vendor | Command Line | Please see DBD-MySQL | |
| DBD-sqlite | vendor | Command Line | Please see DBD-SQLite | |
| DEXSeq | RSE | Command Line | Please see Bioapps | |
| diamond | vendor | Command Line | Please see diamond | |
| Disambiguate | vendor | Command Line | Please see Disambiguate | |
| Docker | vendor | Command Line | See our Docker guide in our container tools section | |
| Doppio | RSE | Non-commercial, academic use | Desktop GUI | See CCP-EM Suite container]. | | Dorado | vendor | | Command Line | Please see [[:advanced:software:dorado|Dorado |
| Eigen | vendor | Command Line | Please see Eigen | |
| EMDA | RSE | Command Line | Please see CCP-EM Suite container | |
| EMDB Validation Analysis | RSE | Command Line | Please see CCP-EM Suite container | |
| FastQC | vendor | Desktop GUI | Please see FastQC | |
| FFTW | vendor | Command Line | Please see FFTW and FFTW.MPI | |
| flye | vendor | Command Line | Please see flye | |
| Freesurfer | vendor | Desktop GUI | Please see Freesurfer | |
| FSL | vendor | Desktop GUI | FSL | |
| GATK | vendor | Command Line | Please see GATK | |
| Gaussian | vendor | Commercial | Command Line | Please see Gaussian / GaussView |
| GaussView | vendor | Commercial | Desktop GUI | Please see Gaussian / GaussView |
| Generic Mapping Tools | vendor | Command Line | Please see Generic Mapping Tools | |
| GipsyX | RSE | Restricted License | Command Line + Desktop GUI | Please see GipsyX |
| Gmsh | vendor | Desktop GUI | Please see Gmsh | |
| GNU g++ | vendor | Command Line | GCC | |
| GNU gcc | vendor | Command Line | GCC | |
| GNU gfortran | vendor | Command Line | GCC | |
| GNU gnuplot | vendor | Command Line | Please see gnuplot | |
| gprMax | vendor | Command Line | Please see gprMax | |
| GRASS | vendor | Desktop GUI | Please see GRASS | |
| Gromacs | vendor | Command Line | gromacs / CUDA / OpenCL | |
| Guppy | vendor | Command Line | See Guppy. | |
| Hail | vendor | Command Line | Please see Hail | |
| HDF5 | vendor | Command Line | Please see HDF5 | |
| HISAT2 | vendor | Command Line | Please see Bioapps | |
| HTSeq | vendor | Command Line | Please see Bioapps | |
| HTSlib | vendor | Command Line | Available standalone, see HTSlib - also installed within Bioapps container for any tools requiring it. | |
| Hybracter | vendor | Command Line | Please see Hybracter | |
| ISSM / Ice Sheet and Sea Level System Model | vendor | Command Line | Please see Ice Sheet and Sea Level System Model | |
| JAGS | vendor | Command Line | Please see JAGS | |
| JARS | vendor | Command Line | Please see JARS | |
| Java | vendor | Command Line | Please see Java | |
| jmol | vendor | Desktop GUI | Please see jmol | |
| Julia | vendor | Command Line | Please see Julia | |
| Jupyter Lab | vendor | Desktop GUI | Jupyter | |
| LAMMPS | vendor | Command Line | Please see LAMMPS | |
| last | vendor | Command Line | Please see last | |
| ldsc | vendor | Command Line | Please see ldsc | |
| libncurses | vendor | Command Line | ncurses | |
| libXmu | vendor | Command Line | Included in the module load X11 environment - see also X11 Desktop |
|
| Linux X11 desktop | vendor | Desktop GUI | Please see X11 Desktop | |
| Locscale | RSE | Command Line | Please see CCP-EM Suite container | |
| MACS2 | vendor | Command Line | Please see MACS2 | |
| Mamba | vendor | Command Line | See the alternative Miniforge | |
| Matlab | vendor | Commercial | Command Line | Matlab |
| Matlab | vendor | Commercial | Desktop GUI | Matlab |
| matplotlib | vendor | Command Line | Please see matplotlib | |
| MBX | RSE | Command Line | Please see Amber MD | |
| megan | vendor | Command Line | Please see megan | |
| merlin | vendor | Command Line | Now installed. See Merlin. | |
| MetalCoord | RSE | Command Line | Please see CCP-EM Suite container | |
| metaSPAdes | vendor | Command Line | Parts of the SPAdes toolkit - please see SPAdes | |
| METIS | vendor | Command Line | Please see METIS | |
| Model Angelo | RSE | Command Line | See CCP-EM Suite. | |
| Modeller (Salilabs) | RSE | Non-commercial, academic use | Command Line | Please see CCP-EM Suite container |
| Mono | vendor | Command Line | Please see Mono | |
| Mrtrix | vendor | Desktop GUI | Please see Mrtrix | |
| MultiQC | vendor | Command Line | Please see MultiQC | |
| MUMPS | vendor | Command Line | Please see MUMPS | |
| MuSpAn | self install | Command Line | Please see the MuSpAn install guide | |
| NBO | vendor | Command Line | Please see NBO | |
| Nektar++ | vendor | Command Line | Please see Nektar++ | |
| Netcdf-c | vendor | Command Line | Please see NetCDF-C | |
| Netcdf-fortran | vendor | Command Line | Please see NetCDF-Fortran | |
| Nextflow | vendor | Command Line | Please see Netxtflow | |
| numpy | vendor | Command Line | numpy | |
| Nvidia CUDA SDK | vendor | Command Line | CUDA SDK | |
| Nvidia HPC SDK | vendor | Command Line | HPC SDK | |
| OpenBLAS | vendor | Command Line | Please see OpenBLAS | |
| OpenCascade CE | vendor | Command Line | Please see OpenCascade CE | |
| OpenCL | vendor | Command Line | OpenCL | |
| OpenFOAM | vendor | Command Line | Please see OpenFOAM | |
| OpenGeoSys | vendor | Command Line | Please see OpenGeoSys | |
| OpenGL (MESA) | vendor | Desktop GUI | MESA | |
| OpenGL (Nvidia) | vendor | Desktop GUI | VirtualGL / Nvidia OpenGL | |
| OpenMP | vendor | Command Line | Please see OpenMP | |
| OpenMPI | vendor | Command Line | Please see OpenMPI | |
| OpenMS | vendor | Command Line | Now installed. See OpenMS. | |
| OpenSeesPy | vendor | Command Line | Please see OpenSeesPy | |
| OpenSSL | vendor | Command Line | Please see OpenSSL | |
| ORCA | vendor | Command Line | Please see Orca | |
| parallel | vendor | Command Line | Please see Parallel | |
| Paraview | vendor | Command Line and Desktop GUI | Please see Paraview | |
| Perl | vendor | Command Line | Please see Perl | |
| pgap | RSE | Command Line | Please see pgap | |
| Picard | vendor | Command Line | Please see Bioapps | |
| PISM | vendor | Command Line | Please see PISM | |
| Plink | vendor | Command Line | Please see Plink | |
| PLUMED | RSE | Command Line | Please see Amber MD | |
| Podman | vendor | Command Line | Podman is one of the supporter container tools on Comet. Also consider browsing our Containers guide. | |
| PRSice | vendor | Command Line | Please see PRSice | |
| PTSCOTCH | vendor | Command Line | PT-SCOTCH refers to SCOTCH when running in parallel mode | |
| Pysam | vendor | Command Line | Please see PySAM | |
| Python | vendor | Command Line | Please see Python | |
| Python JAX | vendor | Command Line | Please see Python JAX| | |
| Python OpenTURNS | vendor | Command Line | Please see Python OpenTURNS | |
| Python RAY | vendor | Command Line | Please see Python RAY | |
| PyTorch | vendor | Command Line | PyTorch | |
| QCTOOL | vendor | Command Line | Please see OCTOOL | |
| quantum-espresso | vendor | Command Line | Please see Quantum Espresso| | |
| R | vendor | Command Line | R | |
| R Studio | vendor | Desktop GUI | R Studio | |
| R.avaflow | vendor | Desktop GUI | Please see R.avaflow | |
| R.keras | vendor | Command Line | Please see R.keras | |
| R.piecewiseSEM | vendor | Command Line | Please see R.Piecewise SEM | |
| R.stan | vendor | Command Line | Please see R.Stan - also Stan | |
| Regenie | vendor | Command Line | See Regenie. | |
| Relion | RSE | Command Line | See CCP-EM Suite. | |
| Relion | RSE | Desktop GUI | Please see CCP-EM Suite container | |
| Remora | vendor | Command Line | Please see Remora | |
| Rerio | vendor | Command Line | Please see Rerio | |
| Resmap | RSE | Command Line | Please see CCP-EM Suite container | |
| RIBFIND | RSE | Command Line | Please see CCP-EM Suite container | |
| SAIGE | vendor | Command Line | Please see SAIGE | |
| Salmon | vendor | Command Line | Please see Salmon | |
| Sambamba | vendor | Command Line | Please see Bioapps | |
| Samtools | vendor | Command Line | Please see Bioapps | |
| SCOTCH | vendor | Command Line | Please see SCOTCH | |
| Singularity | vendor | Command Line | The functionality of Singularity has been replaced by Apptainer on Comet. Also consider browsing our Containers guide. | |
| SMINA | vendor | Command Line | Please see SMINA | |
| Snakemake | vendor | Command Line | Please see Snakemake | |
| SPAdes | vendor | Command Line | Please see SPAdes | |
| Stan | vendor | Command Line | Please see Stan | |
| STAR | vendor | Command Line | Please see STAR | |
| StarCCM+ | vendor | Command Line + Desktop GUI | StarCCM+ | |
| Stata/MP | vendor | Command Line | Please see StataMP | |
| StringTie | vendor | Command Line | Please see Bioapps | |
| Subread | vendor | Command Line | Please see Subread | |
| Suitesparse | RSE | Command Line | Please see Amber MD | |
| Szip | vendor | Command Line | Please see SZip | |
| tabix | vendor | Command Line | Please see tabix | |
| TEMPy | RSE | Command Line | Please see CCP-EM Suite container | |
| TEMPy-REFF | RSE | Command Line | Please see CCP-EM Suite container | |
| Tensorflow | vendor | Command Line | Tensorflow | |
| Tetgen | vendor | Command Line | Please see Tetgen | |
| TinyXML | vendor | Command Line | Please see TinyXML | |
| Topaz | RSE | Command Line | Please see CCP-EM Suite container | |
| Tophat / Tophat 2 | RSE | Command Line | Please see Bioapps | |
| Torchani | RSE | Command Line | Please see Amber MD | |
| Triangle | vendor | Command Line | Please see Triangle | |
| Tricycler | vendor | Command Line | Please see Tricycler | |
| Trim Galore | vendor | Command Line | Please see Trim Galore | |
| UCSF Motioncor 3 | RSE | Command Line | Please see CCP-EM Suite container | |
| Unicycler | vendor | Command Line | Please see Unicycler | |
| VCFTools | vendor | Command Line | Please see VCF Tools | |
| VEP | vendor | Command Line | Please see VEP | |
| VINA | vendor | Command Line | Please see VINA | |
| VirtualGL | vendor | Desktop GUI | VirtualGL / Nvidia OpenGL | |
| Visual Studio Code / VSCode | vendor | Desktop GUI | Please see VSCode | |
| vLLM | RSE | Command Line | Please see vLLM | |
| Vtk | vendor | Command Line | Please see VTK | |
| XengSort | vendor | Command Line | Please see XengSort | |
| xmds | vendor | Command Line | Please see xmds | |
| zlib | vendor | Command Line | zlib |
These titles were requested as part of the initial installation on Comet, require additional work before they can be progressed or are currently missing due to other reasons.
| Title | Category | License | Interface | Help |
|---|---|---|---|---|
| Abaqus | ||||
| bgenix | ||||
| BUGS | ||||
| CryoSPARC | ||||
| GRASS | ||||
| JARS | ||||
| jmol | ||||
| Mrtrix | ||||
| OpenCascade CE | ||||
| octool | ||||
| PISM | ||||
| R.avaflow | ||||
| R.piecewise SEM | ||||
| Stan | ||||
| Tetgen | ||||
| Tricycler | ||||
| VINA |
We sometimes choose to provide software via container environments either due to their complexity, need for additional libraries or dependencies that are difficult to manage via software module, or simply because the developer already provides a pre-built container.
These containers are available for your use on Comet, and we would strongly recommend that you use them in preference to building the software yourself, or requesting a central software module install. Click on the title to see further information on that container, including how to run the software.
In all cases the container can (and should) be run from where it currently sits in the /nobackup containers directory - you should not make duplicate copies of these container images.
| Title / Wiki Page | Container Location | Size | Description |
|---|---|---|---|
| CASTEP | /nobackup/shared/containers/castep-25.12.sif | 720 MB | Includes the CASTEP application binaries and optimised libraries (LAPACK, OpenBLAS, FFTW3) compiled for the AMD Epyc CPU architecture used on Comet. |
| DNAscent | /nobackup/shared/containers/mboemo_dnascent_dnascent.sif | 5 GB | Developer provided runtime image. Obtained from: https://cloud.sylabs.io/library/mboemo/dnascent/dnascent |
| R-GIS-Pipeline | /nobackup/shared/containers/R-gis-pipeline.sif | 800 MB | A custom R GIS image with latest version of R, GCC, Abseil C++ libraries and a large number of custom R packages: tidyverse, terra, sf, matrix, lme4, openxsls, data.table … and more. All AMD Epyc CPU optimised. |
| Bioapps | /nobackup/shared/containers/bioapps.2026.03.sif | 1 GB | Runtime container with an extensive collection of bioinformatics tools. Intended to be used in preference to the standalone software modules already installed on Comet. The tools used in this container are all AMD Epyc optimised and can be used regardless of any other software modules loaded at the same time - no need to load/unload software due to conflicting dependencies. |
| FSL | /nobackup/shared/containers/fsl.6.0.7.19.sif | 7.5 GB | Runtime environment containing the FSL application and all optional components. Please read our documentation guide for assistance. |
| CNVKit | /nobackup/shared/containers/cnvkit.0.9.13.sif | 1.3 GB | Uses the published Docker container from https://github.com/etal/cnvkit - converted to a local Apptainer image. Please read our documentation guide for assistance. |
| Amber MD | /nobackup/shared/containers/ambermd.24.25.sif | 10 GB | Amber MD suite of biomolecular simulation tools. Available in both CPU and GPU accelerated versions. |
| ComfyUI | N/A | A build recipe and instructions are provided to build this on a per-user basis. | |
| Ubuntu LTS | N/A | 120 MB | Sample Ubuntu LTS container recipe. |
| Ubuntu LTS + development tools | N/A | 350 MB | Sample Ubuntu LTS container recipe with standard C, C++, Fortran and Python development tools. |
| Nvidia CUDA/CUDNN | N/A | 5.9 GB | Sample Nvidia CUDA/CUDNN container recipe built on Ubuntu LTS. |
| CCP-EM Suite | /nobackup/shared/containers/ccpemsuite.2026.03.sif | 42 GB | CCP-EM, CCPEM2, CCP4, Doppio, Relion 5 and other, related tools. |
| OpenGeoSys | /nobackup/shared/containers/ogs.2026.03.sif | 1 GB | OpenGeoSys Python environment, including Jupyter Lab for running OGS notebooks. |
| Ice Sheet and Sea Level System Model | /nobackup/shared/containers/issm.2026.03.sif | 3 GB | ISSM is used in large scale ice flow modelling. This container image has ready-to-run ISSM binaries packaged with the required Python runtime needed to allow you to call ISSM functions in your own scripts. |
| ldsc | /nobackup/shared/containers/ldsc.2026.03.sif | 360 MB | ldsc is a command line tool for estimating heritability and genetic correlation from GWAS summary statistics. ldsc also computes LD Scores. This container has a version of ldsc which is targetted for a specific Python version and has difficulty running with other versions of its dependencies. |
| Freesurfer | /nobackup/shared/containers/freesurfer.8.0.20.sif | 10 GB | Freesurfer is installed within a container as it has requirement for multiple system libraries which would otherwise need to be installed on each compute node. This container works in both command-line as well as X11/desktop mode. |
| vLLM | /nobackup/shared/containers/vllm.0.19.1.sif | 7 GB | Container based install of the vLLM application plus Python, PyTorch and the vLLM examples. |
| ANSYS | /nobackup/shared/containers/ansys.2025r2.sif | 50 GB | Later releases of ANSYS on Comet will be provisioned as container environments. This allows us to provide ANSYS on a supported Linux OS, iwth all of the dependencies needed by the ANSYS software without adding multiple, duplicate software modules across the entire system. ANSYS 2025 R2 and above also now works correctly in the graphical X11 Desktop environment provided by Open OnDemand. |
| GipsyX | N/A - restricted to specific project groups | 720 MB | Restricted-license software which is only available to certain HPC rpoejct groups. |
Any additional software requests received since Comet was commissioned are recorded here. These will be taken to the Directors of the AHPC service, considered, prioritised and submitted to the our HPC vendor for installation and commissioning. Email the support team if you'd like to request software which is not listed on this page.
| Title / Wiki Page | Help | Website | License | Interface | Requested By | Action | Status |
|---|---|---|---|---|---|---|---|
| screen | System tool, no module needed | RedHat system package | Open Source | shell | multiple users | Approved | Installed |
| tmux | System tool, no module needed | RedHat system package | Open Source | shell | multiple users | Approved | Installed |
| Gaussian | Use module load Gaussian | link | Commercial - existing University license | shell | Keith Izod, Jack Hemingway, Nick Walker, Sam Power | Purchased | Installed |
| GaussView | Use module load GaussianView | link | Commercial - existing University license | X11 / Open OnDemand | Keith Izod, Jack Hemingway, Nick Walker, Sam Power | Purchased | Installed |
| gromacs / CUDA | Use module load GROMACS/2026-cuda | link | Open Source | shell | Finlay Clark | Approved | Installed |
| gromacs / OpenCL | Use module load GROMACS/2026-opencl | link | Open Source | shell | Finlay Clark | Approved | Installed |
| emacs | System tool, no module needed | RedHat system package | Open Source | shell | multiple users | Approved | Installed |
| bc | System tool, no module needed | RedHat system package | Open Source | shell | multiple users | Approved | Installed |
| VSCode | Use module load VSCode - or launch from the Open OnDemand desktop menu | link | Proprietary, permissive distribution: https://code.visualstudio.com/license | X11 / Open OnDemand | multiple users | Approved | Installed |
| Miniforge | Use module load Miniforge | link | Open Source | shell | multiple users | Approved | Installed |
| BCL Convert | Use module load BCL-Convert - start with bcl-convert. Also see Bioapps | link | Commercial | shell | Matthew Teasdale and other BSU users | Approved | Installed |
| slurm-seff | SchedMD GitHub repository | Open Source | shell | Carol Booth | Approved | Installed | |
| imagemagick | System tool, no module needed | RedHat system package | Open Source | shell | Approved | Installed | |
| Stata MP 2 core | Use module load Stata | link | Commercial - existing University license for 2 core version | shell | multiple users in Business School | Approved | Installed |
| Hypre | Use module load Hypre | link | Open Source | shell | Francesco Zonta | Approved | Installed |
| | top. | RedHat system package | Open Source | shell | installed on login02, multiple users | Approved | |
| CASTEP | Installed as a container - see our CASTEP guide | link | Cost-Free source code license | shell | Ioan Bogdan Magdau, Panagiotis Kourtis, Alex Christison | Approved | Installed |
| ORCA | Use module load Orca | link | Free for academic/personal use | shell | Multiple - alternative to Gaussian | Approved | Installed |
| LAPACK | Use module load LAPACK/3.12.0 | link | Open Source | shell | multiple users | Approved | Installed |
| Avogadro 1 & 2 | Use module load Avogadro - only usable on Open OnDemand GPU desktops | link | Open Source | X11 / Open OnDemand | Used alongside ORCA - alternative to Gauss View | Approved | Installed |
| ChimeraX | Use module load ChimeraX - only usable on Open OnDemand desktops (preferably GPU) | link | Free for academic, government, nonprofit, and personal use | X11 / Open OnDemand | Used alongside ORCA - alternative to Gauss View | Approved | Installed |
| seqkit | Please see Bioapps | Open Source | shell | Common bioinformatics tools - requested by many users. Existing versions in modules have conflicting dependencies. | Approved | Installed via container | |
| bwa-mem2 | Please see Bioapps | Open Source | shell | Common bioinformatics tools - requested by many users. Existing versions in modules have conflicting dependencies. | Approved | Installed via container | |
| bwa-meth | Please see Bioapps | Open Source | shell | Common bioinformatics tools - requested by many users. Existing versions in modules have conflicting dependencies. | Approved | Installed via container | |
| Methyldackel | Please see Bioapps | Open Source | shell | Common bioinformatics tools - requested by many users. Existing versions in modules have conflicting dependencies. | Approved | Installed via container | |
| DEXSeq | Please see Bioapps | link | Open Source | shell | Ogo Ajayi | Approved | Installed via container |
| AmberMD | Please see Amber MD | link | Open Source | shell | Shangyuwen Yang | Approved | Installed via container |
| MuSpAn | Please see MuSpAn | link | Free Academic-use only license | shell | Craig Stamp | Approved | User Install |
| bash-completion | System tool, no module needed | RedHat system package | Open Source | shell | Michael Beaty | Approved | Installed |
| csh | System tool, no module needed | RedHat system package | Open Source | shell | Achraf Koulali | Approved | Installed |
| RClone | System tool, no module needed | RedHat system package | Open Source | shell | Michael Beaty | Approved | Installed |
| Nextflow | Link | Open Source | shell / service | Jordan Cuff, Monika Gonka, Ahlam Alqahtani | Investigating | ||
| Globus connect personal | link | shell / X11 | multiple users | ||||
| Globus cli | link | shell | multiple users | ||||
| Tophat | Please see Bioapps | link | Open Source | shell | Ogo Ajayi | Approved | Installed via container |
| Freesurfer | link | Open Source | Karoline Leiberg | Approved | Installed via container | ||
| vLLM | Please see vLLM | link | Open Source | shell | Jiajie Luo | Approved | Installed via container |
| Matlab 2026a | Update module to latest University version | University License | shell / X11 | Approved | Installed | ||
| SAS | link | University License | shell / X11 | Steven Wang, Dexter Canoy, Misty Troutt, Hemant Patle, John Casement | Investigating | ||
| Convert3D | Please see Bioapps | link | Open Source | shell | Gerard Hall | Approved | Installed via container (inside Bioapps container) |
| GipsyX | link | Restricted License | shell / X11 | Peter Clarke | Approved | Installed via container within project folder |