High Performance Computing guides and policies for the University of Queensland.
Updated: 26 August 2026
The operating system installations on Bunya nodes are relatively lightweight. This is done for a variety of sound technical reasons.
Most software, even some things that would normally be considered part of the standard operating system, are installed separately. Access to this software is facilitated by the modules mechanism. Some software is made available through GUI menus in onBunya
For more information, please refer to these documents
Most of the software listed here is freely available to use. Some software requires agreement to license conditions and/or authorised membership of a special access group.
[!NOTE]
These lists have been created on login nodes.
Software built under /sw/auto will have an architecture specific installation location (login nodes are “epyc3”).
Software built under /sw/local will only be available on the architectures where they have been installed (e.g. “epyc3” but not “epyc4”).
Software built under /sw/local/…/noarch can be used on any architecture that makes sense to use.
The noarch software is either provided by software containers, or, is a commercial software product (e.g. MATLAB).
GPU nodes will have additional software for utilising (e.g. CUDA for NVidia GPU nodes) and GPU specific software.
This list is grouped by installation branch.
It shows the name of the module and the number of distinct versions available.
--------------------- /sw/auto/rocky9a/epyc3/modules/all ----------------------
abricate (1) gtk2 (1) netcdf (4)
alsa-lib (1) gtk3 (2) nettle (3)
anaconda3 (2) guile (1) networkx (3)
ansys-dependencies (1) gzip (4) nextflow (3)
ant (1) harfbuzz (3) nghttp2 (1)
any2fasta (1) hatchling (3) nghttp3 (1)
aocl-blas (1) hdf (4) ngtcp2 (1)
archive-zip (1) hdf5 (5) ninja (4)
archspec (2) help2man (5) nlohmann_json (4)
armadillo (3) hifiasm (1) nlopt (2)
arpack-ng (3) hisat2 (2) nodejs (3)
assimp (1) hmmer (2) nspr (3)
at-spi2-atk (2) htseq (1) nss (3)
at-spi2-core (2) htslib (3) numactl (4)
atk (2) humann (1) openbabel (1)
augustus (1) hwloc (4) openblas (4)
autoconf (5) hypothesis (4) openexr (3)
automake (5) icu (4) openfoam (1)
autotools (5) iimpi (4) openjpeg (4)
bamtools (4) imagemagick (2) openmpi (4)
bbmap (2) imath (3) openpgm (1)
bcftools (2) imkl-fftw (4) openssl (2)
bcl2fastq2 (1) imkl (4) p11-kit (1)
beagle-lib (2) impi (4) pandoc (1)
beagle (1) intel-compilers (4) pango (3)
beautifulsoup (1) intel (4) parallel (2)
bedtools (4) interproscan (1) paraview (1)
binutils (10) interproscan_data (1) patchelf (3)
bio-db-hts (1) intervaltree (1) pcre (4)
bio-searchio-hmmer (1) intltool (3) pcre2 (4)
bioperl (2) ipython (1) perl-bundle-cpan (2)
biopython (2) isa-l (1) perl (6)
bison (6) jags (1) picard (1)
blast+ (2) jansson (1) pigz (1)
blast (1) jasper (3) pillow (2)
blat (2) java (3) pixman (3)
blis (4) jbigkit (4) pkg-config (1)
boost.python (1) jellyfish (2) pkgconf (5)
boost (4) jemalloc (3) plink (1)
bowtie (2) json-c (3) plotly.py (1)
bowtie2 (2) json-fortran (1) plumed (3)
brotli (4) jsoncpp (4) pmix (4)
brunsli (3) judy (2) pocl (1)
build (2) julia (1) poetry (3)
busco (1) jupyter-server (1) popt (1)
bwa (2) jupyterlab (1) postgresql (2)
bzip2 (4) kallisto (2) pplacer (1)
c-ares (1) kim-api (2) prodigal (2)
cairo (3) kraken2 (1) proj (4)
canu (1) kronatools (1) prokka (1)
capnproto (1) lame (3) prrte (2)
catch2 (3) lammps (2) psutil (1)
cd-hit (1) lapack (1) pybigwig (1)
cellranger-arc (1) lerc (3) pybind11 (4)
cellranger (1) libaec (1) pydantic (1)
cereal (2) libaio (2) pysam (1)
cffi (3) libarchive (4) python-bundle-pypi (3)
cfitsio (3) libcerf (1) python-isal (1)
cgal (1) libde265 (3) python (6)
checkm-database (1) libdeflate (4) pyyaml (2)
checkm (1) libdrm (3) qhull (5)
clang (2) libepoxy (2) qiime2 (1)
cmake (6) libev (1) qt5 (2)
compress-raw-zlib (1) libevent (5) qt6 (1)
coordgenlibs (1) libfabric (4) quantumespresso (2)
cp2k (1) libffi (4) quast (1)
cpio (2) libgd (2) r-bundle-cran (2)
cppy (2) libgeotiff (4) r (4)
cryptography (3) libgit2 (2) rapidjson (1)
cunit (1) libglu (4) re2c (3)
curl (4) libglvnd (3) rjags (1)
cutadapt (1) libheif (3) rsem (1)
cython (3) libiconv (4) ruby (1)
db (2) libidn2 (2) rust (5)
db_file (2) libint (1) salmon (2)
dbd-mysql (1) libjpeg-turbo (4) samtools (3)
dbus (3) libnsl (1) scafacos (2)
deeptools (1) libogg (2) scalapack (4)
dendropy (2) libopus (2) scikit-build-core (1)
dftd4 (1) libpciaccess (4) scikit-build (3)
diamond (1) libpng (4) scipy-bundle (4)
dirac (1) libpsl (2) scotch (1)
double-conversion (3) libreadline (4) sdl2 (3)
doxygen (4) libsndfile (2) sepp (2)
easybuild (1) libsodium (1) seqlib (1)
eigen (4) libsoup (1) seqtk (4)
elfutils (1) libtasn1 (1) setuptools-rust (3)
elpa (2) libtiff (4) skani (1)
expat (4) libtirpc (4) smithwaterman (1)
fastahack (1) libtool (5) snakemake (1)
fastp (1) libunistring (2) snappy (3)
fastqc (1) libunwind (3) spaceranger (2)
fasttree (1) libvorbis (2) spades (1)
fermi-lite (1) libvori (1) spectra (1)
ffmpeg (3) libwebp (3) spin (1)
ffnvcodec (3) libxc (2) sqlite (4)
fftw.mpi (4) libxml2 (6) sra-toolkit (2)
fftw (4) libxslt (3) ssw (1)
file (2) libxsmm (1) star (2)
filevercmp (1) libyaml (2) stringtie (1)
flac (2) lit (3) suitesparse (1)
flex (8) littlecms (2) swig (4)
flexiblas (4) llvm (3) szip (4)
flit (3) lmdb (3) tabixpp (1)
flye (1) lpsolve (2) tbb (3)
fontconfig (3) lua (1) tbl2asn (1)
fonttools (1) lxml (1) tcl (4)
foss (4) lz4 (4) tk (3)
freebayes (1) lzo (2) tkinter (2)
freetype (3) m4 (8) tmux (1)
fribidi (3) maeparser (1) tqdm (1)
fsom (1) mafft (1) trimmomatic (1)
gatk (2) make (4) trinity (1)
gc (1) makeinfo (2) typing-extensions (1)
gcc (5) mako (3) ucc (4)
gcccore (5) mariadb (2) ucx (4)
gcta (1) mash (1) udunits (2)
gdal (3) matplotlib (2) unzip (4)
gdk-pixbuf (3) maturin (2) util-linux (3)
geos (4) maxquant (1) vcflib (1)
gettext (7) mctc-lib (1) vcftools (2)
gfbf (4) mdi (2) vep (1)
gffcompare (1) megahit (1) virtualenv (3)
gffread (1) mesa (3) voro++ (2)
ghostscript (2) meson-python (3) vscode (1)
giflib (4) meson (4) vtk (2)
git (4) metaeuk (2) wayland (2)
gitpython (1) metis (1) wfa2 (1)
glib-networking (1) miller (1) wget (1)
glib (3) miniconda3 (2) x11 (3)
glpk (2) minimap2 (1) x264 (3)
gmap-gsnap (2) miniprot (1) x265 (3)
gmp (3) mono (1) xerces-c++ (3)
gnuplot (1) motif (1) xml-libxml (2)
gnutls (1) mpfr (3) xorg-macros (4)
go (4) mpi4py (3) xtb (1)
gobject-introspection (3) mrbayes (2) xvfb (2)
gompi (8) mstore (1) xxd (3)
googletest (4) multicharge (1) xz (4)
gperf (3) multichoose (1) yasm (3)
graphite2 (3) multiqc (1) z3 (2)
groff (3) mummer (1) zeromq (1)
gromacs (3) nasm (4) zip (1)
gsl (3) ncbi-vdb (2) zlib (9)
gtdb-tk (1) ncurses (7) zstd (4)
--------------------- /sw/local/rocky8/epyc3/rcc/modules ----------------------
bolt-lmm (1) hdf5 (1) lisflood-fp (4) rjags (1)
dirac (1) jags (1) r-bundle-cran (1) vasp (6)
eagleimp (1) libaec (1) r (2)
--------------------- /sw/local/rocky8/noarch/rcc/modules ---------------------
alphafast (1) epi2me (1) openfold (3)
alphafold (4) esa-snap (1) orca (1)
alphapickle (1) evobind (1) osca (1)
amst2 (1) fastfold (1) paraview (1)
ansys (3) fbpic (1) perceval-quandela (1)
ansysem (1) fiji (3) porechop_abi (1)
asreml-sa (3) fragpipe (1) post (1)
asreml-sa_test (1) freesurfer (1) prism (1)
aviary (4) fsl (1) proteina-complexa (1)
bagel (1) gaussian (1) proteinfold (1)
bakta (1) gromacs (4) proteinmpnn (1)
basespace (1) gtdb-tk (3) pyem (1)
binchicken (1) gurobi (4) qctool (1)
bindcraft (3) humann (1) quilt (1)
bioformats2raw (1) huygens (4) qupath (3)
boltz (3) ilastik (2) r (6)
boltzgen (1) imod (2) relion (9)
carpdock (1) interproscan (1) remora (2)
cebraem (1) ipyrad (1) rfantibody (1)
cellpose (2) itk-snap (1) rfdiffusion (2)
cellprofiler (1) jobstats (1) rosetta (1)
cellsnp-lite (1) julia (1) rstudio (9)
chai-lab (2) ligandmpnn (1) scenicplus (1)
chimerax (1) llama.cpp (3) schrodinger (1)
chrombpnet (1) localcolabfold (3) sglang (1)
cistem (1) mathematica (1) slorado (2)
code-server (4) matlab (3) spisonet (1)
compucell3d (1) medaka (3) spss (1)
coot (2) metabolic (1) star-ccm+ (3)
cramino (1) metaphlan (2) strainberry (1)
crested (2) miniforge (4) subtom (1)
crisflash (1) minimap2 (1) suite2p (2)
cryocare (1) mmseqs (2) tesseract (1)
cryodrgn (2) mobsuite (1) topaz (1)
cuda-q (4) model-angelo (1) transcriptm (1)
deeplabcut (5) mrtrix (1) triqs (1)
diann (2) nastic (1) ultralytics (1)
diffdock (1) nnu-net (1) virtualgl (2)
dl-jupyter (2) ollama (1) vllm (5)
dorado (1) openclip (2) wombat (1)
dynamo (1) openfoam (1) xds (1)
--------------------- /sw/local/rocky9/noarch/rcc/modules ---------------------
ansys (5) deeptmhmm (1) huygens (2) pclai (1)
autodock-gpu (1) diamond (1) lastools (1) proteinix (1)
autodock-vina (1) eggnog-mapper (1) lexicmap (1) space (1)
clustal-omega (1) evo2 (1) macs2 (1) star-ccm+ (1)
coverm (1) group_envs (1) nanomotif (1) vasp (1)
crest (1) gtdb-tk (1) parabricks (1)
-------------------- /sw/local/rocky8/noarch/qcif/modules ---------------------
3d-dna (1) isoseq3 (1) raxml (1)
biobakery_workflows (1) juicer (1) regenie (1)
blast (1) kallisto (1) repeatmasker (1)
braker3 (1) kofamscan (1) repeatmodeler (1)
cellbender (1) ldsc (1) rmats-turbo (1)
celseq2 (1) maker (1) rsem (1)
circlator (1) medaka (1) salsa2 (1)
dadi (1) mikado (1) screen_assembly (1)
dfam (1) mira (1) scvelo (1)
diamond (1) mixer (1) shovill (1)
dram (1) mlst (1) shpc (1)
drep (1) mmseqs2 (1) singlem (1)
edirect (1) mtag (1) snap (1)
enrichm (1) nanocompore (1) sortmerna (1)
exonerate (1) nanopolish (1) sqanti3 (1)
f5c (1) nextpolish (1) sra-tools (1)
fastool (1) nextpolish2 (1) srst2 (1)
gcta (1) ont-fast5-api (1) star (1)
gff3sort (1) parsnp (1) suppa (1)
gmap (1) pb-assembly (1) syri (1)
gtdbtk (1) pear (1) transdecoder (1)
hapflk (1) qapa (1) trinity (1)
harvesttools (1) qiime2-amplicon (1) trinotate (1)
hisat2 (1) qiime2-shotgun (1) unicycler (1)
ipyrad (2) racon (1) xpore (1)
iqtree (1) ratatosk (1)
TO BE COMPLETED
| Application | Category 1 | Category 2 |
|---|---|---|
| 3dslicer (4.10.1) | General-Imaging | Neuroimaging |
| 3dslicer (5.12.0) | General-imaging | Neuroimaging |
| 3dslicer (5.12.3) | General-imaging | Neuroimaging |
| 3dslicer (5.8.1) | General-imaging | Neuroimaging |
| Adxv | Crystallography | General-scientific |
| AFNI | Imaging | Neuroimaging |
| AlphaFold 2.3.2 | AI-ML | Struct-bio |
| ANTs | Misc | General-imaging |
| BIDScoin | Imaging | Neuroimaging |
| Blender | Misc | General-imaging |
| Cellpose 3.1.0 | Misc | Struct-bio |
| Cellpose-SAM | Misc | Struct-bio |
| Cellprofiler 4.2.1 | Misc | Cytometry |
| Cellprofiler 4.2.8.1 | Misc | Cytometry |
| ChimeraX 1.12 | Misc | Cryo-EM |
| CisTEM 2 | CryoEM | Cryo-EM |
| CisTEM | CryoEM | Cryo-EM |
| ComfyUI | AI-ML | |
| CompuCell3D | Misc | Struct-bio |
| Coot 0.9.8.92 | Misc | Struct-bio |
| Cryolo | Misc | Struct-bio |
| CryoSPARC | CryoEM | Struct-bio |
| CryoSPARC updater (to 5.0.4) | CryoEM | Struct-bio |
| Crystfel | CryoEM | Cryo-EM |
| Cytoscape | Bioinformatics | Cytometry |
| DeepLabCut 2.3.11 (AMD GPU) | AI-ML | Struct-bio |
| DeepLabCut 2.3.8 (NVidia GPU) | AI-ML | Struct-bio |
| DeepLabCut 3.0.0rc10 (AMD GPU) | AI-ML | Struct-bio |
| DeepLabCut 3.0.0rc10 (NVidia GPU) | AI-ML | Struct-bio |
| DIA-NN | Bioinformatics | |
| Diffusion Toolkit | Imaging | Neuroimaging |
| Dynamo 1.1.532 | Misc | General-scientific |
| EMAN 2.3 | CryoEM | Struct-bio |
| Empanada (Napari) | General-imaging | Cryo-EM |
| EPI2ME | Bioinformatics | |
| ESA SNAP 10.0.0 | Misc | General-scientific |
| ESA SNAP 9.0 | Misc | General-scientific |
| Eye of MATE Image Viewer | Misc | General-imaging |
| Fiji 1.53 | Fiji | |
| Fiji 1.54h | Fiji | |
| Fiji 1.54h (No Cellpose) | Fiji | |
| Fiji 1.54k | Fiji | |
| Fiji 1.54k (No Cellpose) | Fiji | |
| Fiji 1.54p | Fiji | |
| Fiji 1.54q | Fiji | |
| Fiji 1.54t | Fiji | |
| FoldDock | AI-ML | Struct-bio |
| FragPipe | Struct-bio | |
| Freesurfer 7.3.2 | Imaging | Neuroimaging |
| FSL 5.0 | Imaging | Neuroimaging |
| FSL 6.0.7.9 | Imaging | Neuroimaging |
| HRM Online - Huygens Core | Scientific | Volume |
| Huygens Essential | Scientific | Volume |
| Huygens Localizer | Scientific | Volume |
| Huygens Professional | Scientific | Volume |
| IGV | Bioinformatics | |
| Ilastik 1.4.1 | Misc | Cytometry |
| IMOD 4.11.4 | Misc | General-imaging |
| IMOD 4.12.62 | Misc | General-imaging |
| IMOD 4.9.9 | Misc | General-imaging |
| IMOD 5.1.1 | Misc | General-imaging |
| IMOD-RAZA | Misc | General-imaging |
| ITK-SNAP (4.2.0) | Misc | General-imaging |
| ITK-SNAP (4.4.0) | Misc | General-imaging |
| Jupyter notebook | Misc | General-scientific |
| LabGym 2.8.1 | AI-ML | |
| LiberTEM | Misc | Cryo-EM |
| LibreOffice | Misc | General-scientific |
| LLAma.cpp | AI-ML | |
| Mathematica 14.0 | Misc | General-scientific |
| Matlab 2022a6 | Misc | General-scientific |
| Matlab 2023b5 | Misc | General-scientific |
| Matlab MCR (v93, for R2017b) | Misc | General-scientific |
| Matlab MCR (v97, for R2019b) | Misc | General-scientific |
| MIB | Crystallography | Struct-bio |
| Minc Tools | Imaging | Neuroimaging |
| Model-angelo | CryoEM | Cryo-EM |
| MolSketch | Misc | General-imaging |
| MrTrix 3.0.8 | Imaging | Neuroimaging |
| MrTrix 3 | Imaging | Neuroimaging |
| MrTrix | Imaging | Neuroimaging |
| Napari (0.4.10) | Misc | General-imaging |
| Napari (0.5.3) | Misc | General-imaging |
| Napari (0.6.2) | Misc | General-imaging |
| NoiseTransfer2Clean | CryoEM | Struct-bio |
| Octave 9.2.0 | Misc | General-scientific |
| Olex2 | Crystallography | Struct-bio |
| OMERO.insight | Misc | Light-microscopy |
| Open WebUI | AI-ML | |
| Paraview | Misc | General-imaging |
| Phenix 1.20.1 | Crystallography | Struct-bio |
| Phenix 1.21.1 | Crystallography | Struct-bio |
| Phenix 2.1 (no GPU) | Crystallography | Struct-bio |
| Phenix 2.1 (NVidia GPU) | Crystallography | Struct-bio |
| PyEM | Misc | Cryo-EM |
| PyMOL | Misc | General-imaging |
| QGIS | Misc | General-imaging |
| QuPath 0.7.0 | Cytometry | General-imaging |
| Relion 4.0 | CryoEM | Struct-bio |
| Relion 5.0.1 | CryoEM | Struct-bio |
| Rstudio 2024.04.2 (R 4.4.1) | Misc | General-scientific |
| Rstudio 2024.12.0 (R 4.4.2, 25k pkgs) | Rstudio | |
| Rstudio 2024.12.1 (R 4.4.2, 1200 pkgs) | Rstudio | |
| Rstudio 2025.05.1 (R 4.5.1) | Rstudio | |
| Rstudio 2026.01.0 (R 4.5.2) | Rstudio | |
| Rstudio 2026.07.0 (R 4.6.1) | Rstudio | |
| Schrodinger Maestro | Misc | Struct-bio |
| ScigetApp | Misc | General-scientific |
| Scipion3 | Misc | Struct-bio |
| Scipion3 (with Relion) | Misc | Struct-bio |
| Scipion3 (with XmippSrc) | Misc | Struct-bio |
| SHELX | Crystallography | Struct-bio |
| ShelXle | Crystallography | Struct-bio |
| Sir2019 | CryoEM | Cryo-EM |
| SPHIRE 1.4 | CryoEM | Struct-bio |
| SPM 12 | Imaging | CVL |
| Spyder | Misc | General-scientific |
| StaMPS | Misc | General-scientific |
| Suite2p | Misc | General-imaging |
| THUNDER | CryoEM | Cryo-EM |
| TomoBear 0.6.0 | CryoEM | Struct-bio |
| Topaz | CryoEM | Cryo-EM |
| TrackVis | Imaging | Neuroimaging |
| TrackVis shell | Imaging | Neuroimaging |
| VESTA | Crystallography | Struct-bio |
| VLC Media Player | Misc | General-imaging |
| VMD 2.0.1a1 | Misc | General-imaging |
| VMD | Misc | General-imaging |
| XDS 2021 | Crystallography | Struct-bio |
| XDS 2025 | Crystallography | Struct-bio |
#Module Overview List
module --show-hidden -w 80 -t overview
#onBunya List
/sw/admin/davidg/bin/createOnBunyaAppsList