Using software on the HPC¶
Software on the Genomics England HPC is managed through the module system framework.
Module system commands¶
You can list the software available with:
module avail
Software available 14th January 2026
aliview/1.28 hmftools/2024-02-06 nf-test/0.8.2
annovar/2019Nov htslib/1.18 nf-test/0.9.0
annovar/2024-03-14 htslib/1.21 openrefine/3.7.4
ant/1.9.16 inkscape/1.3 openssl/1.1.1o
bamtools/2.5.2 java/1.8 openssl/1.1.1t
bcftools/1.16 java/11.0.2 openssl/3.6.0
bcftools/1.21 java/17.0.2 perl/5.38.2
beagle/5.4 java/19.0.2 picard/3.1.1
bedtools/2.30.0 java/21.0.2 plink/1.9
bedtools/2.31.1 java/23.0.1 plink/2.0
bison/3.8.0 jq/1.7.1 plink/2.00a3.3LM
blat/1.0 king/2.3.2 postgresql/17.4
boost/1.83 kraken/1.1.1 proj/8.2.1
boost/1.84 kraken2/2.1.3 python/3.11
cargo/0.10.5 libdeflate/1.20 python/3.13.9
cmake/3.24.0 libffi/3.4.7 qgrs-cpp/1.0
cmake/ECM libgit2/1.6.2 qt/6.10.1
conform/240524 libpcre/8.45 R/4.3.3
cromwell/v65 libpng/1.6.43 R/4.5.1
curl/7.81.0 libtiff/4.7.0 regenie/3.4.1
eigen/3.3.9 locuszoom/1.4 REViewer/0.2.7
exomiser/13.3.0 m4/1.4.19 rust/1.91.1
exonerate/2.2.0 magma/1.10 samtools/1.16.1
fetk/1.9.3 maven/3.9.6 samtools/1.21
flex/2.6.4 miniconda/23.11.0 singularity/3.8.3
gatk/4.5.0.0 mpc/1.3.1 singularity/4.1.1
gcc/10.4.0 MPFR/4.2.0 singularity/4.1.1-test3
gdal/3.7.0 ncurses/6.4 sqlite3/3.38.1
geos/3.12.2 nextflow/22.10.5 tabix/1.21
gmp/6.2.1 nextflow/23.04 udunits/2.2.28
go/1.25.0 nextflow/23.10 xz/5.4.7
gsl/2.7 nextflow/23.10-with-plugins yt-dlp/2025-12-08
haplocheck/1.3.3 nextflow/24.04.2-with-plugins zlib/1.3
hipstr/0.7 nf-core/0.3.1
hla-la/1.0.3 nf-test/0.7.3
Changes to installed packages
The upgrade to Ubuntu has caused incompatibilities with a number of software packages. Many packages that were previously available on the HPC are no longer there, and many are only available in updated versions.
If there is a package you need to use that is not available, we recommend that you use containers to access it. Many bioinformatics containers are available from biocontainers.
To load software, run:
module load R/4.5.1
Always specify the version of the software that you want to load, to avoid errors and unexpected results.
To unload software, run:
module unload R/4.5.1
Or you can switch to a different version of the same software (required software to be loaded first):
module switch R/4.3.3
Video tutorial¶
Python package and environment management¶
You can use conda in the RE to access pre-made Python environments as well as creating your own. To install packages to your environments, you will need to use proxy paths.
Bringing in software with containers¶
If you require software that is not available on the HPC, you can bring software in using containers with Singularity. If your workflow is written in Docker, Singularity is able to read Dockerfiles and convert them into Singularity images.