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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 3rd June 2024
AdapterRemoval/2.3.3            kraken/1.1.1
AutoDock_Vina/1.2.5             kraken2/2.1.3
BWA/0.7.17                      ldsc/1.0.1
BerkeleyDB/3.01                 ldstore/2.0
Bio-DB-HTS/3.01                 libgit2/1.6.2
CADD/1.6                        libtiff/3.4
CNView/1.0                      libtiff/4.5.0           (D)
CNVnator/0.4.1                  libunwind/1.8.0
CaVEMan/1.15.3                  liftover/1.0
GSL/2.7                         linasm/1.13
MEDICC2/1.0.2                   llvm/16.0.6
MPFR/4.2.0                      locuszoom/1.4
R/3.6.3                         lollipop/0.3.0
R/4.2.1                         lumpy/0.3.1
R/4.3.3                  (D)    mafft/7.520
REViewer/0.2.7                  magma/1.10
aliview/1.28                    manta/1.6.0
ampliconArchitect/1.3.r7        maven/3.9.6
ampliconClassifier/1.1.1        meme/5.5.5
annotSV/3.3.7                   metal/1.0
annovar/2019Nov                 miniconda3/23.11.0
annovar/2024-03-14       (D)    miniforge3/23.11.0-0
ant/1.9.16                      minimap2/2.26
apbs/3.4.1                      mosaicHunter/2024-02-14
asmc-asmc/2024-02-26            mplayer/1.5
automake/1.15                   msisensor-pro/1.2.0
bamtools/2.5.2                  msisensor/0.6
bcftools/1.16                   multiqc/1.19
beagle/5.4                      music2/0.2
bedops/2.4.41                   mutserve/2.0.0-rc15
bedtools/2.30.0                 ncurses/6.4
bedtools/2.31.0          (D)    new_fugue/2010-06-02
blast+/2.15                     nextflow/22.10.5
blat/1.0                        nextflow/23.04
bolt-lmm/2.4.1                  nextflow/23.10          (D)
boost/1.83                      nf-test/0.7.3
bowtie2/2.5.2                   nf-test/0.8.2           (D)
canvas/1.40.0.1613              nodejs/16.9.0
circos/0.69-9                   openrefine/3.7.4
clang/16.0.6                    openssl/1.1.1o
cmake/3.24.3                    perl/5.38.2
cpan/1.7047                     picard/3.1.1
cromwell/v65                    pindel/0.2.5b8
curl/7.81.0                     platypus/0.8.1
cython/3.0.8                    plink/1.9
delly/1.2.6                     plink/2.0               (D)
denovoGear/1.1.1                popdel/1.5.0
discover/0.9.5                  prsice-2/2.3.5
dotnet/2.0.0                    pycircos/1.0.2
dotnet/8.0.1             (D)    pysam/0.22.0
drop/1.2.4                      python/3.8
eigen/3.3.9                     python/3.8.1
exomiser/13.3.0                 python/3.11             (D)
fastqc/0.12.1                   readline/8.0
fetk/1.9.3                      regenie/3.4.1
ffmpeg/6.0                      repeatDetector/1.0
fribidi/1.0.12                  rtg-tools/3.12.1
gatk/4.5.0.0                    rvtests/2.1.0
gauchian/1.0.2                  saige/1.0.9
gcc/10.4.0                      salmon/1.10.0
gcta/1.94                       samtools/1.16.1
gistic/2.0.23                   shapeit4/4.2.2
gmp/6.2.1                       sniffles/1.0.11
gnu-parallel/20190222           somalier/0.2.19
gnu/4.4                         sqlite3/3.40.0
gradle/8.5                      squirls/2.0.1
guppy/3.4.5                     star/2.7.2a
gvcfgenotyper/2019.02.26        star/2.7.11a            (D)
haplocheck/1.3.3                strelka/2.9.10
hipstr/0.7                      superSTR/1.0.1
hisat2/2.2.1                    svanna/1.0.4
hla-la/1.0.3                    tabix/1.18
hmftools/2024-02-06             trimmomatic/0.39
homer/4.11                      udunits/2.2.28
htslib/1.18                     vcf2maf/1.6.21
igv/2.17.1                      vcfanno/0.3.4
imagemagick/7.1.0               vcflib/1.0.9
java/11.0.2                     vcftools/0.1.16
java/17.0.2                     verifyBamID/2.0.1
java/19.0.2              (D)    vt/0.57721
jq/1.7.1                        zlib/1.3
kallisto/0.50.1                 zulu/21.0.1
king/2.3.2                      aws-cli/2.15    
singularity/3.8.3    singularity/4.1.1 (D)

To load software, run:

module load R/3.6.3

Always specify the version of the software that you want to load, to avoid errors and unexpected results.

For instance, Running module load R will load version 4.2.1 instead of my desired version of 3.6.3.

To unload software, run:

module unload R/3.6.3

Or you can switch to a different version of the same software (required software to be loaded first):

module switch R/4.2.1

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.

Container support

The HPC supports Singularity for containerised workflows. If your workflow is written in Docker, Singularity is able to read Dockerfiles and convert them into Singularity images. Note that the usage of Singularity/Docker is optional. Softwares and tools can be loaded using module as before.