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 13th August 2024
AdapterRemoval/2.3.3 ldstore/2.0
AutoDock_Vina/1.2.5 libdeflate/1.20
BWA/0.7.17 libgit2/1.6.2
BerkeleyDB/3.01 libtiff/3.4
Bio-DB-HTS/3.01 libtiff/4.3.0
CADD/1.6 libtiff/4.5.0 (D)
CNView/1.0 libunwind/1.8.0
CNVnator/0.4.1 liftover/1.0
CaVEMan/1.15.3 linasm/1.13
ExpansionHunter/3.2.2 llvm/16.0.6
ExpansionHunter/4.0.2 (D) locuszoom/1.4
ExpansionHunterDenovo/0.9.0 lollipop/0.3.0
GSL/2.7 lumpy/0.3.1
MEDICC2/1.0.2 mafft/7.520
MPFR/4.2.0 magma/1.10
R/3.6.3 manta/1.6.0
R/4.2.1 matlab/8.1
R/4.3.3 (D) matlab/24.1 (D)
REViewer/0.2.7 maven/3.9.6
aliview/1.28 meme/5.5.5
ampliconArchitect/1.3.r7 metal/1.0
ampliconClassifier/1.1.1 miniconda3/23.11.0
annotSV/3.3.7 miniforge3/23.11.0-0
annovar/2019Nov minimap2/2.26
annovar/2024-03-14 (D) mosaicHunter/2024-02-14
ant/1.9.16 mplayer/1.5
apbs/3.4.1 msisensor-pro/1.2.0
asmc-asmc/2024-02-26 msisensor/0.6
automake/1.15 multiqc/1.19
bamtools/2.5.2 music2/0.2
bcftools/1.16 mutserve/2.0.0-rc15
beagle/5.4 mutsig2cv/3.11
bedops/2.4.41 ncurses/6.4
bedtools/2.30.0 new_fugue/2010-06-02
bedtools/2.31.0 (D) nextflow/22.10.5
blast+/2.15 nextflow/23.04
blat/1.0 nextflow/23.10-with-plugins
bolt-lmm/2.4.1 nextflow/23.10
boost/1.83 nextflow/24.04.2-with-plugins (D)
bowtie2/2.5.2 nf-core/0.3.1
canvas/1.40.0.1613 nf-test/0.7.3
circos/0.69-9 nf-test/0.8.2
clang/16.0.6 nf-test/0.9.0 (D)
cmake/3.24.3 nodejs/16.9.0
cpan/1.7047 openrefine/3.7.4
cromwell/v65 openssl/1.1.1o
curl/7.81.0 pandoc/3.3
cython/3.0.8 perl/5.38.2
cytoscape/3.10.1 picard/3.1.1
delly/1.2.6 pindel/0.2.5b8
denovoGear/1.1.1 platypus/0.8.1
discover/0.9.5 plink/1.9
dotnet/2.0.0 plink/2.00a3.3LM
dotnet/8.0.1 (D) plink/2.0 (D)
drop/1.2.4 plink_seq/0.10
eigen/3.3.9 popdel/1.5.0
exomiser/13.3.0 proj/8.2.1
exonerate/2.2.0 prsice-2/2.3.5
fastqc/0.12.1 pycircos/1.0.2
fetk/1.9.3 pysam/0.22.0
ffmpeg/6.0 python/3.8
fribidi/1.0.12 python/3.8.1
gatk/4.5.0.0 python/3.11 (D)
gauchian/1.0.2 readline/8.0
gcc/10.4.0 regenie/3.4.1
gcta/1.94 repeatDetector/1.0
gdal/3.7.0 rtg-tools/3.12.1
geos/3.12.1 rvtests/2.1.0
gistic/2.0.23 saige/1.0.9
gmp/6.2.1 salmon/1.10.0
gnu-parallel/20190222 samtools/1.16.1
gnu/4.4 shapeit4/4.2.2
gradle/8.5 sniffles/1.0.11
guppy/3.4.5 somalier/0.2.19
gvcfgenotyper/2019.02.26 sqlite3/3.40.0
haplocheck/1.3.3 squirls/2.0.1
hipstr/0.7 stack/2.15.7
hisat2/2.2.1 star/2.7.2a
hla-la/1.0.3 star/2.7.11a (D)
hmftools/2024-02-06 strelka/2.9.10
homer/4.11 superSTR/1.0.1
htslib/1.18 svanna/1.0.4
igv/2.17.1 tabix/1.18
imagemagick/7.1.0 trimmomatic/0.39
java/1.8 udunits/2.2.28
java/11.0.2 vcf2maf/1.6.21
java/17.0.2 vcfanno/0.3.4
java/19.0.2 (D) vcflib/1.0.9
jq/1.7.1 vcftools/0.1.16
kallisto/0.50.1 verifyBamID/2.0.1
king/2.3.2 vt/0.57721
kraken/1.1.1 xz/5.4.7
kraken2/2.1.3 zlib/1.3
lapack/3.12.0 zulu/21.0.1
ldsc/1.0.1 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
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.