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:
To load software, run:
module load lang/R/3.5.1-foss-2018b
Always specify the version of the software that you want to load, to avoid errors and unexpected results.
For instance, Running
module load lang/R will load version 3.6.2 instead of my desired version of 3.5.1.
To unload software, run:
module unload lang/R/3.5.1-foss-2018b
Or you can switch to a different version of the same software (required software to be loaded first):
module switch lang/R/3.6.2-foss-2019b
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.
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.