Software and Modules

Championing reproducibility in scientific tooling

The HPC team maintain software stacks and GNU modules for widely-used software across the institute. This includes modules for compilers, languages and low-level use-cases as well as high-level applications such as specific bioinformatics software.

We champion repeatable and reproducible science by promoting and supporting containerisation in bioinformatics software development and usage. We run a centralised Singularity/Apptainer service internally and host standardised images to enable teams to maintain reproducible workflows either on the cloud or on the farm.

GitLab

The option of hosting collaboration code on an internal GitLab server is provided to users, granting the benefits of the security of the Sanger system.

CI/CD pipelines can be run by dedicated runner machines which are created as instances in OpenStack, allowing for a versatile range of automation for testing, building, and deploying production-level code.

The research computing team are available for assistance with constructing CI/CD workflows and are happy to advise and collaborate with users.

RStudio Platform

We host a local RStudio platform that runs interactive R sessions on the farm to enable users a lightweight interface to statiscal analysis of their datasets.