Research Environment Training Session: Importing data and tools to use in the RE

Working with the extensive genomic data in the Genomics England Research Environment requires the use of specialised software tools, and comparison to other data. While a vast array of bioinformatics tools and public data are made available in the HPC, you may have further tools and datasets you are keen to use, including those you have written yourself, that you would like to use to analyse GEL data.

This training sessions will take you through the various methods available to you for self-installation of tools, including using conda environments, CRAN, containers and Airlock. You will also learn how to query the catalogue of previously installed tools, and how to make requests for installation.

You are only allowed to attend this session if you are eligible for data access. This means that you are a Research Network or Discovery Forum member that has met the necessary verification checks and passed our Information Governance training course. If you do not meet this criterion by 10th February 2025 you will be unregistered for this session.

Timetable

13.30 Welcome and introduction
13.35 What is already in the RE

13.45 Personal conda environments

13.55 Importing R packages with CRAN and Bioconductor

14.05 Importing containers with Singularity

14.15 Using Airlock to bring data/software in

14.25 Making a software request

14.35 Software licensing requirements
14.45 Getting help and questions

Learning objectives

After this training you will know:

• How to find all the available software and data on the RE
• Methods for self-import and installation of data and tools
• How and when to request software installation of the RE

Target audience

This training is aimed at researchers who:

• Are working in the Genomics England RE
• Are comfortable working on the command line
• Would like to work with external tools and software on the RE