Importing tools and data to use in the Research Environment, February 2024¶
Description¶
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.
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 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:
- working with the Genomics England Research Environment
- comfortable using the command line
- who can programme in python and/or R
Date¶
13th February 2024
Materials¶
You can access the redacted slides and video below. All sensitive data has been censored.