Archive training session
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Importing tools and data to use in the Research Environment, February 2025¶
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 session 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
13.50 Importing R packages with CRAN and Bioconductor
14.00 Importing containers with Singularity
14.10 Using Airlock to bring data/software in
14.15 Making a software request
14.25 CloudOS – importing tools and pipelines on the Cloud
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¶
12th February 2025
Materials¶
You can access the redacted slides and video below. All sensitive data has been censored.
Slides¶
Video¶
Give us feedback on this tutorial
Q&A¶
Q&A
I’m guessing everything in terms of containers runs through singularity, not docker, correct?
live answered
Can we link to EHR data for patients?
Hi Shikta! Could you elaborate on your question - do you mean linking to data from LabKey tables in the RE?
yes if I am interested in a particular cancer type - can I link it to EHR information? Or do you have a dataset which is already linked data.
I have linked documentation to accessing and linking clinical data via LabKey: https://re-docs.genomicsengland.co.uk/clinical_data/ . EHR information is available as part of our dataset, and you will have to carry out some data wrangling to link this data to your desired cohort (as all types of clinical/phenotypic data sit in different LabKey tables).
Do you offer mamba support?
I have checked the documentation and it is just conda
Hi Hamzah, can this be accessed with my RE access or does this require other access?
CloudOS requires extra access, which you can request
If I have my own software which exists as a private, password protected docker image, am i correct in reasoning that the correct way to import it would be airlock rather than singularity?
Yes, you can import containers as an image through Airlock if it’s not possible to make it public