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Running workflows on the HPC and Cloud, December 2025

The Genomics England Research Environment provides access to a High Performance Cluster (HPC) where you can access our genomic and clinical data and run large-scale analyses on these, using pre-installed bioinformatics tools, your own code and imported tools and software. This training introduces the HPC, including the compute and the queues available. We will show you how to access the available tools, including interactive coding tools, via the HPC, and how to run jobs using them. We will also cover bringing in tools and software from outside of the RE.

This training will be taught by our experts, including our HPC squad who create and maintain the cluster, and our bioinformaticians, who develop, install and work with the tools and workflows on the HPC.

Timetable

  1. Welcome and introduction
  2. What is the High Performance Cluster?
  3. Queues available on the HPC
  4. How to create and monitor jobs on the HPC
  5. Tools and software available and how to load them
  6. Interactive coding tools
  7. Bringing in your own tools and software
  8. CloudOS – batch and interactive jobs on the Cloud
  9. Questions

Learning objectives

After this training you will be able to:

  • Access the Genomics England Research Environment HPC
  • Work with the available software to submit jobs to the different queues
  • Create and work with your own software on the HPC

Target audience

This training is aimed at researchers:

  • working with the Genomics England Research Environment
  • comfortable working on the command line
  • who can program in python and/or R

Time

9th December 2025, 1.30pm

Materials

You can access the redacted slides and video below. All sensitive data has been censored.

Slides

Slides

Video

Give us feedback on this tutorial

Q&A

Q&A

Normally, if i just want to do some small interactive job with R or python (without accessing to HPC), based on your showcase, i need to use ClouldOS to do it? or i can directly open Rstudio or Vscode as IDE to do that on amazon desktop

live answered

what is the local memory and computing power without loging into the HPC?

Each execution node has 24 cpu cores and ~80GB of memory

Is there a cost involved in using CloudOS?

live answered