Research Environment Training Sessions: Running workflows on the HPC and Cloud

The Genomics England Research Environment (RE) 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.

You are only allowed to attend this session if you are eligible for data access. This means that you are a GECIP 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 11 December 2023, you will be unregistered for this session.

You can find materials from past training sessions and information on upcoming training sessions on the Genomics England Research Environment User Guide.

Agenda

13.30 Introduction and admin

13.35 What is the High Performance Cluster

13.50 Why use the HPC

13.55 Queues and nodes available on the HPC

14.05 How to create and monitor jobs on the HPC

14.15 Tools and software available and how to load them

14.25 Interactive coding tools

14.35 Bringing in your own tools and software

14.45 Getting help and 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 programme in python and/or R