Using R on the CCB cluster

Using R on the CCB cluster.

Overview #

As well as the standard R versions that you would normally expect, the CCB team additionally preinstalled hundreds of additional packages available for all to use. These are available via the R-cbrg module.

Basic usage #

If you just want to get up and running with set of commonly used bioinformatics packages curated by the CCB team, you can do so with a single command:

module load R-cbrg

Request additional packages #

If you need to use a package which is not already installed, please contact the CCB team via the address below before attempting to install a local copy. In many cases the CCB team can easily add it to the central installation.

Advanced usage #

The setup of the R-cbrg module uses the following system.

The R-base module contains fixed, unchanging installations of the base language. This is for safety –- they cannot be accidentally overwritten causing unexpected changes of behaviour. The module R-cbrg contain separate package and library repositories for each version of Python. Because packages and library versions also change over time, we take a snapshot of the state on a monthly basis and then lock this to prevent changes causing unexpected behaviour. A single current version for each provides a continual rolling ‘head’ where changes are applied. Loading the R-cbrg module will automatically pull in the latest stable base and all packages or libraries.

For instance:

module load R-cbrg
module list

However, if you want to use a different version of the base, you can do that by loading it manually first:

module load R-base/3.6.3
module load R-cbrg
module list

Simmilarly, if you want to use a different version of the libraries, for example because a recent update broke something you relied on, you can do that by loading it manually:

module load R-cbrg/202108
module list

Getting help #

You can email the CCB team using the email address genmail@molbiol.ox.ac.uk. Using this address ensures your email is logged and assigned a tracking number, and will go to all the core team, which means the appropriate person or people will be able to pick it up.

Copyright #

This text is copyright University of Oxford and MRC and may not be reproduced or redistributed without permission.

Author #

Duncan Tooke (duncan.tooke@imm.ox.ac.uk) and Kevin Rue-Albrecht (kevin.rue-albrecht@imm.ox.ac.uk).