Using Python on the CCB cluster

Using Python on the CCB cluster.

Overview #

As well as the standard Python 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 python-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 python-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 python-cbrg module uses the following system.

The python-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 python-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 python-cbrg module will automatically pull in the latest stable base and all packages or libraries.

For instance:

module load python-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 python-base/3.6.10
module load python-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 python-cbrg/202104
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).