PYTHON-CBRG

Section: CCB Python (7)
Updated:
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OVERVIEW

As well as the standard R and Python versions that you'd normally expect, we've additionally preinstalled hundreds of additional packages for you to use. These are available via the R-cbrg and python-cbrg modules.  

BASIC USAGE

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

$ module load python-cbrg

or

$ module load R-cbrg

Note that the Spyder IDE is included in the standard Python installations, and that R-Studio is a separate module called rstudio  

REQUESTING ADDITIONAL PACKAGES

If you need to use a package which isn't already installed, please contact us via the address below before attempting to install a local copy. In many cases we can easily add it to the central installation.  

ADVANCED USAGE

The setup of the R-cbrg and python-cbrg modules uses the following system.

python-base and R-base contain fixed, unchanging installations of the base languages. This is for safety – they cannot be accidentally overwritten causing unexpected changes of behaviour. python-cbrg and R-cbrg contain separate package and library repositories for each version of Python and R. 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 or R-cbrg module will automatically pull in the latest stable base and all packages or libraries:

$ module load python-cbrg
Loading python-cbrg/current
  Loading requirement: python-base/3.8.3
$ module list
Currently Loaded Modulefiles:
  1) python-base/3.8.3(default) 2) python-cbrg/current(default)

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
Currently Loaded Modulefiles:
   1) python-base/3.6.10 2) python-cbrg/current(default)

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
Loading python-cbrg/202104
  Loading requirement: python-base/3.8.3
$ module list
Currently Loaded Modulefiles:
   1) python-base/3.8.3(default) 2) python-cbrg/202104
 

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>  

SEE ALSO

R-cbrg(7)


 

Index

OVERVIEW
BASIC USAGE
REQUESTING ADDITIONAL PACKAGES
ADVANCED USAGE
GETTING HELP
COPYRIGHT
AUTHOR
SEE ALSO