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How do I use bioinformatics software in Python and R?

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.
To see all modules available for use, use the command:
$ module avail

 

ADVANCED USAGE

The setup 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)