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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)