Package Management with ModuleFiles

How to view the list of available packages in the facility?

On Sharanga, users can use the following command to view the list of installed packages (with the versions).

$ module avail
--------------------------------- /share/module-------------------------------
   2brad_denovo/2019-01-22_giteec5016            meshclust2/2.1.0
   2brad_gatk/2019-01-22_git1fcc9e8              metal/2010-02-08
   admixture/1.3.0                               metal/2011-03-25
   angsd/0.923                                   metalge/2010-02-08
   annovar/2018apr                               minimac2/2014-09-15
   artemis/18.0.3                                minimac3/2.0.1
   augustus/3.3.2                                minimac4/1.0.0
   bamtools/2.5.1                                mirdeep2/0.1.0
   bamutil/1.0.14                                mixcr/3.0.3
   basemount/0.15.103.3011                       mmap/2018-04-07
   basespace-cli/0.8.12.590                      morgan/3.2
   basespace-cli/0.9.17                          morgan/3.4
   basespace-cli/0.10.8                          mosdepth/0.2.6
   bayescan/2.1                                  mothur/1.35.0
   bbmap/38.16                                   multiqc/1.6
   bcbio/1.1.1                                   mummer/3.23

How to load and unload a package(s)?

Users can use the module load command to load a package into their current environment. For example, a user who wishes to use PETSc library can use the following syntax.

$ module load petsc

If a user wishes to unload the PETSc library from their user environment, they can use the module rm command.

$ module rm petsc

If a user wishes to unload all the loaded libraries from their user environment, then they can use the following command.

$ module purge

How to view the list of loaded packages?

Users can use the following command to find the list of currently loaded modules.

$ module list

How do I check the version of the package installed?

Users can type the following command to find the version of the installed package.

$ module spider <package name>

Note that the user may get additional information about the package by using the following command

$ module help <package name>

After submitting a job, I am getting messages like "module: command not found". Why am I getting this message?

Modulefiles are by default sourced by the default shell /bin/bash. You may get this message if you have changed the shell to something other than bash. We request you to change the shell back to bash for optimal functioning. Users can use the chsh shell command to change their user shell environment back to bash. Another reason could be due to the unavailability of the desired package.