Installation by users

Domain specific folders for executables and libraries

Many packages and applications can be installed locally in the $HOME directory. Users of each of the groups (e.g. 'WUR/ABGC') can deposit a map with executables or library files that can be of interest to multiple users

 /cm/shared/apps/WUR/ABGC/

Preparing modules for local or domain specific use

Example of making a very simple module that would load a specific version of the short-read aligner bwa to your environment. Simple example, but demonstrates the principle. The example assumes that the executable file(s) are in:

 /cm/shared/apps/WUR/ABGC/bwa/bwa-0.5.9/

create a module file

All users can store executable or library files in:

 /cm/shared/apps/WUR/ABGC/

Within that folder, a modules folder was created where modules can be stored.

 /cm/shared/apps/WUR/ABGC/modules

In the case of bwa, there are quite a few versions, and users may have a preference for a newer or older version, depending on your pipeline.

The first step is to create a 'root' bwa directory, where multiple module files, one for each version, can be created.

mkdir /cm/shared/apps/WUR/ABGC/modulefiles/bwa

note that this may already have been done by somebody else; pay attention not to remove existing module files.

The next step involves making a small TCL-based script. The name of the script is the version of the software that the module pertains. In this case 0.5.9.

vi  /cm/shared/apps/WUR/ABGC/modulefiles/bwa/0.5.9

A basic module script may look like this:

#%Module1.0#######################################################################
## bwa 0.5.9 modulefile
##
proc ModulesHelp { } {

        puts stderr "\tAdds bwa v0.5.9 to your environment"
}

module-whatis   "Adds bwa v0.5.9 to your environment"

set             bwa_059_root        /cm/shared/apps/WUR/ABGC/bwa/bwa-0.5.9/

prepend-path     PATH             $bwa_059_root

Adding a custom module directory to your environment

To allow the module program to find the custom module directory, the location of that directory has to be added to MODULEPATH variable.

export MODULEPATH=$MODULEPATH:/cm/shared/apps/WUR/ABGC/modulefiles

This can be made permanent by adding this line of code to the .bash_profile file in the root of your home folder. To then load the modified MODULEPATH variable you have to load .bash_profile again:

source .bash_profile

This needs to be done only once. Next time you login, .bash_profile will be loaded automatically.

You can check if the modules are found.

module avail

This should give output that includes something similar to this:

 ----------------------------------- /cm/shared/apps/WUR/ABGC/modulefiles -----------------------------------
 bwa/0.5.9  bwa/0.7.5a

See also

• Anunna
• Environment Modules
• Control R environment using modules
• Create a shortcut for the ssh log-in command
• Installing R packages locally
• ABGC specific modules

External links

• http://modules.sourceforge.net
• http://www.admin-magazine.com/HPC/Articles/Environment-Modules