galaxy already has tool-dependencies which can be used.
for example, velvet's tool XML would include:
<requirements> <requirement type="package">velvet</requirement> </requirements>
the above will use the default version; or to specify a specific version:
<requirements> <requirement type="package" version="1.2.07">velvet</requirement> </requirements>
in your tool-dependencies dir (as defined in universe_wsgi.ini):
mkdir velvet cd velvet mkdir 1.2.07 mkdir DEFAULT ln -s DEFAULT/ default echo "module load velvet/1.2.07" > 1.2.07/env.sh echo "module load velvet" > DEFAULT/env.sh
notes: - type must be "package" - "default" must be a symlink - we had to add "-S /bin/bash -shell y" to DRMAA native spec to get the bash module function we use to work; may not be an issue with you.
Ed
On Tue, Aug 28, 2012 at 7:28 AM, Fabien Mareuil fabien.mareuil@pasteur.frwrote:
Dear Colleagues,
Many teams use module, a user interface for the Modules package. The Modules package enable to manage easily several versions of a program with a dynamic modification of the user's environment via modulefiles. I would like to know if it is planned to integrate the ability to load modules via galaxy? For example, we could imagine a configuration file that would link the name and version of a tool with the module name and allowing to load the module before running the tool locally or on a cluster.
Thank you for your answer, Best regards,
Fabien Mareuil
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