galaxy already has tool-dependencies which can be used.
for example, velvet's tool XML would include:
the above will use the default version; or to specify a specific version:
<requirement type="package" version="1.2.07">velvet</requirement>
in your tool-dependencies dir (as defined in universe_wsgi.ini):
ln -s DEFAULT/ default
echo "module load velvet/1.2.07" > 1.2.07/env.sh
echo "module load velvet" > DEFAULT/env.sh
- 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.
On Tue, Aug 28, 2012 at 7:28 AM, Fabien Mareuil
> 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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