for example, velvet's tool XML would include:

<requirement type="package">velvet</requirement>

</requirements>

the above will use the default version; or to specify a specific version:

<requirement type="package" version="1.2.07">velvet</requirement>

</requirements>

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 <fabien.mareuil@pasteur.fr> wrote:

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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