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.mare...@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 > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ >
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
