we run galaxy on a cluster and real user job sumission (via DRMAA).
The problem is getting the Galaxy standard tools to work with
We use environment-modules to fit the environment to the needs of a
job and want to do the same for galaxy jobs. I highly expect the need
to handle different versions of the same program on our galaxy instance.
It is no problem to configure indivdual evironments for new tools, as
we can simply set the necessary <requirement type="package"
version="xyz"> entries in the tool.xml and set a 'module load xyz' in
the corresponding env.sh files.
The challenge is to get the galaxy standard tools to work. Several of
them do not define a requirement-package tag. Instead one finds the
types "binary" or "python-module". But these are not handeled by
Managed Tool Dependencies (env.sh). Especially tools that require
python-module=rpy, should also have a package=R, or: if
python-module=Gnuplot I would also need a package='gnuplot' entry to
trigger the corresponding module load command.
I also found binary=gnuplot, or binary=R... these also need to be
loaded on our system.
The only way I can think of solving this, is by editing these
tool.xmls by hand or do you guys think there is a more general
solution? Are there by chance any methods to resolve binaries and
python-modules? (could not find anything about it)
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