I need to get Galaxy to use tools that are not located in the system path. At
the command line I can export the PATH either manually or with environment
modules 'module load foo'. However, there doesn't seem to be a clear way to
pass the $PATH and other environmental variables to the pbs runner. For
instance, I use Torque with a dedicated "galaxy" queue. So, I configured the
"default_cluster_job_runner = pbs:///galaxy/" in universe_wsgi.ini. The problem
is that the pbs runner does not pass the environment to the scheduler. I sort
of circumvented this by sourcing an environment setup file from 'pbs_template'
in pbs.py, but I keep wondering about a better way to do it.
I currently use tools set up using environment modules, so this is what I
added the following to pbs_template:
. /etc/profile.d/modules.sh
module load bio
Thanks,
Alex
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