Providing the correct environment using the .bashrc for the user that the pbs jobs are submitted under works for me. Many thanks to Glen Beane! Cheers, Alex On Sep 14, 2011, at 9:03 AM, Nate Coraor wrote:
Glen Beane wrote:
On Sep 13, 2011, at 6:01 PM, "Oleksandr Moskalenko" <om@hpc.ufl.edu<mailto:om@hpc.ufl.edu>> wrote:
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
I load modules in the .bashrc for the galaxy user on our cluster
This would be the preferred way over modifying the PBS template, to avoid conflicts from updates to pbs.py upstream.
--nate
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