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" >> <o...@hpc.ufl.edu<mailto:o...@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 > >> ___________________________________________________________ >> 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/
