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

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