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
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