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