I feel like someone should respond to this but I must admin I don't have a lot of ideas. I assume you are able to use qsub to submit jobs from the Galaxy server? This is worth verifying that before anything else. If that doesn't work - the system configuration needs to be modified. I think there are a couple different implementations of DRMAA for PBS: http://apps.man.poznan.pl/trac/pbs-drmaa (I think this is recommend one). http://sourceforge.net/projects/pbspro-drmaa/ It might be worth trying to compile the latest and great of one or both and target both. Galaxy also has a PBS runner that many people use for communicating with Torque. I think the DRMAA runner should work - but this is a fallback option as well just to get going. -John