Hi,

I am trying to set up Galaxy to interface with a Cray system which runs Torque/PBS.

After reading this Galaxy wiki page: https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS

I was able to scramble torque egg with the following command:

LIBTORQUE_DIR=/opt/torque/2.4.11/lib/libtorque.so.2 python scripts/scramble.py -e pbs_python

I do not fully understand the "parameters and configuration" part in PBS section of the wiki page. Where exactly the "runner" XML snippet with <plugin> and <destinations> should be placed?

Also wondering if the snippet will be required for all tools that I want to run on compute nodes or is it a global setting? Can I tell existing tools to use this setup?

Another question is, can I configure Galaxy to submit jobs to compute cluster as a mortal user and not an admin of the system?

Thanks,
--
Ketan