Re: [galaxy-dev] RPy dependency and paths

Andreas Kuntzagk wrote:

What cluster management are you running. As I learned on this list for SGE you need to set the .sge_request of the galaxy user to set PYTHONPATH (and other environment staff. e.q. LD_LIBRARY_PATH for R libraries)

Andreas is correct, you'll need to configure it in your user's environment. The Galaxy server itself starts with 'python -ES' to avoid conflicts, but when tools are run (either locally or on the node) they inherit the PYTHONPATH from the user's environment. In PBS we do this via the user's .profile, and the method Andreas uses works for SGE. --nate