From: galaxy-dev-bounces ... On Behalf Of Adam Brenner On our HPC setup, we use the modules system but its the same issue you are running into.
Another vote for the excellent modules system from us at AgResearch. I think it's the only sane way to manage PATH, etc, when you have multiple versions of tools installed. http://modules.sourceforge.net/ I know I've said this before here. Tell all your friends. ;-)
A number of methods exists for setting up the correct path, for you, I believe the easiest would be one of the two:
1) In your init script: source (or setup) PATHS as you have them in your .bash_profile. /etc/init.d/galaxy
OR
2) Within Galaxy, edit universe_wsgi.ini and look for: environment_setup_file and create a file that will setup the correct $PATH for you.
We use (2), which is better than (1), as it will continue to work when you start running your jobs on a cluster, whereas the PATH you set in (1) will not be picked up on the cluster (as far as I remember from our early experience). cheers, Simon ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================