> 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.
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).


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