Hi everyone, I figured it out, in the end has nothing to do with the --daemon mode it had to do with my Galaxy init script! I was accidentally sourcing the function library at the top of my init script: # Source function library. . /etc/rc.d/init.d/functions This resets PATH to only essential dirs, oops. Dont' do this... Now it works fine in --daemon mode thanks everyone for trying to help me out, Leandro On Mon, Jul 19, 2010 at 1:51 AM, Ry4an Brase <ry4an+galaxy@msi.umn.edu<ry4an%2Bgalaxy@msi.umn.edu>
wrote:
On Sun, Jul 18, 2010 at 10:00:51PM +0200, Leandro Hermida wrote:
Is there a way to tell Galaxy in daemon mode to keep the $PATH of the user running the process?
It's inelegant, but I just put the desired path at the top of run.sh. Unless you have multiple users running it in daemon mode that should work out fine.
-- Ry4an Brase 612-626-6575 University of Minnesota Supercomputing Institute for Advanced Computational Research http://www.msi.umn.edu