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> 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