I have added information to the galaxy user's .profile

export TEMP=/mnt/ngswork/galaxy/tmp export PATH="/mnt/ngswork/galaxy/sw/bin:$PATH" export PYTHONPATH="/mnt/ngswork/galaxy/sw/lib/python2.6/site-packages"

and added a .sgerequest # set up temp and path environment variables for jobs -v TEMP=/mnt/ngswork/galaxy/tmp -v PATH=/mnt/ngswork/galaxy/sw/bin:/usr/bin:/bin/:/usr/local/bin #-V

On Aug 25, 2012, at 7:41 AM, Christophe Antoniewski <drosofff@gmail.commailto:drosofff@gmail.com> wrote:

Hi everybody,

I am getting troubles when I try running our galaxy instance as a daemon service in ubuntu, using the procedure provided by James Casbon and available in the /contrib galaxy directory (briefly, installing the galaxy.debian-init in the /etc/init.d directory) Everything is OK, *except* that third party softwares that are installed in /bin of the galaxy home directory fail. I suspect a problem of $PATH when the service is launched with the command : start-stop-daemon --chuid $USER --group $GROUP --start --make-pidfile \ --pidfile $PIDFILE --background --chdir $DIR --exec $PYTHON -- $OPTS; in the James bash script. However, R scripts for instance are run correctly. Taking this observation into account, we added /home/galaxy/bin in the /etc/environment unfortunately without success.

Any advices for fixing this irritating bug is welcome !

Chris

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-- Brad Langhorst langhorst@neb.commailto:langhorst@neb.com 978-380-7564

Hi everybody,

I figured out the problem. Here is our solution, inspired from http://serverfault.com/questions/139970/how-to-tell-start-stop-daemon-to-upd..., which may help others:

In the galaxy.debian-init script provided by James Casbon, a line may be added after the variable assignments and before invoking the start-stop-daemon command:

export PATH="${PATH:+$PATH:}/home/galaxy/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin"

whose purpose is to populate the galaxy $PATH environmental variable, as it turns out that the start-stop-daemon, even as galaxy user, does not pass through the galaxy shell, the .profile conf file, etc...

Everything seems to works fine now and we have Galaxy running as a service.

Chris

2012/8/25 Christophe Antoniewski drosofff@gmail.com

Hi everybody,

I am getting troubles when I try running our galaxy instance as a daemon service in ubuntu, using the procedure provided by James Casbon and available in the /contrib galaxy directory (briefly, installing the galaxy.debian-init in the /etc/init.d directory) Everything is OK, *except* that third party softwares that are installed in /bin of the galaxy home directory fail. I suspect a problem of $PATH when the service is launched with the command : start-stop-daemon --chuid $USER --group $GROUP --start --make-pidfile \ --pidfile $PIDFILE --background --chdir $DIR --exec $PYTHON -- $OPTS; in the James bash script. However, R scripts for instance are run correctly. Taking this observation into account, we added /home/galaxy/bin in the /etc/environment unfortunately without success.

Any advices for fixing this irritating bug is welcome !

Chris