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-update-home-and-user-accordingly-to-chuid-p?answertab=active#tab-top, 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