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