I figured out the problem. Here is our solution, inspired from
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
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.
2012/8/25 Christophe Antoniewski <droso...@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
> unfortunately without success.
> Any advices for fixing this irritating bug is welcome !
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at: