Hi everybody,

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
start-stop-daemon command:


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
> /etc/environment
> unfortunately without success.
> Any advices for fixing this irritating bug is welcome !
> Chris
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:


Reply via email to