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 <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
>
>
>
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