The solution was rather simple, once I figured it out.
The /etc/init.d/galaxy script was invoking scripts/paster.py script directly so
.venv/bin/activate was not being sourced. The solution was to modify
/etc/init.d/galaxy to call a startup script that sourced .venv/bin/activate
before starting Galaxy. I can write my solution up in more detail, but now I
am having some problems setting the pid file correctly.
If I use the --make-pidfile and --pidfile options for start-stop-daemon in
/etc/init.d/galaxy then /var/run/galaxy.pid contains the pid of the startup
script and not the pid of the Galaxy instance.
If I try to set the pid in the startup script Galaxy won't start as the script
(now running as the Galaxy user) can't create/write the /var/run/galaxy.pid
My hack-around has been to touch the pid file (in case it doesn't exist) and
then chown it to the galaxy user in /etc/init.d/galaxy, but this doesn't strike
me as the correct way to do this. Do any sysadmin gurus have any better
> On Nov 1, 2015, at 9:31 PM, Keith Suderman <suder...@cs.vassar.edu> wrote:
> I am trying to upgrade our Galaxy instance to the latest stable code from
> master and now our instance won't start using my /etc/init.d/galaxy script.
> That is:
>> sudo service galaxy start
> no longer works. It says it does (i.e. prints "[OK]"), but Galaxy isn't
> running and nothing is written to the log. I am using the init.d script from
> simison , which is basically the same as the one posted to the Galaxy wiki
> , both of which are quite old.
> Galaxy does start with:
>> sudo su galaxy
>> ./run.sh --daemon
> so I have left Galaxy running in a screen session for now, but that is less
> than ideal.
> I suspect something to do with the .venv as `./run.sh --skip-venv` also fails
> and I don't recall Galaxy being that finicky about a venv being active. Does
> anyone know how I can get the /etc/init.d/galaxy script (i.e.
> start-stop-daemon) to activate the venv for paster.py?
> 1. http://simison.com/brian/GalaxyAdmin_notes.html
> Research Associate
> Department of Computer Science
> Vassar College
> Poughkeepsie, NY
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