Hi Will,

Thanks for the response, but I am still not having any luck.  The script you attached is almost identical to what I have with a few minor exceptions:

1. You include -ES parameters when invoking python.
2. You export PYTHON_EGG_CACHE
3. Your config is in universe_wsgi.ini (in, I assume, /home/galaxy/galaxy-dist) while mine is in config/galaxy.ini
4. You source the virtualenv from /home/galaxy/galaxy_env/bin/activate while mine is in /home/galaxy/galaxy_dist/.venv/bin/activate

I have made the changes for #1 and #2, #3 shouldn't be an issue, which leaves #4 as the only possible remaining culprit.  I have attached my .venv/bin/activate in case you can spot any differences, but since this is generated automatically it shouldn't be the problem.  I am starting to think I might just have to live with my hack-around for now.

Thanks for the help.
Cheers,
Keith

On Nov 5, 2015, at 7:44 PM, Will Holtz <who...@lygos.com> wrote:

Hi Keith,

I use start-stop-daemon to launch python and I pass --chuid and --group to start-stop-daemon so that galaxy does not run as root. It is my understanding that start-stop-daemon creates the pid file as root before changing user, as my /var/run/galaxy.pid is owned by root:root. I have attached my /etc/init.d/galaxy script. This is from a Ubuntu 12.04 system.

-Will



On Wed, Nov 4, 2015 at 8:13 AM, Suderman Keith <suder...@cs.vassar.edu> wrote:
Hi Will,

I tried that and it didn’t work for me.  Are you using start-stop-daemon to launch python?  Or do you run “python scripts/paster.py serve” from /etc/init.d/galaxy?

If I use start-stop-daemon then python does not seem to be picking up the .venv.  I suspect it has something to do with .venv/bin/activate being sourced as root in one process and then python running as the galaxy user in another process.

If I run “python scripts/paster.py serve” in the /etc/init.d/galaxy script then Galaxy is running as the root user and this is (will be) a production server so that is not an option.

If I run python as the galaxy user from the /etc/init.d/galaxy script then I am back to the problem of python not being able to write to /var/run/galaxy.pid

Keith

On Nov 3, 2015, at 7:39 PM, Will Holtz <who...@lygos.com> wrote:

Hi Keith,

I've dealt with similar situations by adding the sourcing of .venv/bin/activate to the etc/init.d/galaxy script. Then none of the pre-existing pid code needs to be changed.

-Will


On Tue, Nov 3, 2015 at 8:55 AM, Suderman Keith <suder...@cs.vassar.edu> wrote:
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 file.

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 suggestions?

Cheers,
Keith

> On Nov 1, 2015, at 9:31 PM, Keith Suderman <suder...@cs.vassar.edu> wrote:
>
> Greetings,
>
> 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 [1], which is basically the same as the one posted to the Galaxy wiki [2], 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?
>
> Cheers,
> Keith
>
> 1. http://simison.com/brian/GalaxyAdmin_notes.html
> 2. https://wiki.galaxyproject.org/Events/GCC2012/TrainingDay/WS5?highlight=%28init.d%29
>
> ------------------------------
> Research Associate
> Department of Computer Science
> Vassar College
> Poughkeepsie, NY
>
>
> ___________________________________________________________
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