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 
> <mailto: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 
> > <mailto: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 
> > <http://simison.com/brian/GalaxyAdmin_notes.html>
> > 2. 
> > https://wiki.galaxyproject.org/Events/GCC2012/TrainingDay/WS5?highlight=%28init.d%29
> >  
> > <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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