Hi Keith, Sorry for the delayed response, as I was on vacation. Your activate script is the same as mine except for the obvious directory name differences. Unfortunately I am out of ideas.
-Will On Fri, Nov 6, 2015 at 6:23 PM, Suderman Keith <suder...@cs.vassar.edu> wrote: > 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 >>> > >>> > >>> > ___________________________________________________________ >>> > Please keep all replies on the list by using "reply all" >>> > in your mail client. 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