Re: [galaxy-dev] Galaxy Startup Failing

[Suderman Keith]

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_CACHE3. Your config is in universe_wsgi.ini (in, I assume, /home/galaxy/galaxy-dist) while mine is in config/galaxy.ini4. You source the virtualenv from /home/galaxy/galaxy_env/bin/activate while mine is in /home/galaxy/galaxy_dist/.venv/bin/activateI 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,KeithOn Nov 5, 2015, at 7:44 PM, Will Holtz  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.-WillOn Wed, Nov 4, 2015 at 8:13 AM, Suderman Keith  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.pidKeithOn Nov 3, 2015, at 7:39 PM, Will Holtz  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.-WillOn Tue, Nov 3, 2015 at 8:55 AM, Suderman Keith  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  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.  To manage your subscriptions to this
> and other Galaxy lists, please use the 

Re: [galaxy-dev] Galaxy Startup Failing

[Will Holtz]

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 
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  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 
> 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 
>> 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.  To manage your subscriptions to this
>> > and other Galaxy lists, please use the interface at:
>> >  https://lists.galaxyproject.org/
>> >
>> > To search Galaxy mailing lists use the unified search at:
>> >  http://galaxyproject.org/search/mailinglists/
>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>
>
>
>
> --
> The information contained in this 

[galaxy-dev] Galaxy Startup Failing

[Keith Suderman]

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"
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  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/