Hi,
I've just resolved a similar problem running uwsgi under supervisord, which
turned out to be a typo setting the path environment variable in the
supervisord config file. Most things worked ok but some things produced errors
finding pysam and sqlalchemy (since the system python was being used in
preference to the galaxy venv), while jobs would mysteriously fail with a 'file
not found' error.
Took some tracking down...
James
--
Dr. James Abbott
Lead Bioinformatician
Bioinformatician Data Science Group
Imperial College London
________________________________
From: galaxy-dev <galaxy-dev-boun...@lists.galaxyproject.org> on behalf of
Gudrun Amedick <amed...@itsc.uni-luebeck.de>
Sent: Wednesday, June 28, 2017 1:49:44 PM
To: Maximilian Friedersdorff
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Python modules not found when starting with init
system
Hi,
I know. To my understaunding of virtual environments, this shouldn't make a
difference. As I said, I don't really get it. It looks like Python tries
to find pysam outside of the virtual environment for some reason, that's why
I'm guessing PATH.
I'm curious though, and if someone knows why this solution works, I'd be happy
to hear it too.
Glad I could help.
Gudrun Amedick
Gudrun Amedick
IT-Systemtechnik
UNIVERSITÄT ZU LÜBECK
IT-Service-Center
Ratzeburger Allee 160
23562 Lübeck
Tel +49 451 3101 2035
Fax +49 451 3101 2004
amed...@itsc.uni-luebeck.de
www.itsc.uni-luebeck.de<http://www.itsc.uni-luebeck.de>
Am Mittwoch, den 28.06.2017, 10:59 +0100 schrieb Maximilian Friedersdorff:
> On Tue, Jun 27, 2017 at 03:41:27PM +0200, Gudrun Amedick wrote:
> >
> > Hi,
> >
> > i ran into that too (on debian 8). I'm not that familiar with virtual
> > environments but this is what I found out.
> >
> > It looks like the virtual environment doesn't get activated properly in the
> > shipped ini.d-file (it is the shipped one, right?).
> > If I add ". /path/to/.venv/bin/activate" to it, everything runs just fine.
> > "run.sh" has this line. The init.d-file hasn't. It just calls the
> > .venv-
> > python directly. It seems like that's not fully equivalent to activating
> > .venv and running python in there. I don't really know why. I'm guessing
> > PATH-magic.
> >
> > Hope that helps a bit.
> >
> > Gudrun Amedick
> Hi,
>
> The thing is that running the python interpreter in the virtual
> environment _should_ take care of that anyway. The provided debian init
> script even says as much: "A simple way to activate this virtualenv is
> to use the python interpreter in <GALAXY_DIR>/.venv".
>
> In any case, explicitly activating the virtualenv solves the problem.
> Thanks for the pointer Gudrun.
>
> Maybe a dev can chime in here.
>
> Many Thanks
>
> Max
>
>
> --------------------------------------------------------------------
> Un o’r 4 prifysgol uchaf yn y DU a’r orau yng Nghymru am fodlonrwydd myfyrwyr.
> (Arolwg Cenedlaethol y Myfyrwyr 2016)
> www.aber.ac.uk<http://www.aber.ac.uk>
>
> Top 4 UK university and best in Wales for student satisfaction
> (National Student Survey 2016)
> www.aber.ac.uk<http://www.aber.ac.uk>
___________________________________________________________
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/
