We had something similar breaking when using run-as-real-user, where config/galaxy.ini setting external_chown_script which defaults to scripts/external_chown_script.py was being run on the cluster nodes using the system default Python.
Here we created a wrapper shell script which invoked the Python script via the correct Python 2.7 used by the main Galaxy instance: external_chown_script = scripts/external_chown_script.sh The symptoms were the same though - Galaxy's dependencies could not be found. Peter On Mon, Apr 11, 2016 at 1:30 PM, Marius van den Beek <m.vandenb...@gmail.com> wrote: > Hi Eric, > > Take a look at this > https://docs.galaxyproject.org/en/master/admin/framework_dependencies.html#wheel-interaction-with-other-software > . > I hope that should be sufficient. > > Cheers, > Marius > > On 11 April 2016 at 14:25, Eric Kuyt <eric.ku...@wur.nl> wrote: >> >> Hi Marius, >> >> Now I ran in to some problems. >> >> When trying to change metadata of a file, the python path changes (these >> tools run using drmaa) to the normal system version. Here tools are ending >> in error becaus sqlalchemy.orm cannot be found. I can ofcourse install >> sqlarchemy-python systemwide. But this woudn't make me very happy. >> >> in File: <galaxy>/lib/galaxy_ext/metadata/set_metadata.py >> a sys.path.insert to .venv/lib should be added. I don't know what the >> right plcae for this is. >> >> Do you hava any better ideas for this matter? >> >> Eric >> >> >> >> >> On 8 April 2016 at 16:15, Eric Kuyt <eric.ku...@wur.nl> wrote: >>> >>> Thanks, works like a charm! Clean easy fix, Now why I couldn't come up >>> with this myself. >>> >>> On 2 April 2016 at 11:49, Marius van den Beek <m.vandenb...@gmail.com> >>> wrote: >>>> >>>> ld have been mentioned with the release notes. >>>> I didn't test this, but it might be sufficient to replace >>>> PYTHON="/usr/bin/python" >>>> with PYTHON="<path/to/venv/bin/python>". >>>> If that is sufficient for you, let us know and we will update the wiki >>>> and adjust the script in >>> >>> >>> >>> >>> >>> -- >>> Central Veterinary Institute of Wageningen UR (CVI) >>> Department of Infection Biology >>> PO box 65, 8200 AB Lelystad, NL >>> Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad >>> >>> Tel: +31-(0)320-293391 >>> Fax: +31-(0)320-238153 >>> E-mail: eric.ku...@wur.nl >>> Web: http://www.cvi.wur.nl >> >> >> >> >> -- >> Central Veterinary Institute of Wageningen UR (CVI) >> Department of Infection Biology >> PO box 65, 8200 AB Lelystad, NL >> Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad >> >> Tel: +31-(0)320-293391 >> Fax: +31-(0)320-238153 >> E-mail: eric.ku...@wur.nl >> Web: http://www.cvi.wur.nl > > > > ___________________________________________________________ > 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/
