On Wed, Mar 2, 2016 at 5:27 PM, Nate Coraor <n...@bx.psu.edu> wrote: > On Wed, Mar 2, 2016 at 12:07 PM, Peter Cock <p.j.a.c...@googlemail.com> > wrote: >> >> On Wed, Mar 2, 2016 at 4:59 PM, Nate Coraor <n...@bx.psu.edu> wrote: >> > On Mon, Feb 29, 2016 at 12:10 PM, Peter Cock <p.j.a.c...@googlemail.com> >> > wrote: >> >> >> >> Hello all, >> >> >> >> QUESTION: When submitting jobs to the cluster as the real user, >> >> how should sudo scripts/drmaa_external_runner.py be told which >> >> Python to use, and how would it activate the venv if needed for >> >> the DRMAA dependency? >> > >> > >> > Hi Peter, >> > >> > I think the easiest solution to this is probably to write a wrapper >> > script >> > that sets up the environment for drmaa_external_runner.py and call this >> > wrapper (with the same args), which can then pass the args to >> > drmaa_external_runner.py. >> > >> > --nate >> >> Thanks Nate, >> >> So we'd write a shell script called drmaa_external_runner.py which >> setups the Python environment and then calls a copy of the original >> Python script drmaa_external_runner.py - has anyone else tried this? > > > The name of the run job script to call is controlled by the > drmaa_external_runjob_script variable in galaxy.ini: > > https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.ini.sample#L1073 > > Here you can change this to your wrapper.
Thanks Nate - I should have realised this was a configuration option. >> Clearly using Python 2.7 on a system with a Python 2.6 default (CentOS 6) >> is part of the problem. Maybe we can just install the Python DRMAA under >> the system Python 2.6 instead? > > This part would work, but wouldn't you still need the environment variables > to be set? > > --nate Good point. The custom script option with hard coded environment variables sounds more straightforward that fighting the Linux OS settings. Peter ___________________________________________________________ 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/
