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.


> 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


>
> Thanks,
>
> Peter
>
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