On Wed, Mar 2, 2016 at 12:07 PM, Peter Cock email@example.com wrote:
On Wed, Mar 2, 2016 at 4:59 PM, Nate Coraor firstname.lastname@example.org wrote:
On Mon, Feb 29, 2016 at 12:10 PM, Peter Cock email@example.com wrote:
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?
I think the easiest solution to this is probably to write a wrapper
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.
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:
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?