drmaa library threads and munge: Invalid Credential Format

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drmaa
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galaxy_1809

#21

How difficult would it be to create and use a Job Plugin for SGE (e.g., sge.py) that is in essence a copy of

galaxy/lib/galaxy/jobs/runners/util/cli/job/torque.py

with the required SGE parameters for qsub,qstat,qdel…etc.?

As it stands drmaa-python is broken for SGE and the CLI Shell runner needs help to correctly monitor and manage jobs within galaxy.


#22

It shouldn’t be difficult if you want to have a go at it. The major issue is that I don’t think SGE is open source, so it’d be difficult to set up automated tests for this.
It looks like the failure is with monitoring the job. What does qstat -x return ? It should be xml.
If that command doesn’t exist we probably just need to write a parser for the text output of qstat or qstat -a.


#23

We are using Son of Gride Engine… Same but different I suppose. Thanks for the tip on qstat -x. I was able to find the correct parameter to output qstat in xml on our system. Progress is a new error Type Error for NoneType. As it stands I believe we can close out the issue, SoGE will require a JobShell of its own to work properly. If I do get it written I will submit it for review. Thanks Again.