Question: Using DRMAA from Python to submit & monitor SGE jobs
gravatar for steve
6 months ago by
steve30 wrote:

I am having issues configuring, submitting, and monitoring SGE HPC cluster jobs from within Python using DRMAA. I know that Galaxy uses Python and supports DRMAA, so I was trying to figure out how this is implemented there. I saw the docs here:

and I was looking at the implementation here:

It appears that Galaxy is using subprocess to issue qsub commands. Is that correct?

I was assuming that Galaxy would be using something like drmaa-python for this, but that appears to not be the case? I had tried that one and couldn't figure out how to properly configure my qsub jobs, but the developer hasn't replied so I was hoping that maybe the Galaxy team would have some insight into this.


sge cluster qsub drmaa • 338 views
ADD COMMENTlink modified 6 months ago by Nate Coraor3.2k • written 6 months ago by steve30
gravatar for Nate Coraor
6 months ago by
Nate Coraor3.2k
United States
Nate Coraor3.2k wrote:

It only uses the subprocess if you're using the "run-as-real-user" mode, and even then the default scripts still use drmaa, they just have to be run through some permissions-granting executable (e.g. sudo).

As per your question to python-drmaa, in Galaxy you can set these SGE-specific options in a <param id="nativeSpecification"></param> on the relevant <destination>.

ADD COMMENTlink written 6 months ago by Nate Coraor3.2k
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