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CoBrALab / qbatch

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Add --parsable option #156

Open gdevenyi opened 6 years ago

gdevenyi commented 6 years ago

qbatch needs an option where it only returns the jobids of jobs submitted.

This would allow qbatch to be used in other pipelines that may want to monitor job IDs themselves rather than using the cluster's proper dependency tracking (see ANTs pipelines...)

gdevenyi commented 6 years ago

Best way to implement is a combination of proper options to the submission and parsing the outputs so that the qbatch outputs are always consistent.

In addition, parsing the outputs is important for eventual python module qbatch.

gdevenyi commented 6 years ago

Related to #163

gdevenyi commented 5 years ago

SLURM will report back:

JOBID:CLUSTERNAME

With option sbatch --parsable

gdevenyi commented 5 years ago

SGE uses qsub -terse to report only job IDs

gdevenyi commented 5 years ago

PBS isn't documented very well, but it looks like it just returns Job ids by default: http://www.arc.ox.ac.uk/content/torque-job-scheduler#PBScondExecution