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UCSF-Costello-Lab / LG3_Pipeline

The original LG3 pipeline
https://github.com/UCSF-Costello-Lab/LG3_Pipeline
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Passing parameters to qsub #171

Open ivan108 opened 2 years ago

ivan108 commented 2 years ago

I am thinking, if we want the user to be able to edit qsub options (e.g. increase memory or time) then the options should be passed directly to qsub in the _run_* files, e.g. :

qsub "${QSUB_OPTS}" -l ppn=6,vmem=20G,time=10:00:00 ...

and not in *.pbs files, e.g.

#PBS -l nodes=1:ppn=12,vmem=64gb
#PBS -l walltime=00:30:00

since *.pbs files are readonly for users using module version of the pipeline.

HenrikBengtsson commented 2 years ago

FWIW, I think any options pass to qsub via the command line will override the corresponding declarations in the PBS script, i.e. you can keep the defaults in the PBS script.