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sbatch submission failures do not continue #1

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18 changes: 15 additions & 3 deletions profiles/slurm/submit
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Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,18 @@ fi
export DEP_STRING
export SBATCH_ARGS

# need to return just the job ID part to enable snakemake to build dependencies correctly
# $@ should still contain the job execution script generated by snakemake
sbatch ${DEP_STRING} ${SBATCH_ARGS} $@ | cut -f4 -d' '
# Submit the job, retrying if sbatch fails to submit the job.
# It is important to not continue after a failure otherwise the JOBID is reported as an empty string.
JOBID=''
while true
do
# need to return just the job ID part to enable snakemake to build dependencies correctly
# $@ should still contain the job execution script generated by snakemake
JOBID=$(sbatch ${DEP_STRING} ${SBATCH_ARGS} $@ | cut -f4 -d' ')
if [ "$JOBID" != '' ]; then
break
fi
echo "Failed to submit job to slurm, waiting 10 seconds" 1>&2
sleep 10
done
echo -n $JOBID