condor_sub_snake

#!/bin/bash
#
# condor_sub_snake
#
# Submit Snakefile to Condor scheduler 
#
# Copyright (C) 2019 Matthew Stone <mrstone3@wisc.edu>
# Distributed under terms of the MIT license.

set -e 

snakefile=$1
shift
rerun=$@

snakename=$(basename $snakefile)
snakename="${snakename%.*}"

# TODO: submit driver Snakemake job to Condor
# TODO: fix requst_cpus typo in /usr/bin/condor_qsub
# bsub -q normal -o logs/${snakename}.out -sla miket_sc -J ${snakename}_MASTER "
snakemake \
  -s ${snakefile} \
  --cluster-config cluster.yaml \
  --cluster 'condor_qsub -o {cluster.stdout} -e {cluster.stderr} -l file={cluster.disk} -l mem={cluster.mem} -v "Log={cluster.log}" -v "JobBatchName={cluster.jobname}" {cluster.flags}' \
  --jobs 10000 \
  ${rerun}
  # ${rerun}"