sgesnake.sh

#!/bin/sh
#
# Adopts and submit a snakemake cluster job script to SGE queue
#
#  by Hyeshik Chang
#

JOBSCRIPT_SNAKEMAKE=$1
JOBSCRIPT_SGE="`dirname $1`/sge`basename $1`"

SGE_QUEUE="shared"

THREADS="`grep '^#threads:' $JOBSCRIPT_SNAKEMAKE|cut -d' ' -f2`"
RULENAME="`grep '^#rule:' $JOBSCRIPT_SNAKEMAKE|cut -d' ' -f2`"
UNIQNO=$$

if [ "$THREADS" -ge 24 ]; then
  THREADS="24-32" # for ribose
fi

cat > $JOBSCRIPT_SGE << END
#!/bin/sh
#$ -pe $SGE_QUEUE $THREADS
#$ -cwd
#$ -N "$RULENAME-$UNIQNO"
#$ -j y
#$ -m n
#$ -o `pwd`/sge-$RULENAME-$UNIQNO.out

export PATH="\$SGE_O_PATH"
END

sed -e 's, -j, -j $NSLOTS,' $JOBSCRIPT_SNAKEMAKE >> $JOBSCRIPT_SGE
chmod 755 $JOBSCRIPT_SGE
qsub $JOBSCRIPT_SGE