msmc_script (example)
#!/bin/bash
##
JOBNAME=$2
cat <<END > $2.status
#! /bin/csh
## set paths
mkdir -p /state/partition1/$USER/\$PBS_JOBID
## copy file to scratch dir.
cd /state/partition1/$USER/\$PBS_JOBID
cp \$PBS_O_WORKDIR/* /state/partition1/$USER/\$PBS_JOBID
## run MSMC
./$1 $2
## copy MSMC files to working dir.
cp *.m* \$PBS_O_WORKDIR
## remove scratch files
rm /state/partition1/$USER/\$PBS_JOBID/*
END
## now submit the job
qsub -l ncpus=$3 -N $JOBNAME $2.status
## wait 1 sec. before exiting script
sleep 1
----