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

----