runFEAT

#!/bin/sh
#
#   Copyright (C) Eugene Duff 2004 University of Oxford
#
#   SHCOPYRIGHT

Usage() {
	function=`basename $0`
	echo function to quickly run multiple feat analyses on cluster
	echo $function [option] feat_files
	echo -p x pause x minutes 
	exit
}

[ "$1" = "" ] && Usage

firstchar=`echo $1 | head -c 1`


while [[ $firstchar == '-' ]]
do
        if [[ $1 == -p ]]
        then   echo sleeping
	       	sleep $2m
        shift 2
        elif [[ $1 == -c ]]
        then    chdirflag=1
        shift 1
        fi

        firstchar=`echo $1 | head -c 1`
done

currdir=`pwd`

for a in $@;do 
    if [[ $chdirflag == 1 ]]
    then 
        cd `dirname $a`
        feat `basename $a`;
        cd $currdir
    else
        feat $a;
    fi
done;