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maq.roadRunner.sh
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maq.roadRunner.sh
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#!/bin/bash
source ./initvars.sh
source $configDir/maq.config.sh
if [ $# -lt 1 ]; then
echo "Usage maq.roadRunner.sh sampleName"
exit;
fi
sampleName=$1
outputpref=$mapDir/$sampleName
readpref=$bfqDir/$sampleName
#outputpref="/nfs/coldfact/awcheng/Bill/Blood/maps.rr/$sampleName"; ##
#readpref="/nfs/coldfact/awcheng/Bill/Blood/bfq/$sampleName"; ###
partdir=$scriptDir
#if [ -e $outputpref ]; then
# echo "$outputpref exists, delete it"
# rm -R $outputpref
#fi;
#echo "making dir $outputpref"
#mkdir $outputpref
cd "$readpref";
#ls
for i in *.bfq;
do
echo "queueing $i";
#echo "-o $outputpref/$i.q.stdout -e $outputpref/$i.q.stderr"
qsub -v READFILENAME=$i,SAMPLENAME=$sampleName,SCRIPTDIR=$scriptDir,LOGPATH=$outputpref/$i.q.stdout -q long "$partdir/maq.roadRunner.part.sh" #### -o "$outputpref/$i.q.stdout" -e "$outputpref/$i.q.stderr"
done;