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bwaQsCoyote.sh
executable file
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bwaQsCoyote.sh
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source ~/.bashrc
source ./initvars.sh
source $configDir/bwa.config.sh
source $tophatshvar
saveIFS=$IFS
IFS=`echo -en ","`
declare -a samples=($Samples)
IFS=$saveIFS
for sample in ${samples[@]}; do
for Qt in ${QThresholds[@]}; do
echo reaching $sample
##PBS -v SAMINPREFIX,SAMSEOUTPREFIX,QTHRESHOLD,SAMPLE,SCRIPTDIR
#qsubcommand="qsub -v SAMINPREFIX=\"$samseDir/\",SAMSEOUTPREFIX=\"$samseDirOutCoyote/\",QTHRESHOLD=$Qt,SAMPLE=\"$sample\",SCRIPTDIR=\"$scriptDir\" -q $jobQueue -m a -M $queueJobEmail $scriptDir/bwaQsCoyoteJob.sh" ###-l nodes=$nodehostname -l nodes=${okNodes[dice]}
qsubcommand="echo $scriptDir/bwaQsCoyoteJob.sh $samseDir $samseDirOutCoyote $Qt $sample $scriptDir | $bsub_command" ###-l nodes=$nodehostname -l nodes=${okNodes[dice]}
echo $qsubcommand
eval $qsubcommand
done
done