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bowtieMapJobArgListSE.sh
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bowtieMapJobArgListSE.sh
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#!/bin/bash
if [ $# -lt 3 ]; then
echo $0 sampleName lfilelist scriptDir
exit
fi
sampleName=$1
lfilelist=$2
scriptDir=$3
cd $scriptDir
source $scriptDir/initvars.sh
source $configDir/tophat.config.sh
sampleOutputDir=$bowtieOutputDir/$sampleName
stdout_file=$sampleOutputDir/tophat.stdout
stderr_file=$sampleOutputDir/tophat.stderr
if [ ! -d $sampleOutputDir ]; then
mkdir $sampleOutputDir
fi
cd $fastqDir ##use fastq dir the more standard one
#lfilelist=`echo $lfilelist | tr "|" ","`
#rfilelist=`echo $rfilelist | tr "|" ","`
echo BOWTIE_INDEXES=$BOWTIE_INDEXES
#$solexa_quality_flag
command="bowtie $other_options $BOWTIE_INDEXES/$ebwt_base $lfilelist $bowtieOutputDir/$sampleName/accepted_hits.sam >> $stdout_file 2>> $stderr_file"
echo $command > $stdout_file
echo $command > $stderr_file
date >> $stdout_file
date >> $stderr_file
eval $command
date >> $stdout_file
date >> $stderr_file