first commit

bwaMap.sh

@@ -0,0 +1,137 @@
+source ~/.bashrc
+source fileUtils.sh
+source rollDie.sh #for randomizing nodes to run jobs
+source ./initvars.sh
+
+source $configDir/bwa.config.sh
+source $tophatshvar
+
+#bash testNodes.sh testNodes.config.sh BWATESTNODES
+#source okNodes.BWATESTNODES.txt
+
+
+saveIFS=$IFS
+IFS=`echo -en ","`
+declare -a samples=($Samples)
+declare -a okNodes=($okNodes)
+IFS=$saveIFS
+###nodenum=1
+numOKNodes=${#okNodes[*]}
+numOKNodes=`expr $numOKNodes - 1`
+echo numOKNodes=$numOKNodes
+
+for sample in ${samples[*]}; do
+	echo "initiate tophat for sample $sample"
+	vname=${sample}_1
+	lfilelist=${!vname}	
+	vname=${sample}_2
+	rfilelist=${!vname}
+
+	IFS=`echo -en ","`
+	declare -a lfilelist=($lfilelist)	
+	declare -a rfilelist=($rfilelist)
+
+	sizeFile=${#lfilelist[@]}
+
+
+	if [ ! -d $saiDir ]; then
+		mkdir $saiDir
+	fi
+
+
+	if [ ! -d $sampeDir ]; then
+		mkdir $sampeDir
+	fi
+
+	if [ ! -d $samseDir ]; then
+		mkdir $samseDir
+	fi
+
+
+	sampleSampeOutDir=$sampeDir/$sample
+	sampleSamseOutDir=$samseDir/$sample
+
+
+
+	if [ ! -d $sampleSampeOutDir ];then
+		mkdir $sampleSampeOutDir
+	fi
+
+	if [ ! -d $sampleSamseOutDir ]; then
+		mkdir $sampleSamseOutDir
+	fi
+
+	for((i=0;i<$sizeFile;i++)); do
+
+		lfile=${lfilelist[i]}
+		rfile=${rfilelist[i]}
+		echo processing pair $lfile $rfile
+		dice=`roll_die $numOKNodes`
+		dice=`expr $dice - 1`
+		echo dice $dice ${okNodes[dice]}
+
+		header="#!/bin/bash"		
+
+		commandAlnL="bwa aln -n $ALN_N -o $ALN_o -e $ALN_e -d $ALN_d -i $ALN_i $ALN_l_FLAG -k $ALN_k -t $ALN_t -M $ALN_M -O $ALN_O -E $ALN_E $ALN_R_FLAG $ALN_c_FLAG $ALN_N_FLAG -q $ALN_q $genome $fastqDir/${lfile/.txt/.fastq} > $saiDir/${lfile/.txt/.sai} 2> $saiDir/${lfile/.txt/.err}; echo done >> $saiDir/${lfile/.txt/.err};"
+		commandAlnR="bwa aln -n $ALN_N -o $ALN_o -e $ALN_e -d $ALN_d -i $ALN_i $ALN_l_FLAG -k $ALN_k -t $ALN_t -M $ALN_M -O $ALN_O -E $ALN_E $ALN_R_FLAG $ALN_c_FLAG $ALN_N_FLAG -q $ALN_q $genome $fastqDir/${rfile/.txt/.fastq} > $saiDir/${rfile/.txt/.sai} 2> $saiDir/${rfile/.txt/.err}; echo done >> $saiDir/${rfile/.txt/.err};"		
+
+		commandSamseL="bwa samse -n $SAMSE_n $genome $saiDir/${lfile/.txt/.sai} $fastqDir/${lfile/.txt/.fastq} > $sampleSamseOutDir/${lfile/.txt/.sam} 2> $sampleSamseOutDir/${lfile/.txt/.stderr}; echo done >> $sampleSamseOutDir/${lfile/.txt/.stderr};"	
+		commandSamseR="bwa samse -n $SAMSE_n $genome $saiDir/${rfile/.txt/.sai} $fastqDir/${rfile/.txt/.fastq} > $sampleSamseOutDir/${rfile/.txt/.sam} 2> $sampleSamseOutDir/${rfile/.txt/.stderr}; echo done >> $sampleSamseOutDir/${rfile/.txt/.stderr};"	
+
+		commandSampe="bwa sampe -a $SAMPE_a -o $SAMPE_o $genome $saiDir/${lfile/.txt/.sai} $saiDir/${rfile/.txt/.sai} $fastqDir/${lfile/.txt/.fastq} $fastqDir/${rfile/.txt/.fastq} > $sampleSampeOutDir/${lfile/_1.txt/.sam} 2> $sampleSampeOutDir/${lfile/_1.txt/.stderr}; echo done >> $sampleSampeOutDir/${lfile/_1.txt/.stderr};"
+
+		if [ ! -d $configDir/queuejobs ]; then
+			mkdir $configDir/queuejobs
+		fi
+
+		tmpshName=$configDir/queuejobs/bwa_sub_${lfile/.txt/}.${rfile/.txt/}.sh		
+
+
+		echo $header > $tmpshName
+		echo "#$tmpshName" >> $tmpshName
+		echo "source ~/.bashrc" >> $tmpshName		
+		echo $commandAlnL >> $tmpshName
+
+		echo $commandAlnR >> $tmpshName
+		echo $commandSamseL >> $tmpshName
+		echo $commandSamseR >> $tmpshName
+		echo $commandSampe >> $tmpshName
+
+		cat $tmpshName
+
+		qsubcommand="qsub -e $queueJobStdWritePath/$sample.bwa.err -m a -M $queueJobEmail -o queueJobStdWritePath/$sample.bwa.out $tmpshName"
+		#qsubcommand="qsub -l nodes=${okNodes[dice]} -e $queueJobStdWritePath/$sample.bwa.err -m a -M $queueJobEmail -o queueJobStdWritePath/$sample.bwa.out $tmpshName"
+
+
+		echo $qsubcommand
+		eval $qsubcommand
+	done
+
+
+	IFS=$saveIFS
+
+	#echo left file list $lfilelist
+	#echo right file list $rfilelist
+	###nodehostname="episode-0$nodenum"
+
+	#qsubcommand="qsub -v SAMPLENAME=$sample,LFILELIST=\"$lfilelist\",RFILELIST=\"$rfilelist\",SCRIPTDIR=$scriptDir -q $jobQueue  -e $queueJobStdWritePath/$sample.tophatqueue.err -m a -M $queueJobEmail -o queueJobStdWritePath/$sample.tophatqueue.out $scriptDir/tophatMapJob.sh" ###-l nodes=$nodehostname	
+	#echo $qsubcommand
+	#eval $qsubcommand
+
+	###nodenum=`expr $nodenum + 1`
+
+	#declare -a filelist=(${!vname})
+	#for fil in ${filelist[*]}; do
+	#	echo "file $fil"
+	#done
+done
+
+
+
+
+exit;
+
+command="echo 'source ~/.bashrc;  bwa index $indexFlag $genome > $logprefix/$genomeName.bwa_index.stdout 2> $logprefix/$genomeName.bwa_index.stderr' | qsub -l nodes=$nodehostname -q $jobQueue -m a -M $queueJobEmail -"
+
+echo $command
+eval $command

bwaMapPE.sh

@@ -0,0 +1,122 @@
+source ~/.bashrc
+source fileUtils.sh
+source ./initvars.sh
+
+source $configDir/bwa.config.sh
+source $tophatshvar
+
+
+
+saveIFS=$IFS
+IFS=`echo -en ","`
+declare -a samples=($Samples)
+IFS=$saveIFS
+###nodenum=1
+
+
+
+for sample in ${samples[*]}; do
+	echo "initiate tophat for sample $sample"
+	vname=${sample}_1
+	lfilelist=${!vname}	
+	vname=${sample}_2
+	rfilelist=${!vname}
+
+	IFS=`echo -en ","`
+	declare -a lfilelist=($lfilelist)	
+	declare -a rfilelist=($rfilelist)
+
+	sizeFile=${#lfilelist[@]}
+
+
+
+	if [ ! -d $saiDir ]; then
+		mkdir $saiDir
+	fi
+
+
+	if [ ! -d $sampeDir ]; then
+		mkdir $sampeDir
+	fi
+
+	if [ ! -d $samseDir ]; then
+		mkdir $samseDir
+	fi
+
+
+	sampleSampeOutDir=$sampeDir/$sample
+	sampleSamseOutDir=$samseDir/$sample
+
+
+
+	if [ ! -d $sampleSampeOutDir ];then
+		mkdir $sampleSampeOutDir
+	fi
+
+	if [ ! -d $sampleSamseOutDir ]; then
+		mkdir $sampleSamseOutDir
+	fi
+
+	for((i=0;i<$sizeFile;i++)); do
+
+		lfile=${lfilelist[i]}
+		rfile=${rfilelist[i]}
+		echo processing $lfile $rfile
+
+
+		header="#!/bin/bash"		
+
+		commandAlnL="bwa aln -n $ALN_N -o $ALN_o -e $ALN_e -d $ALN_d -i $ALN_i $ALN_l_FLAG -k $ALN_k -t $ALN_t -M $ALN_M -O $ALN_O -E $ALN_E $ALN_R_FLAG $ALN_c_FLAG $ALN_N_FLAG -q $ALN_q $genome $fastqDir/${lfile} > $saiDir/${lfile/.fastq/.sai} 2> $saiDir/${lfile/.fastq/.err}; echo done >> $saiDir/${lfile/.fastq/.err};"
+
+		commandAlnR="bwa aln -n $ALN_N -o $ALN_o -e $ALN_e -d $ALN_d -i $ALN_i $ALN_l_FLAG -k $ALN_k -t $ALN_t -M $ALN_M -O $ALN_O -E $ALN_E $ALN_R_FLAG $ALN_c_FLAG $ALN_N_FLAG -q $ALN_q $genome $fastqDir/${rfile} > $saiDir/${rfile/.fastq/.sai} 2> $saiDir/${rfile/.fastq/.err}; echo done >> $saiDir/${rfile/.fastq/.err};"
+
+		commandSamseL="bwa samse -n $SAMSE_n $genome $saiDir/${lfile/.fastq/.sai} $fastqDir/${lfile} > $sampleSamseOutDir/${lfile/.fastq/.sam} 2> $sampleSamseOutDir/${lfile/.fastq/.stderr}; echo done >> $sampleSamseOutDir/${lfile/.fastq/.stderr};"	
+
+		commandSamseR="bwa samse -n $SAMSE_n $genome $saiDir/${rfile/.fastq/.sai} $fastqDir/${rfile} > $sampleSamseOutDir/${rfile/.fastq/.sam} 2> $sampleSamseOutDir/${rfile/.fastq/.stderr}; echo done >> $sampleSamseOutDir/${rfile/.fastq/.stderr};"	
+
+		commandSampe="bwa sampe -a $SAMPE_a -o $SAMPE_o $genome $saiDir/${lfile/.fastq/.sai} $saiDir/${rfile/.fastq/.sai} $fastqDir/${lfile} $fastqDir/${rfile} > $sampleSampeOutDir/${sample}.sam 2> $sampleSampeOutDir/${sample}.stderr; echo done >> $sampleSampeOutDir/${sample}.stderr;"
+
+		#commandSampe="bwa sampe -a $SAMPE_a -o $SAMPE_o $genome $saiDir/${lfile/.fastq/.sai} $saiDir/${rfile/.fastq/.sai} $fastqDir/${lfile} $fastqDir/${rfile} > $sampleSampeOutDir/${lfile/_1.fastq/.sam} 2> $sampleSampeOutDir/${lfile/_1.fastq/.stderr}; echo done >> $sampleSampeOutDir/${lfile/_1.fastq/.stderr};"
+
+
+		if [ ! -d $configDir/queuejobs ]; then
+			mkdir $configDir/queuejobs
+		fi
+
+		tmpshName=$configDir/queuejobs/bwa_sub_${lfile/.fastq/}.sh		
+
+
+		echo $header > $tmpshName
+		echo "#$tmpshName" >> $tmpshName
+		echo "source ~/.bashrc" >> $tmpshName		
+
+		echo $commandAlnL >> $tmpshName	
+		echo $commandAlnR >> $tmpshName
+		echo $commandSamseL >> $tmpshName
+		echo $commandSamseR >> $tmpshName
+		echo $commandSampe >> $tmpshName
+
+		cat $tmpshName
+
+		#qsubcommand="qsub -e $queueJobStdWritePath/$sample.bwa.err -m a -M $queueJobEmail -o queueJobStdWritePath/$sample.bwa.out $tmpshName"
+
+		bsubcommand="bsub bash $tmpshName"
+		echo $bsubcommand
+		eval $bsubcommand
+	done
+
+
+	IFS=$saveIFS
+
+
+done
+
+
+
+
+exit;
+
+command="echo 'source ~/.bashrc;  bwa index $indexFlag $genome > $logprefix/$genomeName.bwa_index.stdout 2> $logprefix/$genomeName.bwa_index.stderr' | qsub -l nodes=$nodehostname -q $jobQueue -m a -M $queueJobEmail -"
+
+echo $command
+eval $command

bwaMapSE.sh

@@ -0,0 +1,110 @@
+source ~/.bashrc
+source fileUtils.sh
+source ./initvars.sh
+
+source $configDir/bwa.config.sh
+source $tophatshvar
+
+
+
+saveIFS=$IFS
+IFS=`echo -en ","`
+declare -a samples=($Samples)
+IFS=$saveIFS
+###nodenum=1
+
+
+
+for sample in ${samples[*]}; do
+	echo "initiate tophat for sample $sample"
+	vname=${sample}
+	lfilelist=${!vname}	
+
+	IFS=`echo -en ","`
+	declare -a lfilelist=($lfilelist)	
+
+	sizeFile=${#lfilelist[@]}
+
+
+	if [ ! -d $saiDir ]; then
+		mkdir $saiDir
+	fi
+
+
+	if [ ! -d $sampeDir ]; then
+		mkdir $sampeDir
+	fi
+
+	if [ ! -d $samseDir ]; then
+		mkdir $samseDir
+	fi
+
+
+	sampleSampeOutDir=$sampeDir/$sample
+	sampleSamseOutDir=$samseDir/$sample
+
+
+
+	if [ ! -d $sampleSampeOutDir ];then
+		mkdir $sampleSampeOutDir
+	fi
+
+	if [ ! -d $sampleSamseOutDir ]; then
+		mkdir $sampleSamseOutDir
+	fi
+
+	for((i=0;i<$sizeFile;i++)); do
+
+		lfile=${lfilelist[i]}
+		#rfile=${rfilelist[i]}
+		echo processing $lfile
+		#dice=`roll_die $numOKNodes`
+		#dice=`expr $dice - 1`
+		#echo dice $dice ${okNodes[dice]}
+
+		header="#!/bin/bash"		
+
+		commandAlnL="bwa aln -n $ALN_N -o $ALN_o -e $ALN_e -d $ALN_d -i $ALN_i $ALN_l_FLAG -k $ALN_k -t $ALN_t -M $ALN_M -O $ALN_O -E $ALN_E $ALN_R_FLAG $ALN_c_FLAG $ALN_N_FLAG -q $ALN_q $genome $fastqDir/${lfile} > $saiDir/${lfile/.fastq/.sai} 2> $saiDir/${lfile/.fastq/.err}; echo done >> $saiDir/${lfile/.fastq/.err};"
+
+		commandSamseL="bwa samse -n $SAMSE_n $genome $saiDir/${lfile/.fastq/.sai} $fastqDir/${lfile} > $sampleSamseOutDir/${lfile/.fastq/.sam} 2> $sampleSamseOutDir/${lfile/.fastq/.stderr}; echo done >> $sampleSamseOutDir/${lfile/.fastq/.stderr};"	
+
+
+		if [ ! -d $configDir/queuejobs ]; then
+			mkdir $configDir/queuejobs
+		fi
+
+		tmpshName=$configDir/queuejobs/bwa_sub_${lfile/.fastq/}.sh		
+
+
+		echo $header > $tmpshName
+		echo "#$tmpshName" >> $tmpshName
+		echo "source ~/.bashrc" >> $tmpshName		
+		echo $commandAlnL >> $tmpshName
+		echo $commandSamseL >> $tmpshName
+
+
+
+		cat $tmpshName
+
+		#qsubcommand="qsub -e $queueJobStdWritePath/$sample.bwa.err -m a -M $queueJobEmail -o queueJobStdWritePath/$sample.bwa.out $tmpshName"
+
+		bsubcommand="bsub bash $tmpshName"
+		echo $bsubcommand
+		eval $bsubcommand
+	done
+
+
+	IFS=$saveIFS
+
+
+done
+
+
+
+
+exit;
+
+command="echo 'source ~/.bashrc;  bwa index $indexFlag $genome > $logprefix/$genomeName.bwa_index.stdout 2> $logprefix/$genomeName.bwa_index.stderr' | qsub -l nodes=$nodehostname -q $jobQueue -m a -M $queueJobEmail -"
+
+echo $command
+eval $command