initial checkin

SVN: 19087

deep_sequencing_unit/source/bash/ellac_create_srfs.sh

+#!/bin/bash
+# Processing steps needed from the Illumina Output to the SRF files
+
+export RUN_BASE=/net/bs-dsu-data/array0/dsu/runs/ellac
+export LATEST_FOLDER=`ls -1dtr $RUN_BASE/*XX* | tail -1`
+export INTENSITY_FOLDER=Data/Intensities
+export BUSTARD=/usr/local/dsu/GAPipeline/bin/bustard.py
+export CONFIG_FILE=$LATEST_FOLDER/$INTENSITY_FOLDER/config.txt
+export CIF2TXT=/usr/local/dsu/bin/cif2txt.sh
+export LANES2SRF=/usr/local/dsu/bin/lanes2srf_RTA
+export MAILX=/bin/mailx
+export MAIL_LIST="manuel.kohler@bsse.ethz.ch"
+export RM=/bin/rm
+export MAKE=/usr/bin/make
+export GERALD=/usr/local/CASAVA-1.7.0/bin/GERALD.pl
+export LF=`echo $LATEST_FOLDER | cut -d / -f8`
+export RUN_COMPLETED=$LATEST_FOLDER/Run.completed
+export ANALYSIS_STARTED=$LATEST_FOLDER/Analysis.started
+export OPENBIS_SERVER=http://openbis-dsu.bsse.ethz.ch:8080/openbis/openbis
+export PROCESSING=/net/bs-dsu-data/array0/dsu/processing
+export BCL=/usr/local/dsu/OLB/OLB-1.8.0/bin/setupBclToQseq.py
+
+export PRG=`basename $0`
+export USAGE="Usage: ${PRG} <Path_to_Run_Base> <Number_of_Lanes> \n\nEXAMPLE: ${PRG} /array0/Runs/ 8" 
+
+#if [ -z "${RUN_BASE}"  -o -z "${NUMBER_OF_LANES}" ]
+#then
+#   echo "${USAGE}"
+#   exit 1
+#fi
+
+function gerald_basic {
+	cd $LATEST_FOLDER/$INTENSITY_FOLDER
+	export PAIRED_END=`cat  $LATEST_FOLDER/$INTENSITY_FOLDER/RTAConfiguration.xml | grep IsPairedEndRun  | cut -d \> -f2 | cut -d \< -f1`
+	echo "5:ELAND_GENOME /array0/Genomes/PhiX" > $CONFIG_FILE
+	if $PAIRED_END;
+	 then echo "5:ANALYSIS eland_pair" >> $CONFIG_FILE;
+	 else echo "5:ANALYSIS eland_extended" >> $CONFIG_FILE;
+	fi
+	echo "ELAND_SET_SIZE 8" >> $CONFIG_FILE
+	echo "EMAIL_LIST manuel.kohler@bsse.ethz.ch" >> $CONFIG_FILE
+}
+
+function gerald {
+	cd $LATEST_FOLDER/$INTENSITY_FOLDER
+        /usr/local/dsu/openbis-property-client/client/lib/properties.sh $OPENBIS_SERVER $LF
+	sleep 5
+	mv /usr/local/dsu/openbis-property-client/client/lib/config.txt $CONFIG_FILE
+	mv /usr/local/dsu/openbis-property-client/client/lib/bowtie.txt $LATEST_FOLDER/$INTENSITY_FOLDER
+#	chmod -R 755 BaseCalls
+	mkdir -p $PROCESSING/$LF/BaseCalls
+	$GERALD $CONFIG_FILE --EXPT_DIR $LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls --OUT_DIR $PROCESSING/$LF/GERALD --make
+	cd $PROCESSING/$LF/GERALD
+	make -j 10 all
+	wait $!
+	chmod -R 755 .
+	rsync -av . $LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls
+	rm -rf $PROCESSING/$LF	
+	/usr/local/dsu/bin/check_read_numbers.sh
+#	rm -rf Temp
+}
+
+function bowtie {
+	/usr/local/dsu/bin/openBIS_bowtie_alignment.sh
+}
+
+
+# no longer needed with the use of the RTA
+function bustard {
+	$BUSTARD --CIF . --GERALD=$CONFIG_FILE --control-lane=5 --make
+	cd Bustard*
+	echo "Starting parallel make..."
+	make recursive -j 15 2>seq_make.err >seq_make.log
+}
+
+
+function cif2txt {
+	cd $LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls
+	$CIF2TXT $LATEST_FOLDER/$INTENSITY_FOLDER $NUMBER_OF_CYCLES $NUMBER_OF_TILES
+
+}
+
+
+function bcl2qseq {
+	export LF=`echo $LATEST_FOLDER | cut -d / -f8`
+	$BCL -i $LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls/ -p $LATEST_FOLDER/$INTENSITY_FOLDER -o /net/bs-dsu-data/array0/dsu/processing/$LF --in-place --overwrite
+	cd $PROCESSING/$LF
+	make -j15
+	chmod -R 755 .
+	rsync -av . $LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls
+	rm -rf $PROCESSING/$LF
+}
+
+
+function create_srf {
+	export SRF_DIR=Srf
+	export ILLUMINA2SRF=/usr/local/bin/illumina2srf
+	export LF=`echo $LATEST_FOLDER | cut -d / -f8`
+
+	cd $LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls
+	[ -d $SRF_DIR ] || mkdir $SRF_DIR
+	$ILLUMINA2SRF -clobber -b -o $SRF_DIR/"ETHZ_BSSE_"$LF"_1.srf" $LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls/s_1_*_qseq.txt 
+	$ILLUMINA2SRF -clobber -b -o $SRF_DIR/"ETHZ_BSSE_"$LF"_2.srf" $LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls/s_2_*_qseq.txt &
+	$ILLUMINA2SRF -clobber -b -o $SRF_DIR/"ETHZ_BSSE_"$LF"_3.srf" $LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls/s_3_*_qseq.txt &
+	$ILLUMINA2SRF -clobber -b -o $SRF_DIR/"ETHZ_BSSE_"$LF"_4.srf" $LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls/s_4_*_qseq.txt &
+	$ILLUMINA2SRF -clobber -b -o $SRF_DIR/"ETHZ_BSSE_"$LF"_5.srf" $LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls/s_5_*_qseq.txt &
+	$ILLUMINA2SRF -clobber -b -o $SRF_DIR/"ETHZ_BSSE_"$LF"_6.srf" $LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls/s_6_*_qseq.txt &
+	$ILLUMINA2SRF -clobber -b -o $SRF_DIR/"ETHZ_BSSE_"$LF"_7.srf" $LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls/s_7_*_qseq.txt &
+	$ILLUMINA2SRF -clobber -b -o $SRF_DIR/"ETHZ_BSSE_"$LF"_8.srf" $LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls/s_8_*_qseq.txt &
+  	wait $!
+	echo sleeping for 600 secs...
+	sleep 600
+	echo creating srf_info.txt...
+	for i in `ls -1 ${SRF_DIR}/*.srf`; do
+		/usr/local/bin/srf_info -l1 $i >> ${SRF_DIR}/srf_info.txt;
+	done
+	echo creating fastqs...
+	cd ${SRF_DIR}
+	/usr/local/dsu/bin/create_fastq.sh
+	echo removing int and nse files ...
+	rm $LATEST_FOLDER/$INTENSITY_FOLDER/*int* $LATEST_FOLDER/$INTENSITY_FOLDER/*nse*
+}
+
+if [ -f $ANALYSIS_STARTED ];then
+	echo "Analysis already started/done"
+	exit 255
+fi
+
+if [ -f $RUN_COMPLETED ];then
+	touch $ANALYSIS_STARTED
+	echo "Run completed! Starting Analysis..."
+	export NUMBER_OF_LANES=`cat $LATEST_FOLDER/$INTENSITY_FOLDER/RTAConfiguration.xml | grep NumberOfLanes | cut -d \> -f2 | cut -d \< -f1`
+	export NUMBER_OF_TILES=`cat $LATEST_FOLDER/$INTENSITY_FOLDER/RTAConfiguration.xml | grep TilesPerLane | cut -d \> -f2 | cut -d \< -f1`
+	export PAIRED_END=`cat  $LATEST_FOLDER/$INTENSITY_FOLDER/RTAConfiguration.xml | grep IsPairedEndRun  | cut -d \> -f2 | cut -d \< -f1`
+	export NUMBER_OF_CYCLES=`cat  $LATEST_FOLDER/$INTENSITY_FOLDER/RTAConfiguration.xml | grep MaxCycles | cut -d \> -f2 | cut -d \< -f1`
+#	sleep 2700
+
+	#cif2txt
+	#bcl2qseq
+	#create_srf
+	gerald
+	#bowtie
+fi