changed SRF naming schema

SVN: 14355

deep_sequencing_unit/source/bash/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/processing
-export LATEST_FOLDER=`ls -1tr $RUN_BASE | tail -1`
+export LATEST_FOLDER=`ls -1dtr $RUN_BASE/*XX* | tail -1`
 export INTENSITY_FOLDER=Data/Intensities
 export BUSTARD=/usr/local/dsu/GAPipeline/bin/bustard.py
-export CONFIG_FILE=$RUN_BASE/$LATEST_FOLDER/$INTENSITY_FOLDER/config.txt
+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 NUMBER_OF_LANES=`cat $RUN_BASE/$LATEST_FOLDER/$INTENSITY_FOLDER/RTAConfiguration.xml | grep NumberOfLanes | cut -d \> -f2 | cut -d \< -f1`
-export NUMBER_OF_TILES=`cat $RUN_BASE/$LATEST_FOLDER/$INTENSITY_FOLDER/RTAConfiguration.xml | grep TilesPerLane | cut -d \> -f2 | cut -d \< -f1`
-export NUMBER_OF_CYCLES=`ls -1tr $RUN_BASE/$LATEST_FOLDER/$INTENSITY_FOLDER/L00$NUMBER_OF_LANES/ | tail -1 | cut -d . -f1 | cut -d C -f2`
+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 RTAConfiguration.xml | grep IsPairedEndRun  | cut -d \> -f2 | cut -d \< -f1`
+export NUMBER_OF_CYCLES=`ls -1tr $LATEST_FOLDER/$INTENSITY_FOLDER/L00$NUMBER_OF_LANES/ | tail -1 | cut -d . -f1 | cut -d C -f2`
 export MAILX=/bin/mailx
 export MAIL_LIST="manuel.kohler@bsse.ethz.ch"
 export RM=/bin/rm
 export MAKE=/usr/bin/make
 
 export PRG=`basename $0`
-export USAGE="Usage: ${PRG} <Path_to_Run_Base> <Number_of_Lanes> \n\nEXAMPLE: ${PRG} /array0/Runs/ 8"
+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
@@ -26,10 +26,13 @@ then
    exit 1
 fi
 
-cd $RUN_BASE/$LATEST_FOLDER/$INTENSITY_FOLDER
+cd $LATEST_FOLDER/$INTENSITY_FOLDER
 
 echo "5:ELAND_GENOME /array0/Genomes/PhiX" > $CONFIG_FILE
-echo "5:ANALYSIS eland_extended" >> $CONFIG_FILE
+if $PAIRED_END;
+ then echo "5:ANALYSIS eland_pair" >> $CONFIG_FILE;
+ else echo "5:ANALYSIS eland_extended" >> $CONFIG_FILE;
+fi
 echo "ELAND_MULTIPLE_INSTANCES 8" >> $CONFIG_FILE
 echo "EMAIL_LIST manuel.kohler@bsse.ethz.ch" >> $CONFIG_FILE
 
@@ -43,14 +46,33 @@ make -j 8 all
 #echo "Starting parallel make..."
 
 #make recursive -j 15 2>seq_make.err >seq_make.log
-cd $RUN_BASE/$LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls
+cd $LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls
 
-$CIF2TXT $RUN_BASE/$LATEST_FOLDER/$INTENSITY_FOLDER $NUMBER_OF_CYCLES $NUMBER_OF_TILES
+$CIF2TXT $LATEST_FOLDER/$INTENSITY_FOLDER $NUMBER_OF_CYCLES $NUMBER_OF_TILES
 
-$LANES2SRF $RUN_BASE/$LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls/ $NUMBER_OF_LANES
+#$LANES2SRF $LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls $NUMBER_OF_LANES
 #$LANES2SRF /net/bs-dsu-data/array0/dsu/processing/091208_433DAAXX/Data/Intensities/BaseCalls/ 8
 
+export SRF_DIR=Srf
+#export ILLUMINA2SRF=/usr/local/dsu/bin/illumina2srf
+export ILLUMINA2SRF=/usr/local/bin/illumina2srf
+
+[ -d $SRF_DIR ] || mkdir $SRF_DIR
+#for  (( a=1; a<=$NUMBER_OF_LANES; a++ )); do
+#  echo "Starting SRF $a"
+  $ILLUMINA2SRF -clobber -b -o $SRF_DIR/"ETHZ_BSSE_"$LATEST_FOLDER"_1.srf" $LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls/s_1_*_qseq.txt &
+  $ILLUMINA2SRF -clobber -b -o $SRF_DIR/"ETHZ_BSSE_"$LATEST_FOLDER"_2.srf" $LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls/s_2_*_qseq.txt &
+  $ILLUMINA2SRF -clobber -b -o $SRF_DIR/"ETHZ_BSSE_"$LATEST_FOLDER"_3.srf" $LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls/s_3_*_qseq.txt &
+  $ILLUMINA2SRF -clobber -b -o $SRF_DIR/"ETHZ_BSSE_"$LATEST_FOLDER"_4.srf" $LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls/s_4_*_qseq.txt &
+  $ILLUMINA2SRF -clobber -b -o $SRF_DIR/"ETHZ_BSSE_"$LATEST_FOLDER"_5.srf" $LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls/s_5_*_qseq.txt &
+  $ILLUMINA2SRF -clobber -b -o $SRF_DIR/"ETHZ_BSSE_"$LATEST_FOLDER"_6.srf" $LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls/s_6_*_qseq.txt &
+  $ILLUMINA2SRF -clobber -b -o $SRF_DIR/"ETHZ_BSSE_"$LATEST_FOLDER"_7.srf" $LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls/s_7_*_qseq.txt &
+  $ILLUMINA2SRF -clobber -b -o $SRF_DIR/"ETHZ_BSSE_"$LATEST_FOLDER"_8.srf" $LATEST_FOLDER/$INTENSITY_FOLDER/BaseCalls/s_8_*_qseq.txt &
+  wait $!
+#done
+
+
 # clean up
-#chmod -R 755 $RUN_BASE/$LATEST_FOLDER
+#chmod -R 755 $LATEST_FOLDER
 
 echo -e "SRF creation finished for $LATEST_FOLDER :-)" | $MAILX -s "SRF creation finished for $LATEST_FOLDER :-)" $MAIL_LIST
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