diff --git a/openbis_all/source/bash/ellac_create_srfs.sh b/openbis_all/source/bash/ellac_create_srfs.sh
deleted file mode 100755
index fcb8aa397f8243f5dcca5164fbc8834b5228be92..0000000000000000000000000000000000000000
--- a/openbis_all/source/bash/ellac_create_srfs.sh
+++ /dev/null
@@ -1,143 +0,0 @@
-#!/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