- number of lane is now a mandatory parameter

- added parallel usage (backgrounding of one process per lane)

SVN: 13110

deep_sequencing_unit/source/bash/lanes2srf_RTA

 #!/bin/bash
 
 export BUSTARD=$1
+export NUMBER_OF_LANES=$2
 export SRF_DIR=Srf_RTA
 export ILLUMINA2SRF=/usr/local/dsu/bin/illumina2srf
 
+export PRG=`basename $0`
+export USAGE="Usage: ${PRG} <Path_to_Bustard_Folder> <Number_of_Lanes> \n\nEXAMPLE: ${PRG} /array0/Runs/090720_42HUDAAXX/Data/Intensities/Bustard/ 8" 
+
+if [ -z "${BUSTARD}"  -o -z "${NUMBER_OF_LANES}" ]
+then
+   echo "${USAGE}"
+   exit 1
+fi
+
 [ -d $SRF_DIR ] || mkdir $SRF_DIR
-for a in 1 2 3 4 5 6 7 8; do
+for  (( a=1; a<=$NUMBER_OF_LANES; a++ )); do
   echo Converting Lane $a to SRF
-  $ILLUMINA2SRF -b -o $SRF_DIR/s_${a}_RTA.srf $BUSTARD/s_${a}_*_qseq.txt ;
-done
+  $ILLUMINA2SRF -b -o $SRF_DIR/s_${a}_RTA.srf $BUSTARD/s_${a}_*_qseq.txt &;
+done
\ No newline at end of file