- parallel usage: starts one process for each lane

- Number of tile is now a mandatory parameter

SVN: 13108

deep_sequencing_unit/source/bash/cif2txt.sh

@@ -21,13 +21,13 @@
 
 INTENSITY_FOLDER=$1
 CYCLES=$2
+NUMBER_OF_TILES=$3
 NUMBER_OF_LANES=8
-NUMBER_OF_TILES=100
 #INT_NSE_DIR=$1/int_nse
 PRG=`basename $0`
-USAGE="Usage: ${PRG} <Path_to_Intensity_Folder> <Number_of_Cycles> \n\nEXAMPLE: ${PRG} /array0/Runs/090720_42HUDAAXX/Data/Intensities/ 38" 
+USAGE="Usage: ${PRG} <Path_to_Intensity_Folder> <Number_of_Cycles> \n\nEXAMPLE: ${PRG} /array0/Runs/090720_42HUDAAXX/Data/Intensities/ 38 120" 
 
-if [ -z "${INTENSITY_FOLDER}" -o -z "${CYCLES}" ]
+if [ -z "${INTENSITY_FOLDER}" -o -z "${CYCLES}" -o -z "${NUMBER_OF_TILES}" ]
 then
    echo -e "${USAGE}"
    exit 1
@@ -41,8 +41,8 @@ for (( l = 1; l <= $NUMBER_OF_LANES; l++ )); do
  for (( t = 1; t <= $NUMBER_OF_TILES; t++ )); do
   echo Lane $l Tile $t;
   # Convert Signal cif to int
-  /dsf/GAPipeline/bin/cifToTxt -l $l -t $t -n $CYCLES -i $INTENSITY_FOLDER -o $INTENSITY_FOLDER -c none 
+  /dsf/GAPipeline/bin/cifToTxt -l $l -t $t -n $CYCLES -i $INTENSITY_FOLDER -o $INTENSITY_FOLDER -c none &
   # Convert Noise cnf to nse (additional -N)
-  /dsf/GAPipeline/bin/cifToTxt -N -l $l -t $t -n $CYCLES -i $INTENSITY_FOLDER -o $INTENSITY_FOLDER -c none 
+  /dsf/GAPipeline/bin/cifToTxt -N -l $l -t $t -n $CYCLES -i $INTENSITY_FOLDER -o $INTENSITY_FOLDER -c none &
  done
 done