rendered compatible with the updated MPListener

diff --git a/htswdataprod/scripts/MPCollectData b/htswdataprod/scripts/MPCollectData
index 479ff3be74cc7fd21de37f49db432f83e2c2e3da..5811ad9a5126f983d09ad0331fa3f0f9eeded4b7 100755 (executable)
--- a/htswdataprod/scripts/MPCollectData
+++ b/htswdataprod/scripts/MPCollectData
@@ -1,35 +1,45 @@
 #!/bin/sh                                                                                                                                                                                                    
-# Post Solexa Pipeline Data analysis
+# CollectData after Solexa Pipeline + Quality Control Runs
 
-#dir="$HOME/EXPTRACK";
-#exptrackmainsc="$HOME/EXPTRACK/exp_track_main.py"
 exptrackmainsc="exp_track_main.py"
 fcid=$1
-runfolder=$2
+fullpath=$2
+runfolder=`echo $fullpath | sed -e 's/^.*\///'`
 
 # -------- FINISHED LISTENING TO SOLEXA DATA PROCESSING. START OUR DATA ANALYSIS PIPELINE ------------------------ #                                                                                                                   
-echo "Starting CollectReads ..."
+echo "Starting CollectData & QC ..."
 python $exptrackmainsc updsts $fcid $runfolder 4 Collecting_Reads
-CollectReads
+
+## These 2 are for the test
+python $exptrackmainsc updsts $fcid $runfolder 5 Running_QC
+python $exptrackmainsc updsts $fcid $runfolder 6 Copying_Data
+python $exptrackmainsc updsts $fcid $runfolder 7 DONE
+
+echo " TEMP: Exiting ColectData: We need to modify CollectReads to accept fullpath as paramter etc. "
+exit
+
+#CollectReads needs to be run from the RunFolder directory
+./CollectReads
 
 if [ -f ExpTrackLog/OK_CollectReads ]
  then
   echo "CollectReads successfuly finished.\n"
-  python $exptrackmainsc updsts $fcid $runfolder 5 Quality_Control
+  python $exptrackmainsc updsts $fcid $runfolder 5 Running_QC
   mkdir QC
   #make -f ~/EXPTRACK/QC/Flowcell_QC_Makefile -j 8
   make -f QC/Flowcell_QC_Makefile -j 8
   
-  python $exptrackmainsc updsts $fcid $runfolder 5 Copying_Data
+  python $exptrackmainsc updsts $fcid $runfolder 6 Copying_Dat
   scp CollectReads/* ENCODE@171.65.76.194:~Data/Flowcells/DATA_FROM_HA
 
-  python $exptrackmainsc updsts $fcid $runfolder 5 DONE
+  python $exptrackmainsc updsts $fcid $runfolder 7 DONE
   echo "===== END ====="
-else
+ else
   echo "FAILED: collect reads."
   python $exptrackmainsc updsts $fcid $runfolder 4 CollectRead_Failed
 fi
 
+echo " Exiting ColectData "
 exit
 
 ## ----------------------------------------------------