rendered completely runnable from runner bot

diff --git a/htswdataprod/scripts/MainPipelineScript b/htswdataprod/scripts/MainPipelineScript
index 5cd52cae414f5faba24802499a42c821a1377fe6..6dd3eb1be2eda16c0bac78d9bc1fe43caa991b0b 100755 (executable)
--- a/htswdataprod/scripts/MainPipelineScript
+++ b/htswdataprod/scripts/MainPipelineScript
@@ -36,9 +36,9 @@ echo "fcid is $fcid"
 #runfolder=`pwd | sed -e 's/^.*\///'`
 #changed for the HTSW merged
 fullpath=$2
-#echo "fullpath is $fullpath"
+echo "fullpath is $fullpath"
 runfolder=`echo $fullpath | sed -e 's/^.*\///'` 
-#echo "runfolder is $runfolder"
+echo "runfolder is $runfolder"
 
 
 if [ $3 ] && [ $3 == 'init' ]
@@ -57,15 +57,16 @@ fi
 exptrackmainsc="exp_track_main.py"
 # -- Check Image folders and find out cycle number 
 #tocycle=`$HOME/EXPTRACK/CheckImageFolders`
-#tocycle=`CheckImageFolders`
+echo "calling CheckImageFolders"
+tocycle=`./CheckImageFolders $fullpath`
 
 ## Uncomment this if you want to force a cycle number:
-tocycle=36
+#tocycle=36
 
 if [ $tocycle -gt 0 ] && [ $tocycle -lt 37 ]
 then echo "" 
 else
-  echo "PROBLEM: Check Image folders failed to a cycle between 0 and 36. Found: $tocycle"
+  echo "PROBLEM: CheckImagefolders failed to return a cycle number between 0 and 36. Returned: '$tocycle'"
   echo "Note: to input cycle number edit the MainP..Script un-comment ##tocycle=36"
   echo "  --- tocycle  SET to 0 --- "
   echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
@@ -85,7 +86,7 @@ echo "Run Folder: $runfolder"
 echo "FlowcellId: $fcid"
 echo "------------------------------------------------------"
 echo "Config File generation"
-#rm config.txt
+rm config.txt
 python $exptrackmainsc getconfile $fcid $runfolder
 if [ -f config.txt ]
 then 
@@ -94,13 +95,13 @@ else
  echo "ERROR: config.txt not found."
  exit
 fi
-#cat config.txt
+cat config.txt
 
 echo ""
 echo "------------------------------------------------------"
 echo "LaneNames.xml file generation: "
 echo ""
-#rm LaneNames.xml
+rm LaneNames.xml
 python $exptrackmainsc getLanesNames $fcid
 if [ -f LaneNames.xml ]
 then
@@ -109,7 +110,7 @@ else
  echo "ERROR: LaneNames.xml not found."
  exit
 fi
-#cat LaneNames.xml
+cat LaneNames.xml
 echo ""
 echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 echo "Will run Cycles: 1 to $tocycle"
@@ -166,7 +167,7 @@ then
     echo " and Bustard finished.txt found."
     if [ -f $gerfinished ]
     then
-      phaseMsg='It seems like Solexa pipeline has completed (found all 3 finished.txt files). Procees to next steps (CollectReads etc..)'
+      phaseMsg='Looks like Solexa pipeline has completed (found all 3 finished.txt files).'
       #? [Yes/[Any Key]] (Any Key = Start from scratch)'
       nextDo='CollectReads'
       echo " and Gerald finished.txt found."
@@ -191,8 +192,9 @@ else
   if [ $confirm == "Yes" ]
   then
     #Launch MPListener in the background 
-    echo " ..... supposed to run MPListener in the background here ...." 
-    ##NOT READY YET MPListener $fcid $runfolder $tocycle & 
+    echo " ... starting MPListener in the background ..." 
+    #./MPListener $fcid $runfolder $tocycle &
+    ./MPListener $fcid $fullpath $tocycle &
     if [ $nextDo == "Bustard" ]
     then
       #Change dir down to Bustard run folder      
@@ -250,7 +252,7 @@ else
     python $exptrackmainsc updsts $fcid $runfolder 0 ERROR:_Need_Specific_Firecrest_Dir
     exit
   else
-    echo "ERROR: Firecrest directory NOT FOUND."
+    echo "ERROR: Firecrest directory NOT FOUND. Looked for /^C1-$tocycle.*_Firecrest.*/"
     python $exptrackmainsc updsts $fcid $runfolder 0 ERROR:_Firecrest_Dir_Not_Found
     exit
   fi