rendered compatible with the new MainPipelineScript, which is now ran from runner bot

diff --git a/htswdataprod/scripts/CheckImageFolders b/htswdataprod/scripts/CheckImageFolders
index 8e063c8739ae74cf46b418d97dc002f1eecc3d15..904ffcd5dc254bff1c8fa10513358b16ce96e3f8 100755 (executable)
--- a/htswdataprod/scripts/CheckImageFolders
+++ b/htswdataprod/scripts/CheckImageFolders
@@ -1,15 +1,20 @@
 #!/bin/sh
+# -- Checks Image folders and find out cycle number ---------------------                                                                                                                                                               
+
+## ~~~ RAMI AUG 12 008 ~~~
+fullpath=$1
+## Follow /Images and add "$fullpath/" before
+## ~~~ END ~~~ 
 
-# -- Check Image folders and find out cycle number ---------------------                                                                                                                                                               
 
 # -- Get the num of cycles from L001
-if [ ! -d Images/L001 ]
+if [ ! -d $fullpath/Images/L001 ]
 then
   echo "ERROR_L001_not_found."
   exit 127 
 fi
 c=1
-while [ -d Images/L001/C$c.1 ] && [ $c -le 36 ]
+while [ -d $fullpath/Images/L001/C$c.1 ] && [ $c -le 36 ]
 do
  c=`expr $c +  1`
 done
@@ -23,10 +28,10 @@ NumCycles=0
 for ((  l = 2 ;  l <= 8;  l++  ))
 do
   ## echo "lane folder $l"
-  if [ -d Images/L00$l ]
+  if [ -d $fullpath/Images/L00$l ]
   then
     c=1
-    while  [ -d Images/L00$l/C$c.1 ] && [ $c -le 36 ]
+    while  [ -d $fullpath/Images/L00$l/C$c.1 ] && [ $c -le 36 ]
     do 
       NumCycles=$c
       c=`expr $c +  1`