# HG changeset patch
# User bgruening
# Date 1384606232 18000
# Node ID 9441b4e5d2d6ab6b21b029705d507b27cd259279
# Parent  b5da8186454149962a7dba3fc82bb5ee82a924be
Uploaded

diff -r b5da81864541 -r 9441b4e5d2d6 bamCorrelate.xml
--- a/bamCorrelate.xml	Fri Nov 15 11:02:32 2013 -0500
+++ b/bamCorrelate.xml	Sat Nov 16 07:50:32 2013 -0500
@@ -15,6 +15,15 @@
 
         bamCorrelate
 
+        #if $mode.modeOpt == "bins":
+            bins
+            --binSize '$mode.binSize'
+            --numberOfSamples '$mode.numberOfSamples'
+        #else:
+            BED-file
+            --BED $mode.region_file
+        #end if
+
         @THREADS@
 
         --bamfiles #echo " ".join($files)
@@ -31,13 +40,6 @@
             --outFileCorMatrix '$outFileCorMatrix'
         #end if
 
-        #if $mode.modeOpt == "bins":
-            --binSize '$mode.binSize'
-            --numberOfSamples '$mode.numberOfSamples'
-        #else:
-            --BED $mode.region_file
-        #end if
-
         ## options available in both modes
         #if $mode.advancedOpt.showAdvancedOpt == "yes":
 
diff -r b5da81864541 -r 9441b4e5d2d6 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Nov 15 11:02:32 2013 -0500
+++ b/tool_dependencies.xml	Sat Nov 16 07:50:32 2013 -0500
@@ -73,7 +73,7 @@
 
                 <action type="set_environment">
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable action="prepand_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                     <!-- disable the config file of deepTools -->
                     <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
                 </action>