# HG changeset patch
# User fubar
# Date 1370398707 14400
# Node ID 40b80f54e1a7dbe13884be965e4c10d580903973
# Parent  95064b2e024faba20ab0b741556a1a7a5c774155
Uploaded

diff -r 95064b2e024f -r 40b80f54e1a7 FastQC/rgFastQC.xml
--- a/FastQC/rgFastQC.xml	Tue Jun 04 21:36:30 2013 -0400
+++ b/FastQC/rgFastQC.xml	Tue Jun 04 22:18:27 2013 -0400
@@ -1,13 +1,14 @@
 <tool name="FastQC: Comprehensive QC" id="fastqc" version="0.53">
   <description>reporting for short read sequence</description>
   <command interpreter="python">
-    rgFastQC.py -i "$input_file" -d "$html_file.files_path" -o "$html_file" -n "$out_prefix" -f "$input_file.ext" -j "$input_file.name" -e "\$FASTQC_BINARY_PATH"
+    rgFastQC.py -i "$input_file" -d "$html_file.files_path" -o "$html_file" -n "$out_prefix" -f "$input_file.ext" -j "$input_file.name" 
 #if $contaminants.dataset and str($contaminants) > ''
 -c "$contaminants"
 #end if
+-e fastqc
   </command>
   <requirements>
-    <requirement type="set_environment">FASTQC_BINARY_PATH</requirement>
+    <requirement type="set_environment">FASTQC_INSTALL_PATH</requirement>
     <requirement type="package" version="0.10.1">FastQC</requirement>
   </requirements>
   <inputs>
diff -r 95064b2e024f -r 40b80f54e1a7 FastQC/tool_dependencies.xml
--- a/FastQC/tool_dependencies.xml	Tue Jun 04 21:36:30 2013 -0400
+++ b/FastQC/tool_dependencies.xml	Tue Jun 04 22:18:27 2013 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <set_environment version="1.0">
-        <environment_variable name="FASTQC_BINARY_PATH" action="set_to">$INSTALL_DIR/FastQC/fastqc</environment_variable>   
+        <environment_variable name="FASTQC_INSTALL_PATH" action="set_to">$INSTALL_DIR/FastQC/fastqc</environment_variable>   
     </set_environment>
     <package name="FastQC" version="0.10.1">
         <install version="1.0">
@@ -12,6 +12,9 @@
                     <destination_directory>$INSTALL_DIR/FastQC</destination_directory>
                 </action>                
                 <action type="shell_command">chmod ugo+x $INSTALL_DIR/FastQC/fastqc</action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/FastQC</environment_variable>
+                </action>
             </actions>
         </install>
         <readme>You need a working unzip command line executable to install this tool and a suitable working Java run time environment