# HG changeset patch
# User fubar
# Date 1370317997 14400
# Node ID 7ea207f29f71df4ee47ed8844eb3e98d458e737c
# Parent  ed9e8630cda3e1c42fcacd67d0ef6a097e43d729
Uploaded

diff -r ed9e8630cda3 -r 7ea207f29f71 FastQC/tool_dependencies.xml
--- a/FastQC/tool_dependencies.xml	Mon Jun 03 23:37:37 2013 -0400
+++ b/FastQC/tool_dependencies.xml	Mon Jun 03 23:53:17 2013 -0400
@@ -1,13 +1,17 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <set_environment version="1.0">
-        <environment_variable name="FASTQC_BINARY_PATH">$INSTALL_DIR/FastQC/fastqc</environment_variable>
-    </set_environment>
     <package name="FastQC" version="0.10.1">
         <install version="1.0">
             <actions>
                 <action type="download_by_url">http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.10.1.zip</action>
+                <action type="move_directory_files">
+                    <source_directory>FastQC</source_directory>
+                    <destination_directory>$INSTALL_DIR/FastQC</destination_directory>
+                </action>                
                 <action type="shell_command">chmod ugo+x $INSTALL_DIR/FastQC/fastqc</action>
+                <action type="set_environment">
+                    <environment_variable name="FASTQC_BINARY_PATH" action="set_to">$INSTALL_DIR/FastQC/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