# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1349876013 18000
# Node ID 51288d868a5ca3203e36c4511fb2552711fd87ad
# Parent  d90db1d506c42df2a24ff3de9cfd6bf12fa95a60
tool_dependencies.xml

diff -r d90db1d506c4 -r 51288d868a5c metaphlan.xml
--- a/metaphlan.xml	Tue Oct 09 20:54:18 2012 -0500
+++ b/metaphlan.xml	Wed Oct 10 08:33:33 2012 -0500
@@ -1,6 +1,5 @@
 <tool id="metaphlan" name="MetaPhlAn" version="1.7.0">
 <requirements>
-    <requirement type="set_environment">METAPHLAN_BASE</requirement>
     <requirement type="package" version="1.7.0">metaphlan</requirement>
     <requirement type="package">bowtie2</requirement>
 </requirements>
@@ -8,7 +7,7 @@
   <command>
 	  metaphlan.py 
 	  $input  
-	  --bowtie2db ${METAPHLAN_BASE}/bowtie2db/mpa  
+	  --bowtie2db \${METAPHLAN_PATH}/bowtie2db/mpa  
 	  --no_map  
 	  -o $output  
 	  --bt2_ps $PresetsForBowtie2 
diff -r d90db1d506c4 -r 51288d868a5c tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Oct 09 20:54:18 2012 -0500
+++ b/tool_dependencies.xml	Wed Oct 10 08:33:33 2012 -0500
@@ -1,15 +1,20 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <set_environment version="1.0">
-        <environment_variable name="METAPHLAN_BASE" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
-    </set_environment>
     <package name="metaphlan" version="1.7.0">
         <install version="1.0">
             <actions>
                 <action type="shell_command">hg clone http://bitbucket.org/nsegata/metaphlan</action>
+                <action type="move_directory_files">
+                    <source_directory>.</source_directory>
+                    <destination_directory>$INSTALL_DIR</destination_directory>
+                </action>
                 <action type="set_environment">
                     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                 </action>
+                <action type="set_environment">
+                    <environment_variable name="METAPHLAN_PATH" action="set_to">$INSTALL_DIR</environment_variable>
+                </action>
+
             </actions>
         </install>
         <readme>