# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1349815986 18000
# Node ID 868624c77941baab482a139d3ec23ca89ba759a0
# Parent  0ec6c5781381d1af5584da8a9f2bf21202cfde19
Add tool_dependencies.xml

diff -r 0ec6c5781381 -r 868624c77941 metaphlan.xml
--- a/metaphlan.xml	Tue Oct 09 12:13:27 2012 -0400
+++ b/metaphlan.xml	Tue Oct 09 15:53:06 2012 -0500
@@ -1,13 +1,14 @@
-<tool id="metaphlan" name="MetaPhlAn" version="1.6.0">
+<tool id="metaphlan" name="MetaPhlAn" version="1.7.0">
 <requirements>
-<requirement type="package">metaphlan</requirement>
-<requirement type="package">bowtie2</requirement>
+    <requirement type="set_environment">METAPHLAN_BASE</requirement>
+    <requirement type="package" version="1.7.0">metaphlan</requirement>
+    <requirement type="package">bowtie2</requirement>
 </requirements>
   <description>Metagenomic Phylogenetic Analysis</description>
   <command>
 	  metaphlan.py 
 	  $input  
-	  --bowtie2db ${GALAXY_DATA_INDEX_DIR}/shared/metaphlan/bowtie2db/mpa  
+	  --bowtie2db ${METAPHLAN_BASE}/bowtie2db/mpa  
 	  --no_map  
 	  -o $output  
 	  --bt2_ps $PresetsForBowtie2 
diff -r 0ec6c5781381 -r 868624c77941 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Oct 09 15:53:06 2012 -0500
@@ -0,0 +1,22 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <set_environment version="1.0">
+        <environment_variable name="METAPHLAN_BASE" action="set_to">$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 https://bitbucket.org/nsegata/metaphlan -u 43684e5f6dc5</action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+These links provide information for the metaphlan package:
+http://huttenhower.sph.harvard.edu/metaphlan
+https://groups.google.com/forum/#!forum/metaphlan-users
+        </readme>
+    </package>
+</tool_dependency>
+