# HG changeset patch
# User george-weingart
# Date 1461558777 14400
# Node ID 4f3ae60396f9a484f818818291dd5e00ee4a0393
# Parent  16fd605f31deaaae54062e3a260bde36a94e8874
Uploaded

diff -r 16fd605f31de -r 4f3ae60396f9 metaphlan2_hutlab/metaphlan2.xml
--- a/metaphlan2_hutlab/metaphlan2.xml	Mon Apr 25 00:09:30 2016 -0400
+++ b/metaphlan2_hutlab/metaphlan2.xml	Mon Apr 25 00:32:57 2016 -0400
@@ -5,8 +5,8 @@
 
 	<description>metagenomic profiler V2</description>
 	<command interpreter="python">metaphlan2.py $input 
-		--mpa_pkl  \${METAPHLAN2_PATH}/db_v20/mpa_v20_m200.pkl    
-		--bowtie2db \${METAPHLAN2_PATH}/db_v20/mpa_v20_m200 
+		--mpa_pkl   $REPOSITORY_INSTALL_DIR/db_v20/mpa_v20_m200.pkl    
+		--bowtie2db $REPOSITORY_INSTALL_DIR/db_v20/mpa_v20_m200 
 		--input_type  fastq
 		--no_map 
 		--bt2_ps $PresetsForBowtie2  
diff -r 16fd605f31de -r 4f3ae60396f9 metaphlan2_hutlab/tool_dependencies.xml
--- a/metaphlan2_hutlab/tool_dependencies.xml	Mon Apr 25 00:09:30 2016 -0400
+++ b/metaphlan2_hutlab/tool_dependencies.xml	Mon Apr 25 00:32:57 2016 -0400
@@ -1,15 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-        <install version="1.0">
-            <actions>
-                <action type="shell_command">hg clone https://bitbucket.org/biobakery/metaphlan2  metaphlan2_hutlab</action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="METAPHLAN2_PATH" action="set_to">$INSTALL_DIR</environment_variable>
-                </action>
-
-            </actions>
-        </install>
+    <set_environment version="1.0">
+        <environment_variable name="METAPHLAN2_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>   
+    </set_environment>
 </tool_dependency>