Mercurial > repos > jjohnson > metaphlan

diff metaphlan.xml @ 3:51288d868a5c draft

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tool_dependencies.xml
author Jim Johnson <jj@umn.edu>
date Wed, 10 Oct 2012 08:33:33 -0500
parents 868624c77941
children 3468e70d3ed0
line wrap: on
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--- 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