# HG changeset patch
# User george-weingart
# Date 1461559620 14400
# Node ID c7cd6467b570e492e900214a9980ce3372517636
# Parent  0e82a9af69ab2631b90c45ea239ca53444f723bc
Uploaded

diff -r 0e82a9af69ab -r c7cd6467b570 metaphlan2_hutlab/metaphlan2.xml
--- a/metaphlan2_hutlab/metaphlan2.xml	Mon Apr 25 00:35:32 2016 -0400
+++ b/metaphlan2_hutlab/metaphlan2.xml	Mon Apr 25 00:47:00 2016 -0400
@@ -3,8 +3,8 @@
 
 	<description>metagenomic profiler V2</description>
 	<command interpreter="python">metaphlan2.py $input 
-		--mpa_pkl   $REPOSITORY_INSTALL_DIR/db_v20/mpa_v20_m200.pkl    
-		--bowtie2db $REPOSITORY_INSTALL_DIR/db_v20/mpa_v20_m200 
+		--mpa_pkl   $METAPHLAN_PATH/db_v20/mpa_v20_m200.pkl    
+		--bowtie2db $METAPHLAN_PATH/db_v20/mpa_v20_m200 
 		--input_type  fastq
 		--no_map 
 		--bt2_ps $PresetsForBowtie2  
@@ -168,7 +168,9 @@
 	 
 
 	</outputs>
-      
+  <requirements>
+    <requirement type="set_environment">METAPHLAN2_PATH</requirement>
+  </requirements>  
   <help>
 **MetaPhlAn**  is a computational tool for profiling the composition of microbial communities *(Bacteria, Archaea, Eukaryotes and Viruses)* from metagenomic shotgun sequencing data with species level resolution.