# HG changeset patch
# User george-weingart
# Date 1461560645 14400
# Node ID e2de1c7613411a8a1c5eb4efcf656b33ed90b8c0
# Parent  ef38bf0b3208ff31db283cdd92d9704fceb3a34a
Uploaded

diff -r ef38bf0b3208 -r e2de1c761341 metaphlan2_hutlab/metaphlan2.xml
--- a/metaphlan2_hutlab/metaphlan2.xml	Mon Apr 25 00:58:36 2016 -0400
+++ b/metaphlan2_hutlab/metaphlan2.xml	Mon Apr 25 01:04:05 2016 -0400
@@ -3,8 +3,8 @@
 
 	<description>metagenomic profiler V2</description>
 	<command interpreter="python">metaphlan2.py $input 
-		--mpa_pkl   $METAPHLAN2_PATH/db_v20/mpa_v20_m200.pkl    
-		--bowtie2db $METAPHLAN2_PATH/db_v20/mpa_v20_m200 
+		--mpa_pkl   \{$METAPHLAN2_PATH}/db_v20/mpa_v20_m200.pkl    
+		--bowtie2db \{$METAPHLAN2_PATH}/db_v20/mpa_v20_m200 
 		--input_type  fastq
 		--no_map 
 		--bt2_ps $PresetsForBowtie2