# HG changeset patch
# User jjohnson
# Date 1502207950 14400
# Node ID 044f0a2e2a36b06e9fbb40311c68c841fa601a52
# Parent  111d2508ab15df9fa64c95238c1117df83e7e3f6
Uploaded

diff -r 111d2508ab15 -r 044f0a2e2a36 optitype.xml
--- a/optitype.xml	Mon Aug 07 15:46:02 2017 -0400
+++ b/optitype.xml	Tue Aug 08 11:59:10 2017 -0400
@@ -3,10 +3,7 @@
     <requirements>
         <requirement type="package" version="1.2.1">optitype</requirement>
     </requirements>
- <stdio>
-         <exit_code range="1:"    level="fatal" description="Error Running optitype" />
- </stdio>
-    <command>
+    <command detect_errors="aggressive">
 <![CDATA[
 #set $fastqs = []
 #if str( $fastq_input.fastq_input_selector ) == "paired":
@@ -21,9 +18,8 @@
     ln -s "${fastq_input.fastq_input1}" reads.fastq
     #set $fastqs = ['reads.fastq']
 #end if
-&& cp \$OPTITYPE_DIR/config.ini .
-&& sed "s/path_to_razers3/`which razers3`/" '$optitype_config' | sed "s/threads=16/threads=\$GALAXY_SLOTS/" > config.ini
-&& ln -s \$OPTITYPE_DIR/data data
+&& RAZERS3=`which razers3`
+&& sed "s#path_to_razers3#\$RAZERS3#" '$optitype_config' | sed "s/threads=16/threads=\$GALAXY_SLOTS/" > config.ini
 #set $input_fq = ' '.join($fastqs)
 && OptiTypePipeline.py 
 $read_type --input    ${' '.join($fastqs)}