Mercurial > repos > jpetteng > ectyper

diff ecoli_serotyping/ectyper.xml @ 8:06e7c1355431 draft

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author jpetteng
date Fri, 05 Jan 2018 16:21:19 -0500
parents a202cc394af8
children 148199949636
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line diff
--- a/ecoli_serotyping/ectyper.xml	Fri Jan 05 15:58:51 2018 -0500
+++ b/ecoli_serotyping/ectyper.xml	Fri Jan 05 16:21:19 2018 -0500
@@ -19,8 +19,9 @@
         ln -s $jobtype.fastq1 sample_1.fastq;  
         ln -s $jobtype.fastq2 sample_2.fastq;  
       #end if
+	PYTHONPATH=\$PATHONPATH:$__tool_directory__/ecytper/
 
-      $__tool_directory__/ectyper/ectyper.py
+      $__tool_directory__/bin/ectyper.py
       #if $jobtype.select == "asm"
         -m 4
         -i sample.fasta