Mercurial > repos > jpetteng > ectyper

changeset 10:5b52b3842765 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jpetteng
date Sat, 06 Jan 2018 13:32:23 -0500
parents 148199949636
children 8cb863e320e7
files ecoli_serotyping/ectyper.xml
diffstat 1 files changed, 2 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/ecoli_serotyping/ectyper.xml	Fri Jan 05 16:25:18 2018 -0500
+++ b/ecoli_serotyping/ectyper.xml	Sat Jan 06 13:32:23 2018 -0500
@@ -1,6 +1,7 @@
 <tool id="ectyper" name="ectyper" version="2.0">
     <requirements>
       <requirement type="package" version="3.6.3">python</requirement>
+      <requirement type="package">ectyper</requirement>
       <requirement type="package">biopython</requirement>
       <requirement type="package">blast</requirement>
       <requirement type="package">samtools</requirement>
@@ -19,9 +20,7 @@
         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
+		ectyper.py
       #if $jobtype.select == "asm"
         -m 4
         -i sample.fasta