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diff download_align.xml @ 20:083c25559b6b

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updated cutadapt dependency to 1.8 to solve env problem
author Eduardo <eduardoalves@abdn.ac.uk>
date Tue, 04 Aug 2015 12:01:09 +0100
parents d839829f8494
children 92b1945d1f64
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--- a/download_align.xml	Mon Aug 03 17:32:31 2015 +0100
+++ b/download_align.xml	Tue Aug 04 12:01:09 2015 +0100
@@ -1,14 +1,14 @@
 <tool id="download_align" name="Download and align" version="0.0.1">
   <description> Downloads fastq.gz, unzips, trims with cutadapt and alignes to reference</description>
   <requirements>
-      <requirement type="package" version="1.6">cutadapt</requirement>
+      <requirement type="package" version="1.8">cutadapt</requirement>
       <requirement type="package" version="2.2.4">bowtie2</requirement>
       <requirement type="package" version="0.1.19">samtools</requirement>
   </requirements>
   <command>
   #set index_path = ''
   #if str($reference_genome.source) == "history":
-    echo \${PATH} &amp;&amp; bowtie2-build "$reference_genome.own_file" genome &amp;&amp;
+    bowtie2-build "$reference_genome.own_file" genome &amp;&amp;
     ln -s "$reference_genome.own_file" genome.fa &amp;&amp;
     #set index_path = 'genome'
   #else: