# HG changeset patch
# User Eduardo <eduardoalves@abdn.ac.uk>
# Date 1438686069 -3600
# Node ID 083c25559b6b53ed950e4541e7a21f2a1aec5336
# Parent  d839829f8494d322e1846e8cb6b413b799d3396e
updated cutadapt dependency to 1.8 to solve env problem

diff -r d839829f8494 -r 083c25559b6b download_align.xml
--- 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:
diff -r d839829f8494 -r 083c25559b6b tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Aug 03 17:32:31 2015 +0100
+++ b/tool_dependencies.xml	Tue Aug 04 12:01:09 2015 +0100
@@ -6,11 +6,9 @@
     <package name="samtools" version="0.1.18">
       <repository name="package_samtools_0_1_18" owner="devteam"  />
     </package>
-    <package name="cutadapt" version="1.6">
-      <repository name="package_cutadapt_1_6" owner="lparsons" />
+    <package name="cutadapt" version="1.8">
+      <repository name="package_cutadapt_1_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/>
     </package>
 </tool_dependency>
 
-<tool_dependency>
 
-