# HG changeset patch
# User iuc
# Date 1400284012 14400
# Node ID 81a0c1c27ec85298b35ee2b888c9bc8f6cbc206e
# Parent  3480daf4ed27f34e78e35356c1e84df729904ae8
Uploaded

diff -r 3480daf4ed27 -r 81a0c1c27ec8 fastq_screen.xml
--- a/fastq_screen.xml	Fri May 16 19:26:18 2014 -0400
+++ b/fastq_screen.xml	Fri May 16 19:46:52 2014 -0400
@@ -1,8 +1,8 @@
 <tool id="fastq_screen" name="fastq_screen" version="0.4.2">
     <description>Screen for contamination</description>
     <requirements>
+        <requirement type="package" version="2.1.0">bowtie2</requirement>
         <requirement type="package" version="0.4.2">fastq_screen</requirement>
-        <requirement type="package" version="2.1.0">package_bowtie2</requirement>
     </requirements>
     <command> 
     fastq_screen --aligner="bowtie2" --outdir="." --conf="$fastqrunconf"
@@ -62,7 +62,7 @@
     <configfiles>
          <configfile name="fastqrunconf">
 ###### autogenerated by fastq_screen.xml for fastq_screen run
-BOWTIE2 /data/app/bin/bowtie2
+BOWTIE2 bowtie2
 #for $refs in $refGenomes:
 DATABASE    $refs.ref.fields.value $refs.ref.fields.path    BOWTIE2
 #end for
diff -r 3480daf4ed27 -r 81a0c1c27ec8 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri May 16 19:26:18 2014 -0400
+++ b/tool_dependencies.xml	Fri May 16 19:46:52 2014 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="package_bowtie2" version="2.1.0">
+    <package name="bowtie2" version="2.1.0">
         <repository changeset_revision="606d435a57a4" name="package_bowtie2_2_1_0" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="fastq_screen" version="0.4.2">