Mercurial > repos > iuc > fastq_screen

diff fastq_screen.xml @ 2:81a0c1c27ec8 draft default tip

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author iuc
date Fri, 16 May 2014 19:46:52 -0400
parents 3480daf4ed27
children
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--- 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