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comparison rsem_prepare_reference.xml @ 4:30a8343fb0e7

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Change for extra_files_path
author Jim Johnson <jj@umn.edu>
date Mon, 13 Oct 2014 15:32:39 -0500
parents 59459de65740
children 14267d364365
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3:59459de65740 4:30a8343fb0e7
4 <requirement type="package" version="1.1.17">rsem</requirement> 4 <requirement type="package" version="1.1.17">rsem</requirement>
5 <requirement type="package" version="1.0.0">bowtie</requirement> 5 <requirement type="package" version="1.0.0">bowtie</requirement>
6 </requirements> 6 </requirements>
7 <command> 7 <command>
8 echo $reference_name " " | tee $reference_file &amp;&amp; 8 echo $reference_name " " | tee $reference_file &amp;&amp;
9 mkdir $reference_file.extra_files_path &amp;&amp; 9 mkdir $reference_file.dataset.extra_files_path &amp;&amp;
10 cd $reference_file.extra_files_path &amp;&amp; 10 cd $reference_file.dataset.extra_files_path &amp;&amp;
11 rsem-prepare-reference 11 rsem-prepare-reference
12 #if $polya.polya_use == 'add': 12 #if $polya.polya_use == 'add':
13 #if $polya.polya_length: 13 #if $polya.polya_length:
14 --polyA-length $polya.polya_length 14 --polyA-length $polya.polya_length
15 #end if 15 #end if