Mercurial > repos > jjohnson > rsem
comparison rsem_prepare_reference.xml @ 4:30a8343fb0e7
Change for extra_files_path
author | Jim Johnson <jj@umn.edu> |
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date | Mon, 13 Oct 2014 15:32:39 -0500 |
parents | 59459de65740 |
children | 14267d364365 |
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3:59459de65740 | 4:30a8343fb0e7 |
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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 && | 8 echo $reference_name " " | tee $reference_file && |
9 mkdir $reference_file.extra_files_path && | 9 mkdir $reference_file.dataset.extra_files_path && |
10 cd $reference_file.extra_files_path && | 10 cd $reference_file.dataset.extra_files_path && |
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 |