Mercurial > repos > devteam > tophat_fusion_post
diff tophat_fusion_post.xml @ 3:2f75d0317ee5
Use Bowtie rather than Bowtie2 and update wrapper to fix Cheetah syntax bug.
author | devteam@galaxyproject.org |
---|---|
date | Mon, 10 Feb 2014 12:13:22 -0500 |
parents | 75845643f9dd |
children | 51ede4e7d4f0 |
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--- a/tophat_fusion_post.xml Sun Feb 09 15:48:15 2014 -0500 +++ b/tophat_fusion_post.xml Mon Feb 10 12:13:22 2014 -0500 @@ -3,14 +3,14 @@ <version_command>tophat-fusion-post --version</version_command> <requirements> <requirement type="package" version="2.2.28">blast+</requirement> - <requirement type="package" version="2.1.0">bowtie2</requirement> + <requirement type='package' version="0.12.7">bowtie</requirement> </requirements> <command> ## Set up tophat_out structure. mkdir tophat_out; ln -s $accepted_hits tophat_out/accepted_hits.bam; ln -s $fusions tophat_out/fusions.out; ## Set up blast directory structure. - #set blast_db_path = ${__get_data_table_entry__('tophat_fusion_blastdb_indexes', 'dbkey', $accepted_hits.dbkey, 'path')} + #set blast_db_path = $__get_data_table_entry__('tophat_fusion_blastdb_indexes', 'dbkey', $accepted_hits.dbkey, 'path') ln -s ${blast_db_path}/ blast; ## Set up additional files: @@ -25,8 +25,8 @@ --non-human #end if - ## Bowtie2 indices. - ${__get_data_table_entry__('bowtie2_indexes', 'dbkey', $accepted_hits.dbkey, 'path')} + ## Bowtie indices. + ${__get_data_table_entry__('bowtie_indexes', 'dbkey', $accepted_hits.dbkey, 'path')} </command> <inputs>