Mercurial > repos > devteam > tophat_fusion_post

changeset 10:33aafd74bb31

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Fix bugs: (a) use value rather than dbkey to get bowtie indices and (b) point to correct bowtie table.
author devteam@galaxyproject.org
date Thu, 27 Feb 2014 14:58:22 -0500
parents 7d6658b2531a
children 08f88205d596
files tool_data_table_conf.xml.sample tool_dependencies.xml tophat_fusion_post.xml
diffstat 3 files changed, 6 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/tool_data_table_conf.xml.sample	Thu Feb 20 13:19:38 2014 -0500
+++ b/tool_data_table_conf.xml.sample	Thu Feb 27 14:58:22 2014 -0500
@@ -1,7 +1,7 @@
 <tables>
-    <table name="bowtie2_indexes" comment_char="#">
+    <table name="bowtie_indexes" comment_char="#">
         <columns>value, dbkey, name, path</columns>
-	 	<file path="tool-data/bowtie2_indices.loc" />
+	 	<file path="tool-data/bowtie_indices.loc" />
     </table>
     <table name="tophat_fusion_blastdb_indexes" comment_char="#">
         <columns>value, dbkey, name, path</columns>
--- a/tool_dependencies.xml	Thu Feb 20 13:19:38 2014 -0500
+++ b/tool_dependencies.xml	Thu Feb 27 14:58:22 2014 -0500
@@ -1,12 +1,12 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="blast+" version="2.2.28">
-        <repository changeset_revision="23b9ba41ad00" name="package_blast_plus_2_2_28" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository name="package_blast_plus_2_2_28" owner="iuc"/>
     </package>
     <package name="tophat2" version="2.0.9">
-        <repository changeset_revision="8549fd545473" name="package_tophat2_2_0_9" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository name="package_tophat2_2_0_9" owner="devteam"/>
     </package>
     <package name="bowtie" version="0.12.7">
-        <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository name="package_bowtie_0_12_7" owner="devteam"/>
     </package>
 </tool_dependency>
--- a/tophat_fusion_post.xml	Thu Feb 20 13:19:38 2014 -0500
+++ b/tophat_fusion_post.xml	Thu Feb 27 14:58:22 2014 -0500
@@ -27,7 +27,7 @@
         #end if
 
 	    ## Bowtie indices.
-	    ${__get_data_table_entry__('bowtie_indexes', 'dbkey', $accepted_hits.dbkey, 'path')}
+	    ${__get_data_table_entry__('bowtie_indexes', 'value', $accepted_hits.dbkey, 'path')}
     </command>
 
     <inputs>