# HG changeset patch
# User devteam@galaxyproject.org
# Date 1392052402 18000
# Node ID 2f75d0317ee56352753a84d655d966aa75621ed0
# Parent  664f7d96423145361680681790bc01cff67990f2
Use Bowtie rather than Bowtie2 and update wrapper to fix Cheetah syntax bug.

diff -r 664f7d964231 -r 2f75d0317ee5 tool-data/bowtie_indices.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/bowtie_indices.loc.sample	Mon Feb 10 12:13:22 2014 -0500
@@ -0,0 +1,37 @@
+# bowtie_indices.loc.sample
+# This is a *.loc.sample file distributed with Galaxy that enables tools
+# to use a directory of indexed data files. This one is for Bowtie and Tophat.
+# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
+# First create these data files and save them in your own data directory structure.
+# Then, create a bowtie_indices.loc file to use those indexes with tools.
+# Copy this file, save it with the same name (minus the .sample), 
+# follow the format examples, and store the result in this directory.
+# The file should include an one line entry for each index set.
+# The path points to the "basename" for the set, not a specific file.
+# It has four text columns seperated by TABS.
+#
+# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
+#
+# So, for example, if you had hg18 indexes stored in:
+#
+#    /depot/data2/galaxy/hg19/bowtie/
+#
+# containing hg19 genome and hg19.*.ewbt files, such as:
+#    -rw-rw-r-- 1 james   james   914M Feb 10 18:56 hg19canon.fa
+#    -rw-rw-r-- 1 james   james   914M Feb 10 18:56 hg19canon.1.ewbt
+#    -rw-rw-r-- 1 james   james   683M Feb 10 18:56 hg19canon.2.ewbt
+#    -rw-rw-r-- 1 james   james   3.3K Feb 10 16:54 hg19canon.3.ewbt
+#    -rw-rw-r-- 1 james   james   683M Feb 10 16:54 hg19canon.4.ewbt
+#    -rw-rw-r-- 1 james   james   914M Feb 10 20:45 hg19canon.rev.1.ewbt
+#    -rw-rw-r-- 1 james   james   683M Feb 10 20:45 hg19canon.rev.2.ewbt
+#
+# then the bowtie2_indices.loc entry could look like this:
+#
+#hg19	hg19	Human (hg19)	/depot/data2/galaxy/hg19/bowtie/hg19canon
+#
+#More examples:
+#
+#mm10	mm10	Mouse (mm10)	/depot/data2/galaxy/mm10/bowtie/mm10
+#dm3	dm3	      D. melanogaster (dm3)	/depot/data2/galaxy/mm10/bowtie/dm3
+#
+#
diff -r 664f7d964231 -r 2f75d0317ee5 tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Feb 09 15:48:15 2014 -0500
+++ b/tool_dependencies.xml	Mon Feb 10 12:13:22 2014 -0500
@@ -1,9 +1,9 @@
 <?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="bowtie2" version="2.1.0">
-        <repository changeset_revision="017a00c265f1" name="package_bowtie2_2_1_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <package name="bowtie" version="0.12.7">
+        <repository name="package_bowtie_0_12_7" owner="devteam"/>
     </package>
 </tool_dependency>
diff -r 664f7d964231 -r 2f75d0317ee5 tophat_fusion_post.xml
--- 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>