# HG changeset patch
# User big-tiandm
# Date 1418021476 18000
# Node ID f5a2e8308836cba68abf1f2b60cb3d90d6e4124f
# Parent  8b8c356e6db507f5a34aa4f04f31b80f67e9d135
Uploaded

diff -r 8b8c356e6db5 -r f5a2e8308836 tool-data/rfam_bowtie_indices.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/rfam_bowtie_indices.loc.sample	Mon Dec 08 01:51:16 2014 -0500
@@ -0,0 +1,37 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Bowtie indexed sequences data files. You will
+#need to create these data files and then create a bowtie_indices.loc
+#file similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The bowtie_indices.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#<unique_build_id>   <dbkey>   <display_name>   <file_base_path>
+#
+#So, for example, if you had hg18 indexed stored in
+#/depot/data2/galaxy/bowtie/hg18/,
+#then the bowtie_indices.loc entry would look like this:
+#
+#hg18	hg18	hg18	/depot/data2/galaxy/bowtie/hg18/hg18
+#
+#and your /depot/data2/galaxy/bowtie/hg18/ directory
+#would contain hg18.*.ebwt files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.1.ebwt
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.2.ebwt
+#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 hg18.3.ebwt
+#...etc...
+#
+#Your bowtie_indices.loc file should include an entry per line for each
+#index set you have stored. The "file" in the path does not actually
+#exist, but it is the prefix for the actual index files. For example:
+#
+#hg18canon			hg18	hg18 Canonical	/depot/data2/galaxy/bowtie/hg18/hg18canon
+#hg18full			hg18	hg18 Full		/depot/data2/galaxy/bowtie/hg18/hg18full
+#/orig/path/hg19	hg19	hg19			/depot/data2/galaxy/bowtie/hg19/hg19
+#...etc...
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. That is why the
+#hg19 entry above looks odd. New genomes can be better-looking.
+#
diff -r 8b8c356e6db5 -r f5a2e8308836 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Fri Dec 05 01:28:46 2014 -0500
+++ b/tool_data_table_conf.xml.sample	Mon Dec 08 01:51:16 2014 -0500
@@ -5,4 +5,9 @@
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/bowtie_indices.loc" />
     </table>
+    <!-- Locations of indexes in the Bowtie mapper format -->
+    <table name="rfam_bowtie_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/rfam_bowtie_indices.loc" />
+    </table>
 </tables>