# HG changeset patch
# User chrisw
# Date 1573683432 0
# Node ID b456cb342e9e2c562a48aa484f57c6440fc9031f
# Parent  11daa95fdc3ecdb7aa1a8a6f6d9016445ce995a4
Uploaded

diff -r 11daa95fdc3e -r b456cb342e9e data_manager_monorail_index/data_manager_conf.xml
--- a/data_manager_monorail_index/data_manager_conf.xml	Wed Nov 13 21:12:37 2019 +0000
+++ b/data_manager_monorail_index/data_manager_conf.xml	Wed Nov 13 22:17:12 2019 +0000
@@ -1,4 +1,4 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ncoding="utf-8" ?>
 <data_managers>
     <data_manager tool_file="data_manager/monorail_index_fetcher.xml" id="monorail_index_fetcher" version="1.0.0">
     <data_table name="monorail_index">
diff -r 11daa95fdc3e -r b456cb342e9e data_manager_monorail_index/tool-data/monorail_index.loc.sample
--- a/data_manager_monorail_index/tool-data/monorail_index.loc.sample	Wed Nov 13 21:12:37 2019 +0000
+++ b/data_manager_monorail_index/tool-data/monorail_index.loc.sample	Wed Nov 13 22:17:12 2019 +0000
@@ -0,0 +1,26 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of rna-star indexed sequences data files. You will
+#need to create these data files and then create a rnastar_index2.loc
+#file similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The rnastar_index2.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#<unique_build_id>   <dbkey>   <display_name>   <file_base_path>	<with_gene_model>	<version>
+#
+#The <with_gene_model> column should be 1 or 0, indicating whether the index
+#was built with annotations (i.e., --sjdbGTFfile and --sjdbOverhang were used)
+#or not.
+#
+#The <version> column indicates the STAR version that introduced the format of
+#the index, i.e., the oldest STAR version that could make use of the index.
+#
+#Note that STAR indices can become quite large. Consequently, it is only
+#advisable to create indices with annotations if it's known ahead of time that
+#(A) the annotations won't be frequently updated and (B) the read lengths used
+#will also rarely vary. If either of these is not the case, it's advisable to
+#create indices without annotations and then specify an annotation file and
+#maximum read length (minus 1) when running STAR.
+#
+#hg19   hg19    hg19 full   /mnt/galaxyIndices/genomes/hg19/rnastar	0	2.7.1a
+#hg19Ensembl   hg19Ensembl    hg19 full with Ensembl annotation   /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar	1	2.7.1a
+
diff -r 11daa95fdc3e -r b456cb342e9e data_manager_monorail_index/tool_data_table_conf.xml.sample
--- a/data_manager_monorail_index/tool_data_table_conf.xml.sample	Wed Nov 13 21:12:37 2019 +0000
+++ b/data_manager_monorail_index/tool_data_table_conf.xml.sample	Wed Nov 13 22:17:12 2019 +0000
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
 <tables>
     <!-- Locations of gene annotation data -->
-    <table name="gene_annotation" comment_char="#">
+    <table name="monorail_index" comment_char="#" allow_duplicate_entries="False">
         <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/gene_annotation.loc" />
+        <file path="tool-data/monorail_index.loc" />
     </table>
-</tables>
\ No newline at end of file
+</tables>