# HG changeset patch
# User chrisw
# Date 1549987903 18000
# Node ID f0c74414410085974858780804e2edb99b30c710
# Parent  5c92c1163a6d22725c446a8e20fe31485314e6ac
Uploaded

diff -r 5c92c1163a6d -r f0c744144100 README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Tue Feb 12 11:11:43 2019 -0500
@@ -0,0 +1,5 @@
+Monorail Test Repo
+==================
+
+Primarily to test installation from a repo
+to get requirements right.
diff -r 5c92c1163a6d -r f0c744144100 monorail.sh
diff -r 5c92c1163a6d -r f0c744144100 tool-data/rnastar_index2.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/rnastar_index2.loc.sample	Tue Feb 12 11:11:43 2019 -0500
@@ -0,0 +1,22 @@
+#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> <withGTF>
+#
+#The <with_gtf> column should be 1 or 0, indicating whether the index was made
+#with an annotation (i.e., --sjdbGTFfile and --sjdbOverhang were used) or not,
+#respecively.
+#
+#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
+#hg19Ensembl   hg19Ensembl    hg19 full with Ensembl annotation   /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1
diff -r 5c92c1163a6d -r f0c744144100 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Feb 12 11:11:43 2019 -0500
@@ -0,0 +1,6 @@
+<tables>
+    <table name="rnastar_index2" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, path, with-gtf</columns>
+        <file path="tool-data/rnastar_index2.loc" />
+    </table>
+</tables>