--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/old/tool-data/salmon_indexes_versioned.loc.sample	Wed Oct 02 04:31:23 2019 -0400
@@ -0,0 +1,32 @@
+# salmon_indexes_versioned.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 Salmon.
+# 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 salmon_indexes_versioned.loc.sample 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> <version>
+#
+# The <version> column can be retrieved from the header.json file in the index folder. e.g   "IndexVersion": "q5"
+
+
+
+# So, for example, if you had sacCer3 indexes stored in:
+#
+#    /depot/data2/galaxy/sacCer3/salmon_indexes/
+#
+# then the salmon_indexes.loc entry could look like this:
+#
+#sacCer3	sacCer3	S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3)	/depot/data2/galaxy/sacCer3/salmon_indexes/version_3/	q6
+#
+#More examples:
+#
+#mm10	mm10	Mouse (mm10)	/depot/data2/galaxy/salmon_indexes/mm10/version_2	q4
+#dm3	dm3		D. melanogaster (dm3)	/depot/data2/galaxy/salmon_indexes/dm3/version_1	q5
+#
+#