diff tool-data/salmon_indexes.loc.sample @ 6:d22f69a2e80e draft

Uploaded

--- a/tool-data/salmon_indexes.loc.sample	Thu Jan 03 10:51:18 2019 -0500
+++ b/tool-data/salmon_indexes.loc.sample	Tue Jul 23 09:25:04 2019 -0400
@@ -1,28 +1,32 @@
-# salmon_indexes.loc.sample
+# 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 kallisto_indexes.loc file to use those indexes with tools.
+# 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>
+# <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
+#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
-#dm3	dm3		D. melanogaster (dm3)	/depot/data2/galaxy/salmon_indexes/dm3
+#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
 #
 #