diff tool-data/hisat2_indexes.loc.sample @ 0:d3eb4d51b285 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
author iuc
date Sat, 10 Oct 2015 14:53:43 -0400
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/hisat2_indexes.loc.sample	Sat Oct 10 14:53:43 2015 -0400
@@ -0,0 +1,39 @@
+# hisat2_indexes.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 HISAT2.
+# 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 hisat2_indexes.loc 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>
+#
+# So, for example, if you had sacCer3 indexes stored in:
+#
+#    /depot/data2/galaxy/sacCer3/hisat2_indexes/
+#
+# containing sacCer3 genome and sacCer3.*.ht2 files, such as:
+#
+#   -rw-rw-r-- 1 dave dave  12M Sep 23 13:57 sacCer3.1.ht2
+#   -rw-rw-r-- 1 dave dave 2.9M Sep 23 13:57 sacCer3.2.ht2
+#   -rw-rw-r-- 1 dave dave  161 Sep 23 13:57 sacCer3.3.ht2
+#   -rw-rw-r-- 1 dave dave 2.9M Sep 23 13:57 sacCer3.4.ht2
+#   -rw-rw-r-- 1 dave dave 7.3M Sep 23 13:57 sacCer3.5.ht2
+#   -rw-rw-r-- 1 dave dave 3.0M Sep 23 13:57 sacCer3.6.ht2
+#   -rw-rw-r-- 1 dave dave 128K Sep 23 13:57 sacCer3.7.ht2
+#   -rw-rw-r-- 1 dave dave  32K Sep 23 13:57 sacCer3.8.ht2
+#
+# then the hisat2_indexes.loc entry could look like this:
+#
+#sacCer3	sacCer3	S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3)	/depot/data2/galaxy/hisat2_indexes/sacCer3
+#
+#More examples:
+#
+#mm10	mm10	Mouse (mm10)	/depot/data2/galaxy/hisat2_indexes/mm10
+#dm3	dm3		D. melanogaster (dm3)	/depot/data2/galaxy/hisat2_indexes/dm3
+#
+#