Mercurial > repos > ieguinoa > data_manager_salmon_index_builder
comparison tool-data/salmon_indexes_versioned.loc.sample @ 7:954d617c323d draft
Uploaded
| author | ieguinoa |
|---|---|
| date | Tue, 23 Jul 2019 10:50:43 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 6:d22f69a2e80e | 7:954d617c323d |
|---|---|
| 1 # salmon_indexes_versioned.loc.sample | |
| 2 # This is a *.loc.sample file distributed with Galaxy that enables tools | |
| 3 # to use a directory of indexed data files. This one is for Salmon. | |
| 4 # See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup | |
| 5 # First create these data files and save them in your own data directory structure. | |
| 6 # Then, create a salmon_indexes_versioned.loc.sample file to use those indexes with tools. | |
| 7 # Copy this file, save it with the same name (minus the .sample), | |
| 8 # follow the format examples, and store the result in this directory. | |
| 9 # The file should include an one line entry for each index set. | |
| 10 # The path points to the "basename" for the set, not a specific file. | |
| 11 # It has four text columns seperated by TABS. | |
| 12 # | |
| 13 # <unique_build_id> <dbkey> <display_name> <file_base_path> <version> | |
| 14 # | |
| 15 # The <version> column can be retrieved from the header.json file in the index folder. e.g "IndexVersion": "q5" | |
| 16 | |
| 17 | |
| 18 | |
| 19 # So, for example, if you had sacCer3 indexes stored in: | |
| 20 # | |
| 21 # /depot/data2/galaxy/sacCer3/salmon_indexes/ | |
| 22 # | |
| 23 # then the salmon_indexes.loc entry could look like this: | |
| 24 # | |
| 25 #sacCer3 sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) /depot/data2/galaxy/sacCer3/salmon_indexes/version_3/ q6 | |
| 26 # | |
| 27 #More examples: | |
| 28 # | |
| 29 #mm10 mm10 Mouse (mm10) /depot/data2/galaxy/salmon_indexes/mm10/version_2 q4 | |
| 30 #dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/salmon_indexes/dm3/version_1 q5 | |
| 31 # | |
| 32 # |