Mercurial > repos > bgruening > salmonquantmerge
comparison test-data/cached_locally/salmon_indexes_versioned.loc @ 0:43658f594542 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
| author | bgruening |
|---|---|
| date | Mon, 09 Sep 2019 11:12:04 -0400 |
| parents | |
| children | 992c077f6e41 |
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| -1:000000000000 | 0:43658f594542 |
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| 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 # | |
| 33 hg19_transcript_subset hg19 Human (Homo sapiens): hg19 transcript test subset ${__HERE__}/prebuilt_index q5 |