Mercurial > repos > ieguinoa > data_manager_salmon_index_builder
comparison tool-data/salmon_indexes.loc.sample @ 6:d22f69a2e80e draft
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author | ieguinoa |
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date | Tue, 23 Jul 2019 09:25:04 -0400 |
parents | c5dea2080109 |
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5:3888ec1918d0 | 6:d22f69a2e80e |
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1 # salmon_indexes.loc.sample | 1 # salmon_indexes_versioned.loc.sample |
2 # This is a *.loc.sample file distributed with Galaxy that enables tools | 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. | 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 | 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. | 5 # First create these data files and save them in your own data directory structure. |
6 # Then, create a kallisto_indexes.loc file to use those indexes with tools. | 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), | 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. | 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. | 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. | 10 # The path points to the "basename" for the set, not a specific file. |
11 # It has four text columns seperated by TABS. | 11 # It has four text columns seperated by TABS. |
12 # | 12 # |
13 # <unique_build_id> <dbkey> <display_name> <file_base_path> | 13 # <unique_build_id> <dbkey> <display_name> <file_base_path> <version> |
14 # | 14 # |
15 # The <version> column can be retrieved from the header.json file in the index folder. e.g "IndexVersion": "q5" | |
16 | |
17 | |
18 | |
15 # So, for example, if you had sacCer3 indexes stored in: | 19 # So, for example, if you had sacCer3 indexes stored in: |
16 # | 20 # |
17 # /depot/data2/galaxy/sacCer3/salmon_indexes/ | 21 # /depot/data2/galaxy/sacCer3/salmon_indexes/ |
18 # | 22 # |
19 # then the salmon_indexes.loc entry could look like this: | 23 # then the salmon_indexes.loc entry could look like this: |
20 # | 24 # |
21 #sacCer3 sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) /depot/data2/galaxy/sacCer3/salmon_indexes | 25 #sacCer3 sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) /depot/data2/galaxy/sacCer3/salmon_indexes/version_3/ q6 |
22 # | 26 # |
23 #More examples: | 27 #More examples: |
24 # | 28 # |
25 #mm10 mm10 Mouse (mm10) /depot/data2/galaxy/salmon_indexes/mm10 | 29 #mm10 mm10 Mouse (mm10) /depot/data2/galaxy/salmon_indexes/mm10/version_2 q4 |
26 #dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/salmon_indexes/dm3 | 30 #dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/salmon_indexes/dm3/version_1 q5 |
27 # | 31 # |
28 # | 32 # |