Mercurial > repos > devteam > data_manager_bowtie2_index_builder
comparison tool-data/tophat2_indices.loc.sample @ 1:9bf4eb559ed5 draft
planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062
| author | devteam |
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| date | Mon, 10 Aug 2015 16:44:10 -0400 |
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| 0:9458af1ab90b | 1:9bf4eb559ed5 |
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| 1 # tophat2_indices.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 Bowtie2 and Tophat2. | |
| 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 bowtie_indices.loc 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> | |
| 14 # | |
| 15 # So, for example, if you had hg18 indexes stored in: | |
| 16 # | |
| 17 # /depot/data2/galaxy/hg19/bowtie2/ | |
| 18 # | |
| 19 # containing hg19 genome and hg19.*.bt2 files, such as: | |
| 20 # -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa | |
| 21 # -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2 | |
| 22 # -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2 | |
| 23 # -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2 | |
| 24 # -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2 | |
| 25 # -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2 | |
| 26 # -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2 | |
| 27 # | |
| 28 # then the bowtie2_indices.loc entry could look like this: | |
| 29 # | |
| 30 #hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/bowtie2/hg19canon | |
| 31 # | |
| 32 #More examples: | |
| 33 # | |
| 34 #mm10 mm10 Mouse (mm10) /depot/data2/galaxy/mm10/bowtie2/mm10 | |
| 35 #dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/mm10/bowtie2/dm3 | |
| 36 # | |
| 37 # |