Mercurial > repos > jasper > pathoscope_map
comparison tool-data/pathoscope.loc.sample @ 0:94d7100ad5d0 draft default tip
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| author | jasper |
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| date | Sat, 22 Apr 2017 23:47:18 -0400 |
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| -1:000000000000 | 0:94d7100ad5d0 |
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| 1 # pathoscope.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 Pathoscope_Map. | |
| 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 # | |
| 8 # The path points to the "basename" for the set, not a specific file. | |
| 9 # It has four text columns seperated by TABS. | |
| 10 # <unique_build_id> <display_name> <file_base_path> | |
| 11 # | |
| 12 # So, for example, if you had hg18 indexes stored in: | |
| 13 # | |
| 14 # /depot/data2/galaxy/hg19/bowtie2/ | |
| 15 # | |
| 16 # containing hg19 genome and hg19.*.bt2 files, such as: | |
| 17 # -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa | |
| 18 # -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2 | |
| 19 # -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2 | |
| 20 # -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2 | |
| 21 # -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2 | |
| 22 # -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2 | |
| 23 # -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2 | |
| 24 # | |
| 25 # then the bowtie2_indices.loc entry could look like this: | |
| 26 # | |
| 27 #hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/bowtie2/hg19canon | |
| 28 # | |
| 29 #Important: put all reference bowtie index into same directory (including both | |
| 30 #target and filter reference botwie index) | |
| 31 # | |
| 32 #More examples: | |
| 33 #ref_prok_rep_genomes prok /depot/data/ref | |
| 34 #ce11 ce /depot/data/ref |