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comparison tool-data/hisat_indices.loc.sample @ 0:4c7db9cbbbf7 draft default tip

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author jjohnson
date Tue, 22 Jul 2014 08:52:53 -0400
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1 # hisat_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 hisat_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/hisat/
18 #
19 # containing hg19 genome and hg19.*.bt2 files, such as:
20 # -rw-rw-r--. 1 galaxy galaxy 914M Jul 18 09:17 hg19canon.1.bt2
21 # -rw-rw-r--. 1 galaxy galaxy 683M Jul 18 09:17 hg19canon.2.bt2
22 # -rw-rw-r--. 1 galaxy galaxy 3.3K Jul 18 08:22 hg19canon.3.bt2
23 # -rw-rw-r--. 1 galaxy galaxy 683M Jul 18 08:22 hg19canon.4.bt2
24 # -rw-rw-r--. 1 galaxy galaxy 1.2G Jul 18 09:23 hg19canon.5.bt2
25 # -rw-rw-r--. 1 galaxy galaxy 694M Jul 18 09:23 hg19canon.6.bt2
26 # -rw-rw-r--. 2 galaxy galaxy 3.0G Nov 15 2011 hg19canon.fa
27 # -rw-rw-r--. 1 galaxy galaxy 914M Jul 18 10:13 hg19canon.rev.1.bt2
28 # -rw-rw-r--. 1 galaxy galaxy 683M Jul 18 10:13 hg19canon.rev.2.bt2
29 # -rw-rw-r--. 1 galaxy galaxy 1.2G Jul 18 10:20 hg19canon.rev.5.bt2
30 # -rw-rw-r--. 1 galaxy galaxy 694M Jul 18 10:20 hg19canon.rev.6.bt2
31 #
32 # then the hisat_indices.loc entry could look like this:
33 #
34 #hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/hisat/hg19canon
35 #
36 #More examples:
37 #
38 #mm10 mm10 Mouse (mm10) /depot/data2/galaxy/mm10/hisat/mm10
39 #dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/mm10/hisat/dm3
40 #
41 #