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comparison tool-data/bowtie_indices.loc.sample @ 0:119b03a6eaaa draft default tip

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author jjohnson
date Tue, 20 Aug 2013 11:55:20 -0400
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1 #This is a sample file distributed with Galaxy that enables tools
2 #to use a directory of Bowtie indexed sequences data files. You will
3 #need to create these data files and then create a bowtie_indices.loc
4 #file similar to this one (store it in this directory) that points to
5 #the directories in which those files are stored. The bowtie_indices.loc
6 #file has this format (longer white space characters are TAB characters):
7 #
8 #<unique_build_id> <dbkey> <display_name> <file_base_path>
9 #
10 #So, for example, if you had hg18 indexed stored in
11 #/depot/data2/galaxy/bowtie/hg18/,
12 #then the bowtie_indices.loc entry would look like this:
13 #
14 #hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18
15 #
16 #and your /depot/data2/galaxy/bowtie/hg18/ directory
17 #would contain hg18.*.ebwt files:
18 #
19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt
20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt
21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt
22 #...etc...
23 #
24 #Your bowtie_indices.loc file should include an entry per line for each
25 #index set you have stored. The "file" in the path does not actually
26 #exist, but it is the prefix for the actual index files. For example:
27 #
28 #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon
29 #hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full
30 #/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19
31 #...etc...
32 #
33 #Note that for backwards compatibility with workflows, the unique ID of
34 #an entry must be the path that was in the original loc file, because that
35 #is the value stored in the workflow for that parameter. That is why the
36 #hg19 entry above looks odd. New genomes can be better-looking.
37 #