Mercurial > repos > iuc > bwa_mem2

comparison tool-data/bwa_mem2_index.loc.sample @ 0:82217dccdbcf draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
author iuc
date Fri, 08 Oct 2021 10:19:48 +0000
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-1:000000000000 0:82217dccdbcf
1 #This is a sample file distributed with Galaxy that enables tools
2 #to use a directory of BWA indexed sequences data files. You will need
3 #to create these data files and then create a bwa_index.loc file
4 #similar to this one (store it in this directory) that points to
5 #the directories in which those files are stored. The bwa_index.loc
6 #file has this format (longer white space characters are TAB characters):
7 #
8 #<unique_build_id> <dbkey> <display_name> <file_path>
9 #
10 #So, for example, if you had phiX indexed stored in
11 #/depot/data2/galaxy/phiX/base/,
12 #then the bwa_index.loc entry would look like this:
13 #
14 #phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa
15 #
16 #and your /depot/data2/galaxy/phiX/base/ directory
17 #would contain phiX.fa.* files:
18 #
19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb
20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann
21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt
22 #...etc...
23 #
24 #Your bwa_index.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 #phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa
29 #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa
30 #hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa
31 #/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa
32 #...etc...
33 #
34 #Note that for backwards compatibility with workflows, the unique ID of
35 #an entry must be the path that was in the original loc file, because that
36 #is the value stored in the workflow for that parameter. That is why the
37 #hg19 entry above looks odd. New genomes can be better-looking.
38 #