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comparison tool-data/gatk_sorted_picard_index.loc.sample @ 0:7e1ecaa64370 draft default tip

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author devteam
date Tue, 01 Apr 2014 10:49:56 -0400
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1 #This is a sample file distributed with Galaxy that enables tools
2 #to use a directory of Picard dict and associated files. You will need
3 #to create these data files and then create a picard_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 picard_index.loc
6 #file has this format (longer white space is the TAB character):
7 #
8 #<unique_build_id> <dbkey> <display_name> <fasta_file_path>
9 #
10 #So, for example, if you had hg18 indexed and stored in
11 #/depot/data2/galaxy/srma/hg18/,
12 #then the srma_index.loc entry would look like this:
13 #
14 #hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa
15 #
16 #and your /depot/data2/galaxy/srma/hg18/ directory
17 #would contain the following three files:
18 #hg18.fa
19 #hg18.dict
20 #hg18.fa.fai
21 #
22 #The dictionary file for each reference (ex. hg18.dict) must be
23 #created via Picard (http://picard.sourceforge.net). Note that
24 #the dict file does not have the .fa extension although the
25 #path list in the loc file does include it.
26 #