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comparison tool-data/fasta_indexes.loc.sample @ 3:beab768feb92

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Update to the new data table specification.
author Dave Bouvier <dave@bx.psu.edu>
date Wed, 04 Dec 2013 13:24:38 -0500
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children 63b3133e535b
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2:2d6a90609943 3:beab768feb92
1 #This is a sample file distributed with Galaxy that enables tools
2 #to use a directory of Samtools indexed sequences data files. You will need
3 #to create these data files and then create a sam_fa_new_indices.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 sam_fa_new_indices.loc
6 #file has this format (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 hg19 Canonical indexed stored in
11 #
12 # /depot/data2/galaxy/hg19/sam/,
13 #
14 #then the sam_fa_new_indices.loc entry would look like this:
15 #
16 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
17 #
18 #and your /depot/data2/galaxy/hg19/sam/ directory
19 #would contain hg19canon.fa and hg19canon.fa.fai files.
20 #
21 #Your sam_fa_new_indices.loc file should include an entry per line for
22 #each index set you have stored. The file in the path does actually
23 #exist, but it should never be directly used. Instead, the name serves
24 #as a prefix for the index file. For example:
25 #
26 #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa
27 #hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa
28 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
29 #hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa