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comparison sam_fa_indices.loc.sample @ 0:3fdeebd7e710

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author lparsons
date Tue, 04 Sep 2012 13:45:36 -0400
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-1:000000000000 0:3fdeebd7e710
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_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_indices.loc
6 #file has this format (white space characters are TAB characters):
7 #
8 #index <seq> <location>
9 #
10 #So, for example, if you had hg18 indexed stored in
11 #/depot/data2/galaxy/sam/,
12 #then the sam_fa_indices.loc entry would look like this:
13 #
14 #index hg18 /depot/data2/galaxy/sam/hg18.fa
15 #
16 #and your /depot/data2/galaxy/sam/ directory
17 #would contain hg18.fa and hg18.fa.fai files:
18 #
19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.fa
20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.fa.fai
21 #
22 #Your sam_fa_indices.loc file should include an entry per line for
23 #each index set you have stored. The file in the path does actually
24 #exist, but it should never be directly used. Instead, the name serves
25 #as a prefix for the index file. For example:
26 #
27 #index hg18 /depot/data2/galaxy/sam/hg18.fa
28 #index hg19 /depot/data2/galaxy/sam/hg19.fa