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29 lines
1.2 KiB
Plaintext
29 lines
1.2 KiB
Plaintext
#This is a sample file distributed with Galaxy that enables tools
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#to use a directory of Samtools indexed sequences data files. You will need
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#to create these data files and then create a sam_fa_indices.loc file
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#similar to this one (store it in this directory) that points to
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#the directories in which those files are stored. The sam_fa_indices.loc
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#file has this format (white space characters are TAB characters):
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#
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#index <seq> <location>
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#
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#So, for example, if you had hg18 indexed stored in
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#/depot/data2/galaxy/sam/,
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#then the sam_fa_indices.loc entry would look like this:
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#
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#index hg18 /depot/data2/galaxy/sam/hg18.fa
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#
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#and your /depot/data2/galaxy/sam/ directory
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#would contain hg18.fa and hg18.fa.fai files:
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#
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#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.fa
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#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.fa.fai
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#
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#Your sam_fa_indices.loc file should include an entry per line for
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#each index set you have stored. The file in the path does actually
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#exist, but it should never be directly used. Instead, the name serves
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#as a prefix for the index file. For example:
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#
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#index hg18 /depot/data2/galaxy/sam/hg18.fa
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#index hg19 /depot/data2/galaxy/sam/hg19.fa
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