[2] | 1 | #This is a sample file distributed with Galaxy that enables tools |
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| 2 | #to use a directory of Samtools indexed sequences data files. You will need |
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| 3 | #to create these data files and then create a sam_fa_indices.loc file |
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| 4 | #similar to this one (store it in this directory) that points to |
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| 5 | #the directories in which those files are stored. The sam_fa_indices.loc |
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| 6 | #file has this format (white space characters are TAB characters): |
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| 7 | # |
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| 8 | #index <seq> <location> |
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| 9 | # |
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| 10 | #So, for example, if you had hg18 indexed stored in |
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| 11 | #/depot/data2/galaxy/sam/, |
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| 12 | #then the sam_fa_indices.loc entry would look like this: |
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| 13 | # |
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| 14 | #index hg18 /depot/data2/galaxy/sam/hg18.fa |
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| 15 | # |
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| 16 | #and your /depot/data2/galaxy/sam/ directory |
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| 17 | #would contain hg18.fa and hg18.fa.fai files: |
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| 18 | # |
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| 19 | #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.fa |
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| 20 | #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.fa.fai |
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| 21 | # |
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| 22 | #Your sam_fa_indices.loc file should include an entry per line for |
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| 23 | #each index set you have stored. The file in the path does actually |
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| 24 | #exist, but it should never be directly used. Instead, the name serves |
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| 25 | #as a prefix for the index file. For example: |
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| 26 | # |
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| 27 | #index hg18 /depot/data2/galaxy/sam/hg18.fa |
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| 28 | #index hg19 /depot/data2/galaxy/sam/hg19.fa |
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