Mercurial > repos > blankenberg > naive_variant_caller
comparison tool-data/sam_fa_indices.loc.sample @ 1:ae6edc0012ba
Populate naive_variant_caller repository.
| author | Daniel Blankenberg <dan@bx.psu.edu> |
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| date | Thu, 29 Aug 2013 10:54:14 -0400 |
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| 0:0fa83c466e9d | 1:ae6edc0012ba |
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| 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 |