[3] | 1 | #This is a sample file distributed with Galaxy that enables tools |
---|
| 2 | #to use a directory of SRMA indexed sequences data files. You will need |
---|
| 3 | #to create these data files and then create a srma_index.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 srma_index.loc |
---|
| 6 | #file has this format (white space is the TAB character): |
---|
| 7 | # |
---|
| 8 | #<build> <fasta_file> |
---|
| 9 | # |
---|
| 10 | #So, for example, if you had hg18 indexed and stored in |
---|
| 11 | #/depot/data2/galaxy/srma/hg18/, |
---|
| 12 | #then the srma_index.loc entry would look like this: |
---|
| 13 | # |
---|
| 14 | #hg18 /depot/data2/galaxy/srma/hg18/hg18.fa |
---|
| 15 | # |
---|
| 16 | #and your /depot/data2/galaxy/srma/hg18/ directory |
---|
| 17 | #would contain the following three files: |
---|
| 18 | #hg18.fa |
---|
| 19 | #hg18.dict |
---|
| 20 | #hg18.fa.fai |
---|
| 21 | # |
---|
| 22 | #The dictionary file for each reference (ex. hg18.dict) must be |
---|
| 23 | #created via Picard (http://picard.sourceforge.net). Note that |
---|
| 24 | #the dict file does not have the .fa extension although the |
---|
| 25 | #path list in the loc file does include it. |
---|