Mercurial > repos > iuc > gatk2
comparison gatk2_picard_index.loc.sample @ 0:340633249b3d draft
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| author | bgruening |
|---|---|
| date | Mon, 02 Dec 2013 06:18:36 -0500 |
| parents | |
| children | 8bcc13094767 |
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| -1:000000000000 | 0:340633249b3d |
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| 1 #This is a sample file distributed with Galaxy that enables tools | |
| 2 #to use a directory of Picard dict and associated files. You will need | |
| 3 #to create these data files and then create a picard_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 picard_index.loc | |
| 6 #file has this format (longer white space is the TAB character): | |
| 7 # | |
| 8 #<unique_build_id> <dbkey> <display_name> <fasta_file_path> | |
| 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 hg18 hg18 Pretty /depot/data2/galaxy/picard/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. | |
| 26 # | |
| 27 hg18 hg18 hg18 /data/galaxy/ext-tool-data/picard/hg18.fa | |
| 28 hg19 hg19 hg19 /data/galaxy/ext-tool-data/picard/hg19.fa | |
| 29 mm8 mm8 mm8 /data/galaxy/ext-tool-data/picard/mm8.fa | |
| 30 mm9 mm9 mm9 /data/galaxy/ext-tool-data/picard/mm9.fa |