/tool-data/picard_index.loc.sample

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  1. #This is a sample file distributed with Galaxy that enables tools
    2. 

  2. #to use a directory of Picard dict and associated files. You will need
    3. 

  3. #to create these data files and then create a picard_index.loc file 
    4. 

  4. #similar to this one (store it in this directory) that points to 
    5. 

  5. #the directories in which those files are stored. The picard_index.loc 
    6. 

  6. #file has this format (longer white space is the TAB character):
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  7. #
    8. 

  8. #<unique_build_id>		<dbkey>		<display_name>		<fasta_file_path>
    9. 

  9. #
    10. 

  10. #So, for example, if you had hg18 indexed and stored in 
    11. 

  11. #/depot/data2/galaxy/srma/hg18/, 
    12. 

  12. #then the srma_index.loc entry would look like this:
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  13. #
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  14. #hg18	hg18	hg18 Pretty		/depot/data2/galaxy/picard/hg18/hg18.fa
    15. 

  15. #
    16. 

  16. #and your /depot/data2/galaxy/srma/hg18/ directory
    17. 

  17. #would contain the following three files:
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  18. #hg18.fa
    19. 

  19. #hg18.dict
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  20. #hg18.fa.fai
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  21. #
    22. 

  22. #The dictionary file for each reference (ex. hg18.dict) must be 
    23. 

  23. #created via Picard (http://picard.sourceforge.net). Note that
    24. 

  24. #the dict file does not have the .fa extension although the
    25. 

  25. #path list in the loc file does include it.
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  26. #
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