/tool-data/perm_base_index.loc.sample

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  1. #This is a sample file distributed with Galaxy that enables tools to
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  2. #use a directory of PerM indexed sequences data files. You will need
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  3. #to create these data files and then create a perm_base_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 perm_base_index.loc 
    6. 

  6. #file has this format (white space characters are TAB characters):
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  7. #
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  8. #<build_seed_readlength>	<file_base>
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  9. #
    10. 

  10. #Because each PerM index is built with a specific seed and a specific read
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  11. #length, this needs to be specified so the user can choose the appropriate
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  12. #one. So, for example, if you had phiX indexed with seed F3 and read length 
    13. 

  13. #50, and stored in /depot/data/galaxy/phiX/perm_index/,
    14. 

  14. #then the perm_base_index.loc entry would look something like this:
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  15. #
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  16. #phiX_F3_50	/depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index
    17. 

  17. #
    18. 

  18. #and your /depot/data/galaxy/phiX/perm_index/ directory
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  19. #would contain the file phiX_base_F3_50.index:
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  20. #
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  21. #Your perm_base_index.loc file should include an entry per line for each
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  22. #index set you have stored. For example:
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  23. #
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  24. #phiX_F3_50	/depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index
    25. 

  25. #phiX_F4_50	/depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index
    26. 

  26. #hg19_F3_50	/depot/data/galaxy/hg19/perm_index/hg19_base_F3_50.index
    27. 

  27. #hg19_F4_50	/depot/data/galaxy/hg19/perm_index/hg19_base_F3_50.index
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