/tool-data/perm_base_index.loc.sample

https://bitbucket.org/cistrome/cistrome-harvard/ · Unknown · 27 lines · 27 code · 0 blank · 0 comment · 0 complexity · 7ed911660888aedacd2bb6096f5c6776 MD5 · raw file 

    

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

  2. #use a directory of PerM indexed sequences data files. You will need
    3. 

  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 (longer white space characters are TAB characters):
    7. 

  7. #
    8. 

  8. #<build_seed_readlength>	<display_name>		<file_base>
    9. 

  9. #
    10. 

  10. #Because each PerM index is built with a specific seed and a specific read
    11. 

  11. #length, this needs to be specified so the user can choose the appropriate
    12. 

  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:
    15. 

  15. #
    16. 

  16. #phiX_F3_50		phiX: seed=F3, read length=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
    19. 

  19. #would contain the file phiX_base_F3_50.index:
    20. 

  20. #
    21. 

  21. #Your perm_base_index.loc file should include an entry per line for each
    22. 

  22. #index set you have stored. For example:
    23. 

  23. #
    24. 

  24. #phiX_F3_50		phiX: seed=F3, read length=50	/data/galaxy/phiX/perm_index/phiX_base_F3_50.index
    25. 

  25. #phiX_F4_50		phiX: seed=F4, read length=50	/data/galaxy/phiX/perm_index/phiX_base_F3_50.index
    26. 

  26. #hg19_F3_50		hg19: seed=F3, read length=50	/data/galaxy/hg19/perm_index/hg19_base_F3_50.index
    27. 

  27. #hg19_F4_50		hg19: seed=F4, read length=50	/data/galaxy/hg19/perm_index/hg19_base_F3_50.index
    28.