/tool-data/liftOver.loc.sample

https://bitbucket.org/cistrome/cistrome-harvard/ · Unknown · 27 lines · 27 code · 0 blank · 0 comment · 0 complexity · 9ea80002b0215c331103fafceeed679d MD5 · raw file 

    

  1. #This is a sample file distributed with Galaxy that is used by the
    2. 

  2. #liftOver tools.  The liftOver.loc file has this format (white space 
    3. 

  3. #characters are TAB characters):
    4. 

  4. #
    5. 

  5. #<FromSpecies>	<ToSpecies>	<PathToChainFile>
    6. 

  6. #
    7. 

  7. #So, for example, if you had the chain file to convert from anoCar1 to galGal3
    8. 

  8. #located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain, 
    9. 

  9. #then the liftOver.loc entry would look like this:
    10. 

  10. #
    11. 

  11. #anoCar1	galGal3		/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
    12. 

  12. #
    13. 

  13. #and your /depot/data2/galaxy/anoCar1/liftOver directory would 
    14. 

  14. #contain all of your "chain" files (e.g.):
    15. 

  15. #
    16. 

  16. #-rw-rw-r-- 1 gua110 galaxy 24046079 2008-01-16 14:20 anoCar1ToGalGal3.over.chain
    17. 

  17. #-rw-rw-r-- 1 gua110 galaxy 13216668 2008-01-16 14:20 anoCar1ToGasAcu1.over.chain
    18. 

  18. #-rw-rw-r-- 1 gua110 galaxy 29597067 2008-01-16 14:20 anoCar1ToHg18.over.chain
    19. 

  19. #...etc...
    20. 

  20. #
    21. 

  21. #Your liftOver.loc file should include an entry per line for each build you can
    22. 

  22. #convert.  For example:
    23. 

  23. #
    24. 

  24. #anoCar1	galGal3	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
    25. 

  25. #anoCar1	gasAcu1	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGasAcu1.over.chain
    26. 

  26. #anoCar1	hg18	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToHg18.over.chain
    27. 

  27. #...etc...
    28.