/tool-data/alignseq.loc.sample

https://bitbucket.org/cistrome/cistrome-harvard/ · Unknown · 57 lines · 57 code · 0 blank · 0 comment · 0 complexity · 5ebae2e2bd9b9eb29cbf3c9a6214e68b MD5 · raw file 

    

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

  2. #to use alignment data stored as axt files (lines starting with "align")
    3. 

  3. #or nib files (lines starting with "seq").  You will need to index 
    4. 

  4. #them and then create an alignseq.loc file similar to this one (store
    5. 

  5. #it in this directory) that points to the directories in which those 
    6. 

  6. #alignments are stored.  The "align" data referred to by the alignseq.loc 
    7. 

  7. #file has this format (white space characters are TAB characters):
    8. 

  8. #
    9. 

  9. #align	<build1>	<build2>	<dir>
    10. 

  10. #
    11. 

  11. #So, for example, if you had hg18/bosTau2 alignment files stored in 
    12. 

  12. #/depot/data2/galaxy/hg18/align/bosTau2, then the alignseq.loc entry 
    13. 

  13. #would look like this:
    14. 

  14. #
    15. 

  15. #align	hg18	bosTau2	/depot/data2/galaxy/hg18/align/bosTau2
    16. 

  16. #
    17. 

  17. #and your /depot/data2/galaxy/hg18/align/bosTau2 directory would 
    18. 

  18. #contain all of your alignment files (e.g.):
    19. 

  19. #
    20. 

  20. #-rw-rw-r--   1 nate   galaxy 151842783 2006-01-08 01:00 chr10.axt
    21. 

  21. #-rw-rw-r--   1 nate   galaxy     79575 2006-01-08 01:00 chr10_random.axt
    22. 

  22. #-rw-rw-r--   1 nate   galaxy 155015634 2006-01-08 01:01 chr11.axt
    23. 

  23. #...etc...
    24. 

  24. #
    25. 

  25. #Your alignseq.loc file should include an entry per line for each alignment 
    26. 

  26. #file you have stored.  For example:
    27. 

  27. #
    28. 

  28. #align anoGam1 dm1 /depot/data2/galaxy/anoGam1/align/dm1
    29. 

  29. #align anoGam1 dm2 /depot/data2/galaxy/anoGam1/align/dm2
    30. 

  30. #align canFam1 hg17 /depot/data2/galaxy/canFam1/align/hg17
    31. 

  31. #...etc...
    32. 

  32. #
    33. 

  33. #The "seq" data referred to by the alignseq.loc file has this 
    34. 

  34. #format (white space characters are TAB characters):
    35. 

  35. #
    36. 

  36. #seq	<build1>	<dir>
    37. 

  37. #
    38. 

  38. #So, for example, if you had anoGam1 sequence files stored in
    39. 

  39. #/depot/data2/galaxy/anoGam1/seq, then the alignseq.loc entry
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  40. #would look like this:
    41. 

  41. #
    42. 

  42. #seq anoGam1 /depot/data2/galaxy/anoGam1/seq
    43. 

  43. #and your seq anoGam1 /depot/data2/galaxy/anoGam1/seq directory would
    44. 

  44. #contain all of your sequence files (e.g.):
    45. 

  45. #
    46. 

  46. #-rw-rw-r-- 1 nate galaxy 24397551 2006-06-26 12:51 chr2L.nib
    47. 

  47. #-rw-rw-r-- 1 nate galaxy 31362964 2006-06-26 12:51 chr2R.nib
    48. 

  48. #-rw-rw-r-- 1 nate galaxy 20642013 2006-06-26 12:51 chr3L.nib
    49. 

  49. #-rw-rw-r-- 1 nate galaxy 26636071 2006-06-26 12:51 chr3R.nib
    50. 

  50. #
    51. 

  51. #Your alignseq.loc file should include an entry per line for each sequence
    52. 

  52. #file you have stored.  For example:
    53. 

  53. #
    54. 

  54. #seq anoGam1 /depot/data2/galaxy/anoGam1/seq
    55. 

  55. #seq bosTau2 /depot/data2/galaxy/bosTau2/seq
    56. 

  56. #seq bosTau3 /depot/data2/galaxy/bosTau3/seq
    57. 

  57. #...etc...
    58.