/tool-data/binned_scores.loc.sample

https://bitbucket.org/cistrome/cistrome-harvard/ · Unknown · 37 lines · 37 code · 0 blank · 0 comment · 0 complexity · 3b09ee85b9c0f3fdd8432af2415909a9 MD5 · raw file 

    

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

  2. #to use a directory of FileBinnedArray data files.  You will need
    3. 

  3. #to create these data files and then create a binned_scores.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 binned_scores.loc 
    6. 

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

  7. #
    8. 

  8. #<build>	<description>	<dir>
    9. 

  9. #
    10. 

  10. #So, for example, if you had hg16 ENCODE binCons on MLAGAN alignments
    11. 

  11. #stored in /depot/data2/galaxy/binned_scores/hg16/encode_bincons_lagan, 
    12. 

  12. #then the binned_scores.loc entry would look like this:
    13. 

  13. #
    14. 

  14. #hg16    ENCODE binCons on MLAGAN alignments     /depot/data2/galaxy/binned_scores/hg16/encode_bincons_lagan
    15. 

  15. #
    16. 

  16. #and your /depot/data2/galaxy/binned_scores/hg16/encode_bincons_lagan
    17. 

  17. #directory would contain all of your "binned" files (e.g.):
    18. 

  18. #
    19. 

  19. #-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 ENm001
    20. 

  20. #-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 ENm002
    21. 

  21. #-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 ENm003
    22. 

  22. #...etc...
    23. 

  23. #
    24. 

  24. #Your binned_scores.loc file should include an entry per line for each
    25. 

  25. #"binned" file you have stored.  For example:
    26. 

  26. #
    27. 

  27. #hg16	ENCODE binCons on MLAGAN alignments	/depot/data2/galaxy/binned_scores/hg16/encode_bincons_lagan
    28. 

  28. #hg16	ENCODE binCons on TBA alignments	/depot/data2/galaxy/binned_scores/hg16/encode_bincons_tba
    29. 

  29. #hg16	ENCODE GERP on MLAGAN alignment	/depot/data2/galaxy/binned_scores/hg16/encode_gerp_lagan
    30. 

  30. #hg16	ENCODE GERP on TBA alignment	/depot/data2/galaxy/binned_scores/hg16/encode_gerp_tba
    31. 

  31. #hg16	ENCODE phastCons on MLAGAN alignment	/depot/data2/galaxy/binned_scores/hg16/encode_phastcons_lagan
    32. 

  32. #hg16	ENCODE phastCons on TBA alignment	/depot/data2/galaxy/binned_scores/hg16/encode_phatcons_tba
    33. 

  33. #hg17	ENCODE phastCons on TBA alignment	/depot/data2/galaxy/binned_scores/hg17/phastcons_encode_sep2005_tba
    34. 

  34. #hg17	phastCons on 8-species multiz, 16-Jun-2005	/depot/data2/galaxy/binned_scores/hg17/phastcons_mzPt1Mm5Rn3Cf1Gg2Fr1Dr1/
    35. 

  35. #hg17	phastCons on 17-species multiz, 13-Apr-2006	/depot/data2/galaxy/binned_scores/hg17/phastCons17way/ba
    36. 

  36. #hg17	ESPERR Regulatory Potential, 7-species, 23-Jun-2006	/depot/data2/galaxy/binned_scores/hg17/esperr_rp_7way/ba
    37. 

  37. #hg18	phastCons on 17-species multiz, 06-Apr-2006	/depot/data2/galaxy/binned_scores/hg18/phastCons17way/ba
    38.