/tool-data/sequence_index_base.loc.sample

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

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

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

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

  7. #
    8. 

  8. #<build>	<file_base>
    9. 

  9. #
    10. 

  10. #So, for example, if you had phiX indexed stored in 
    11. 

  11. #/depot/data2/galaxy/phiX/base/, 
    12. 

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

  13. #
    14. 

  14. #phiX	/depot/data2/galaxy/phiX/base/phiX.fa
    15. 

  15. #
    16. 

  16. #and your /depot/data2/galaxy/phiX/base/ directory
    17. 

  17. #would contain phiX.fa.* files:
    18. 

  18. #
    19. 

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

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

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

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

  23. #
    24. 

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

  25. #each index set you have stored.  The "file" in the path does not actually
    26. 

  26. #exist, but it is the prefix for the actual index files.  For example:
    27. 

  27. #
    28. 

  28. #phiX	/depot/data2/galaxy/phiX/base/phiX.fa
    29. 

  29. #hg18	/depot/data2/galaxy/hg18/base/hg18.fa
    30.