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/tool-data/sequence_index_color.loc.sample

https://bitbucket.org/cistrome/cistrome-harvard/
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  1. #This is a sample file distributed with Galaxy that enables tools
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  2. #to use a directory of BWA indexed sequences data files.  You will need
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  3. #to create these data files and then create a sequence_index_color.loc file 
    4. 

  4. #similar to this one (store it in this directory) that points to 
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  5. #the directories in which those files are stored. The sequence_index_color.loc 
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  6. #file has this format (white space characters are TAB characters):
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  7. #
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  8. #<build>	<file_base>
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  9. #
    10. 

  10. #So, for example, if you had phiX indexed stored in 
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  11. #/depot/data2/galaxy/phiX/color/, 
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  12. #then the sequence_index_color.loc entry would look like this:
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  13. #
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  14. #phiX	/depot/data2/galaxy/phiX/color/phiX.fa
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  15. #
    16. 

  16. #and your /depot/data2/galaxy/phiX/color/ directory
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  17. #would contain phiX.fa.* files:
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  18. #
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  19. #-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 phiX.fa.amb
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  20. #-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 phiX.fa.ann
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  21. #-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 phiX.fa.bwt
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  22. #...etc...
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  23. #
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  24. #Your sequence_index_color.loc file should include an entry per line for 
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  25. #each index set you have stored.  The "file" in the path does not actually
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  26. #exist, but it is the prefix for the actual index files.  For example:
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  27. #
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  28. #phiX	/depot/data2/galaxy/phiX/color/phiX.fa
    29. 

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