/tool-data/sam_fa_indices.loc.sample

https://bitbucket.org/cistrome/cistrome-harvard/ · Unknown · 28 lines · 28 code · 0 blank · 0 comment · 0 complexity · 57b10cddd84cec4441eabafd133fee56 MD5 · raw file 

    

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

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

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

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

  7. #
    8. 

  8. #index	<seq>	<location>
    9. 

  9. #
    10. 

  10. #So, for example, if you had hg18 indexed stored in 
    11. 

  11. #/depot/data2/galaxy/sam/, 
    12. 

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

  13. #
    14. 

  14. #index	hg18	/depot/data2/galaxy/sam/hg18.fa
    15. 

  15. #
    16. 

  16. #and your /depot/data2/galaxy/sam/ directory
    17. 

  17. #would contain hg18.fa and hg18.fa.fai files:
    18. 

  18. #
    19. 

  19. #-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.fa
    20. 

  20. #-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.fa.fai
    21. 

  21. #
    22. 

  22. #Your sam_fa_indices.loc file should include an entry per line for 
    23. 

  23. #each index set you have stored.  The file in the path does actually
    24. 

  24. #exist, but it should never be directly used. Instead, the name serves
    25. 

  25. #as a prefix for the index file.  For example:
    26. 

  26. #
    27. 

  27. #index	hg18	/depot/data2/galaxy/sam/hg18.fa
    28. 

  28. #index	hg19	/depot/data2/galaxy/sam/hg19.fa
    29.