/tool-data/bwa_index.loc.sample

https://bitbucket.org/cistrome/cistrome-harvard/ · Unknown · 38 lines · 38 code · 0 blank · 0 comment · 0 complexity · 5b5e34001be54ae293fcea6eb9562a0b MD5 · raw file

  1. #This is a sample file distributed with Galaxy that enables tools
  2. #to use a directory of BWA indexed sequences data files. You will need
  3. #to create these data files and then create a bwa_index.loc file
  4. #similar to this one (store it in this directory) that points to
  5. #the directories in which those files are stored. The bwa_index.loc
  6. #file has this format (longer white space characters are TAB characters):
  7. #
  8. #<unique_build_id> <dbkey> <display_name> <file_path>
  9. #
  10. #So, for example, if you had phiX indexed stored in
  11. #/depot/data2/galaxy/phiX/base/,
  12. #then the bwa_index.loc entry would look like this:
  13. #
  14. #phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa
  15. #
  16. #and your /depot/data2/galaxy/phiX/base/ directory
  17. #would contain phiX.fa.* files:
  18. #
  19. #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb
  20. #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann
  21. #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt
  22. #...etc...
  23. #
  24. #Your bwa_index.loc file should include an entry per line for each
  25. #index set you have stored. The "file" in the path does not actually
  26. #exist, but it is the prefix for the actual index files. For example:
  27. #
  28. #phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa
  29. #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa
  30. #hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa
  31. #/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa
  32. #...etc...
  33. #
  34. #Note that for backwards compatibility with workflows, the unique ID of
  35. #an entry must be the path that was in the original loc file, because that
  36. #is the value stored in the workflow for that parameter. That is why the
  37. #hg19 entry above looks odd. New genomes can be better-looking.
  38. #