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bowmanjeffs / paprica

paprica - PAthway PRediction by phylogenetIC plAcement
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output directory #10

Closed bowmanjeffs closed 8 years ago

bowmanjeffs commented 8 years ago

You need to add an output directory in the next version so that the python scripts can be left in a central location. You can probably get away with os.getcwd - does this return the directory the script is in or the directory the script is called from?

bowmanjeffs commented 8 years ago

Ideally workflow should be changed so that:

  1. Scripts are left in a central location (genome_finder/bin)
  2. Central location is added to user's path
  3. Scripts look for included files in their current location, and input files and outputs in cwd.