old_contents: from setuptools import setup, find_packages
  from codecs import open
  from os import path
  
  
  # Get the long description from the relevant file
  here = path.abspath(path.dirname(__file__))
  with open(path.join(here, 'DESCRIPTION.rst'), encoding='utf-8') as f:
      long_description = f.read()
  
  
  setup(
      name = "pannenkoek",
        long_description=long_description,
      version = "0.1.8",
      packages = find_packages(),
      scripts = ['pannenkoek/pannenkoek.py', 'pannenkoek/lefse/format_input.py', 'pannenkoek/lefse/run_lefse.py'],
  
      # Project uses reStructuredText, so ensure that the
      # docutils get installed or upgraded on the target
      # machine
      install_requires = ['rpy2', 'numpy', 'matplotlib', 'argparse', 'pandas', 'biopython'],
  
      package_data = {
          # If any package contains *.txt or *.rst files,
          # include them:
          '': ['*.txt', '*.rst'],
          # And include any *.msg files found in the
          # 'hello' package, too:
          'hello': ['*.msg'],
      },
  
      # metadata for upload to PyPI
      author = "Thomas W. Battaglia",
      author_email = "tb1280@nyu.com",
      description = "A wrapper for Qiime and LEfSe analysis. Split an OTU table by time and make certain comparisons with ease.",
      license = "MIT",
      keywords = "Biology Microbiome LEFSE QIIME Formatting Diversity Python Bioinformatics",
  
      # project home page, if any :
      url = "https://github.com/twbattaglia/pannenkoek",
  
      # could also include long_description, download_url,
      # classifiers, etc.
  )
  
new_contents: from setuptools import setup, find_packages
  from codecs import open
  from os import path
  
  
  # Get the long description from the relevant file
  here = path.abspath(path.dirname(__file__))
  with open(path.join(here, 'DESCRIPTION.rst'), encoding='utf-8') as f:
      long_description = f.read()
  
  
  setup(
      name = "pannenkoek",
        long_description=long_description,
      version = "0.1.8",
      packages = find_packages(),
      scripts = ['pannenkoek/pannenkoek.py', 'pannenkoek/lefse/format_input.py', 'pannenkoek/lefse/run_lefse.py', 'pannenkoek/lefse/lefse.py', 'pannenkoek/pretty_lefse/prettylefse.R'],
  
      # Project uses reStructuredText, so ensure that the
      # docutils get installed or upgraded on the target
      # machine
      install_requires = ['rpy2', 'numpy', 'matplotlib', 'argparse', 'pandas', 'biopython'],
  
      package_data = {
          # If any package contains *.txt or *.rst files,
          # include them:
          '': ['*.txt', '*.rst'],
          # And include any *.msg files found in the
          # 'hello' package, too:
          'hello': ['*.msg'],
      },
  
      # metadata for upload to PyPI
      author = "Thomas W. Battaglia",
      author_email = "tb1280@nyu.com",
      description = "A wrapper for Qiime and LEfSe analysis. Split an OTU table by time and make certain comparisons with ease.",
      license = "MIT",
      keywords = "Biology Microbiome LEFSE QIIME Formatting Diversity Python Bioinformatics",
  
      # project home page, if any :
      url = "https://github.com/twbattaglia/pannenkoek",
  
      # could also include long_description, download_url,
      # classifiers, etc.
  )
  
subject: add pretty lease