old_contents: """Description
  
  Setup script to install RnaChipIntegrator: analyses of peak data with
  genomic feature data
  
  Copyright (C) University of Manchester 2011-19 Peter Briggs, Ian Donaldson, Leo Zeef
  
  """
  
  from setuptools import setup
  import rnachipintegrator
  
  # Package version
  version = rnachipintegrator.get_version()
  
  download_url = 'https://github.com/fls-bioinformatics-core/RnaChipIntegrator/archive/v' + version + '.tar.gz'
  
  # Hack to acquire all scripts that we want to
  # install into 'bin'
  from glob import glob
  scripts = []
  for pattern in ('bin/*.py',):
      scripts.extend(glob(pattern))
  
  # Setup for installation etc
  setup(
      name = "RnaChipIntegrator",
      version = version,
      description = "Analyse genes against peak data, and vice versa",
      url = 'https://github.com/fls-bioinformatics-core/RnaChipIntegrator',
      download_url = download_url,
      author = 'Peter Briggs, Ian Donaldson, Leo Zeef',
      author_email = 'peter.briggs@manchester.ac.uk',
      maintainer = 'Peter Briggs',
      maintainer_email = 'peter.briggs@manchester.ac.uk',
      packages = ['rnachipintegrator'],
      entry_points = { 'console_scripts': [
          'RnaChipIntegrator = rnachipintegrator.cli:main',]
      },
      license = 'Artistic License',
      keywords = ['RnaChipIntegrator',],
      classifiers=[
          'Development Status :: 3 - Alpha',
          'Intended Audience :: Science/Research',
          'Environment :: Console',
          'License :: OSI Approved :: Artistic License',
          'Operating System :: POSIX',
          'Topic :: Scientific/Engineering :: Bio-Informatics',
          'Natural Language :: English',
          "Programming Language :: Python :: 2",
          'Programming Language :: Python :: 2.7',
          "Programming Language :: Python :: 3",
          'Programming Language :: Python :: 3.5',
          'Programming Language :: Python :: 3.6',
          'Programming Language :: Python :: 3.7',
      ],
      install_requires = ['xlsxwriter >= 0.8.4',],
      test_suite = 'nose.collector',
      tests_require = ['nose'],
      scripts = scripts,
      data_files = [ ('RnaChipIntegrator',
                      ['README.rst',
                       'LICENSE',
                       'INSTALL',
                       'CHANGELOG.rst']),],
      include_package_data=True,
      zip_safe = False
  )
  
new_contents: """Description
  
  Setup script to install RnaChipIntegrator: analyses of peak data with
  genomic feature data
  
  Copyright (C) University of Manchester 2011-20 Peter Briggs, Ian Donaldson, Leo Zeef
  
  """
  
  from setuptools import setup
  import rnachipintegrator
  
  # Package version
  version = rnachipintegrator.get_version()
  
  download_url = 'https://github.com/fls-bioinformatics-core/RnaChipIntegrator/archive/v' + version + '.tar.gz'
  
  with open('README.rst') as fh:
      readme = fh.read()
  
  # Hack to acquire all scripts that we want to
  # install into 'bin'
  from glob import glob
  scripts = []
  for pattern in ('bin/*.py',):
      scripts.extend(glob(pattern))
  
  # Setup for installation etc
  setup(
      name = "RnaChipIntegrator",
      version = version,
      description = "Analyse genes against peak data, and vice versa",
      long_description = readme,
      url = 'https://github.com/fls-bioinformatics-core/RnaChipIntegrator',
      download_url = download_url,
      author = 'Peter Briggs, Ian Donaldson, Leo Zeef',
      author_email = 'peter.briggs@manchester.ac.uk',
      maintainer = 'Peter Briggs',
      maintainer_email = 'peter.briggs@manchester.ac.uk',
      packages = ['rnachipintegrator'],
      entry_points = { 'console_scripts': [
          'RnaChipIntegrator = rnachipintegrator.cli:main',]
      },
      license = 'Artistic License',
      keywords = ['RnaChipIntegrator',],
      classifiers=[
          'Development Status :: 3 - Alpha',
          'Intended Audience :: Science/Research',
          'Environment :: Console',
          'License :: OSI Approved :: Artistic License',
          'Operating System :: POSIX',
          'Topic :: Scientific/Engineering :: Bio-Informatics',
          'Natural Language :: English',
          "Programming Language :: Python :: 2",
          'Programming Language :: Python :: 2.7',
          "Programming Language :: Python :: 3",
          'Programming Language :: Python :: 3.5',
          'Programming Language :: Python :: 3.6',
          'Programming Language :: Python :: 3.7',
      ],
      install_requires = ['xlsxwriter >= 0.8.4',],
      test_suite = 'nose.collector',
      tests_require = ['nose'],
      scripts = scripts,
      data_files = [ ('RnaChipIntegrator',
                      ['README.rst',
                       'LICENSE',
                       'INSTALL',
                       'CHANGELOG.rst']),],
      include_package_data=True,
      zip_safe = False
  )
  
subject: Update setup.py to use the contents of README.rst as the 'long description'.