old_contents: """Description
  
  Setup script to install RnaChipIntegrator: analyses of ChIP-Seq and RNA-Seq data
  
  Copyright (C) University of Manchester 2011-15 Peter Briggs, Leo Zeef &
  Ian Donaldson
  
  """
  
  # 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
  from setuptools import setup
  import rnachipintegrator
  setup(
      name = "RnaChipIntegrator",
      version = rnachipintegrator.get_version(),
      description = "Integrate genomic features with expression data",
      long_description = """
  Utility for integrating sets of genomic features (e.g. canonical genes,
  CpG islands) with expression data.
  """,
      url = 'https://github.com/fls-bioinformatics-core/RnaChipIntegrator',
      maintainer = 'Peter Briggs',
      maintainer_email = 'peter.briggs@manchester.ac.uk',
      packages = ['rnachipintegrator'],
      license = 'Artistic License',
      install_requires = ['xlwt >= 0.7.2',
                          'xlrd >= 0.7.1',
                          'xlutils >= 1.4.1'],
      test_suite = 'nose.collector',
      tests_require = ['nose'],
      scripts = scripts,
      data_files = [ ('RnaChipIntegrator',
                      ['README.markdown',
                       'LICENSE',
                       'INSTALL',
                       'ChangeLog']),
                     ('RnaChipIntegrator/doc',
                      ['doc/MANUAL.markdown',
                       'doc/rnachipintegrator_nearestEdgetoPeak.png',
                       'doc/rnachipintegrator_nearestTSStoSummit.png',
                       'doc/rnachipintegrator_nearestTSStoPeak.png']) ],
      include_package_data=True,
      zip_safe = False
  )
  
new_contents: """Description
  
  Setup script to install RnaChipIntegrator: analyses of ChIP-Seq and RNA-Seq data
  
  Copyright (C) University of Manchester 2011-15 Peter Briggs, Leo Zeef &
  Ian Donaldson
  
  """
  
  # 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
  from setuptools import setup
  import rnachipintegrator
  setup(
      name = "RnaChipIntegrator",
      version = rnachipintegrator.get_version(),
      description = "Integrate genomic features with expression data",
      long_description = """
  Utility for integrating sets of genomic features (e.g. canonical genes,
  CpG islands) with expression data.
  """,
      url = 'https://github.com/fls-bioinformatics-core/RnaChipIntegrator',
      maintainer = 'Peter Briggs',
      maintainer_email = 'peter.briggs@manchester.ac.uk',
      packages = ['rnachipintegrator'],
      license = 'Artistic License',
      install_requires = ['xlwt >= 0.7.2',
                          'xlrd >= 0.7.1',
                          'xlutils >= 1.4.1'],
      test_suite = 'nose.collector',
      tests_require = ['nose'],
      scripts = scripts,
      data_files = [ ('RnaChipIntegrator',
                      ['README.rst',
                       'LICENSE',
                       'INSTALL',
                       'ChangeLog']),],
      include_package_data=True,
      zip_safe = False
  )
  
subject: Update setup.py to match changes to README and docs.