old_contents: """Description
  
  Setup script to install RnaChipIntegrator: analyses of ChIP-Seq and RNA-Seq data
  
  Copyright (C) University of Manchester 2011-12 Peter Briggs, Leo Zeef & Ian Donaldson
  
  This code is free software; you can redistribute it and/or modify it
  under the terms of the Artistic License 2.0 (see the file LICENSE included
  with the distribution).
  
  This will install RnaChipIntegrator and its dependencies and provide the
  'RnaChipIntegrator' command.
  """
  
  from setuptools import setup
  import RnaChipIntegrator
  setup(
      name = "RnaChipIntegrator",
      version = RnaChipIntegrator.__version__,
      maintainer = 'Peter Briggs',
      maintainer_email = 'peter.briggs@manchester.ac.uk',
      license = 'Artistic License 2.0',
      py_modules = ['RnaChipIntegrator','Spreadsheet'],
      install_requires = ['xlwt >= 0.7.2',
                          'xlrd >= 0.7.1',
                          'xlutils >= 1.4.1'],
      entry_points = { 'console_scripts':
                           ['RnaChipIntegrator = RnaChipIntegrator:main']
                       },
      data_files = [ ('RnaChipIntegrator', ['README.markdown',
                                            'LICENSE',
                                            'INSTALL',
                                            'ChangeLog']),
                     ('RnaChipIntegrator/doc', ['doc/README.markdown',
                                                'doc/rnachipintegrator_nearestEdgetoPeak.png',
                                                'doc/rnachipintegrator_nearestTSStoSummit.png',
                                                'doc/rnachipintegrator_nearestTSStoPeak.png']) ]
  )
  
new_contents: """Description
  
  Setup script to install RnaChipIntegrator: analyses of ChIP-Seq and RNA-Seq data
  
  Copyright (C) University of Manchester 2011-12 Peter Briggs, Leo Zeef & Ian Donaldson
  
  This code is free software; you can redistribute it and/or modify it
  under the terms of the Artistic License 2.0 (see the file LICENSE included
  with the distribution).
  
  This will install RnaChipIntegrator and its dependencies and provide the
  'RnaChipIntegrator' command.
  """
  
  from setuptools import setup
  import RnaChipIntegrator
  setup(
      name = "RnaChipIntegrator",
      version = RnaChipIntegrator.__version__,
      maintainer = 'Peter Briggs',
      maintainer_email = 'peter.briggs@manchester.ac.uk',
      license = 'Artistic License 2.0',
      py_modules = ['RnaChipIntegrator','Spreadsheet'],
      install_requires = ['xlwt >= 0.7.2',
                          'xlrd >= 0.7.1',
                          'xlutils >= 1.4.1'],
      entry_points = { 'console_scripts':
                           ['RnaChipIntegrator = RnaChipIntegrator:main']
                       },
      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']) ]
  )
  
subject: update doc/README to doc/MANUAL.