old_contents: import ez_setup
  ez_setup.use_setuptools()
  
  import glob
  import os
  import sys
  from setuptools import setup
  from distutils.extension import Extension
  
  if 'setuptools.extension' in sys.modules:
      m = sys.modules['setuptools.extension']
      m.Extension.__dict__ = m._Extension.__dict__
  
  version_py = os.path.join(os.path.dirname(__file__), 'gemini', 'version.py')
  version = open(version_py).read().strip().split('=')[-1].replace('"','')
  long_description = """
  ``gemini`` is a database framework for exploring genetic variation'
  """
  
  setup(
          name="gemini",
          version=version,
          install_requires=['numpy>=1.6.0', 'pyparsing>=1.5.6', 
                            'pysam>=0.6', 'cyvcf>=0.1.3', 
                            'PyYAML >= 3.10', 'pybedtools>=0.6.1',
                            'python-graph-core >= 1.8.2'],
          dependency_links = ['http://github.com/arq5x/cyvcf/tarball/master#egg=cyvcf-0.1.3'],
          requires = ['python (>=2.5, <3.0)'],
          packages=['gemini',
                    'gemini.scripts',
                    'gemini.data'],
          author="Aaron Quinlan and Uma Paila",
          description='A database framework for exploring genetic variation',
          long_description=long_description,
          url="none",
          package_dir = {'gemini': "gemini"},
          package_data = {'gemini': ['data/gemini.conf']},
          zip_safe = False,
          scripts = ['gemini/scripts/gemini'],
          author_email="arq5x@virginia.edu",
          classifiers=[
              'Development Status :: 4 - Beta',
              'Intended Audience :: Science/Research',
              'License :: OSI Approved :: GNU General Public License (GPL)',
              'Topic :: Scientific/Engineering :: Bio-Informatics']
      )
  
new_contents: import ez_setup
  ez_setup.use_setuptools()
  
  import glob
  import os
  import sys
  from setuptools import setup
  from distutils.extension import Extension
  
  if 'setuptools.extension' in sys.modules:
      m = sys.modules['setuptools.extension']
      m.Extension.__dict__ = m._Extension.__dict__
  
  version_py = os.path.join(os.path.dirname(__file__), 'gemini', 'version.py')
  version = open(version_py).read().strip().split('=')[-1].replace('"','')
  long_description = """
  ``gemini`` is a database framework for exploring genetic variation'
  """
  
  setup(
          name="gemini",
          version=version,
          install_requires=['numpy>=1.6.0', 'pyparsing>=1.5.6', 
                            'pysam>=0.6', 'cyvcf>=0.1.3', 
                            'PyYAML >= 3.10', 'pybedtools>=0.6.1',
                            'python-graph-core >= 1.8.2',
                            'python-graph-dot >= 1.8.2'],
          dependency_links = ['http://github.com/arq5x/cyvcf/tarball/master#egg=cyvcf-0.1.3'],
          requires = ['python (>=2.5, <3.0)'],
          packages=['gemini',
                    'gemini.scripts',
                    'gemini.data'],
          author="Aaron Quinlan and Uma Paila",
          description='A database framework for exploring genetic variation',
          long_description=long_description,
          url="none",
          package_dir = {'gemini': "gemini"},
          package_data = {'gemini': ['data/gemini.conf']},
          zip_safe = False,
          scripts = ['gemini/scripts/gemini'],
          author_email="arq5x@virginia.edu",
          classifiers=[
              'Development Status :: 4 - Beta',
              'Intended Audience :: Science/Research',
              'License :: OSI Approved :: GNU General Public License (GPL)',
              'Topic :: Scientific/Engineering :: Bio-Informatics']
      )
  
subject: add dependency for python-graph-dot