old_contents: import os
  from setuptools import setup, find_packages
  
  setup(
      name='Chunky',
      version='0.1.0',
      description='Pipeline design and distribution framework',
      author='Dominic Fitzgerald',
      author_email='dominicfitzgerald11@gmail.com',
      url='https://github.com/djf604/chunky',
      packages=find_packages(),
      entry_points={
          'console_scripts': ['chunky = chunky.util:execute_from_command_line']
      },
      classifiers=[
          'Development Status :: 3 - Alpha',
          'Environment :: Console',
          'Intended Audience :: Developers',
          'Intended Audience :: Science/Research',
          'Programming Language :: Python',
          'Programming Language :: Python :: 2.7',
          'Topic :: Scientific/Engineering',
          'Topic :: Scientific/Engineering :: Bio-Informatics',
          'Topic :: Software Development :: Libraries'
      ]
  )
  
  user_home = os.path.expanduser('~')
  if not os.path.exists(os.path.join(user_home, '.chunky')):
      os.mkdir(os.path.join(user_home, '.chunky'))
  if not os.path.exists(os.path.join(user_home, '.chunky', 'pipelines')):
      os.mkdir(os.path.join(user_home, '.chunky', 'pipelines'))
  os.mknod(os.path.join(user_home, '.chunky', 'pipelines', '__init__.py'), 0o644)
  if not os.path.exists(os.path.join(user_home, '.chunky', 'configs')):
      os.mkdir(os.path.join(user_home, '.chunky', 'configs'))
  
new_contents: import os
  from setuptools import setup, find_packages
  
  setup(
      name='Chunky',
      version='0.1.0',
      description='Pipeline design and distribution framework',
      author='Dominic Fitzgerald',
      author_email='dominicfitzgerald11@gmail.com',
      url='https://github.com/djf604/chunky',
      packages=find_packages(),
      entry_points={
          'console_scripts': ['chunky = chunky.util:execute_from_command_line']
      },
      classifiers=[
          'Development Status :: 3 - Alpha',
          'Environment :: Console',
          'Intended Audience :: Developers',
          'Intended Audience :: Science/Research',
          'Programming Language :: Python',
          'Programming Language :: Python :: 2.7',
          'Topic :: Scientific/Engineering',
          'Topic :: Scientific/Engineering :: Bio-Informatics',
          'Topic :: Software Development :: Libraries'
      ]
  )
  
  user_home = os.path.expanduser('~')
  if not os.path.exists(os.path.join(user_home, '.chunky')):
      os.mkdir(os.path.join(user_home, '.chunky'))
  if not os.path.exists(os.path.join(user_home, '.chunky', 'pipelines')):
      os.mkdir(os.path.join(user_home, '.chunky', 'pipelines'))
  if not os.path.isfile(os.path.join(user_home, '.chunky', 'piplines', '__init__.py')):
      os.mknod(os.path.join(user_home, '.chunky', 'pipelines', '__init__.py'), 0o644)
  if not os.path.exists(os.path.join(user_home, '.chunky', 'configs')):
      os.mkdir(os.path.join(user_home, '.chunky', 'configs'))
  
subject: Put a guard on making the __init__.py file