old_contents: #!/usr/bin/env python
  
  from setuptools import setup
  
  setup(
      name='TEBreak',
      version='0.0.1',
      author='Adam Ewing',
      author_email='adamewing@gmail.com',
      description=("Insertion finder for high throughput sequence data"),
      license='MIT',
      url='https://github.com/adamewing/tebreak',
      packages=['tebreak'],
      install_requires = [
          'pysam>=0.8.1',
          'bx-python>=0.5.0',
          'scipy>=0.14.0',
          'numpy>=1.9.0',
      ],
  
  )
  
  
  
new_contents: #!/usr/bin/env python
  
  from setuptools import setup
  
  setup(
      name='TEBreak',
      version='0.0.1',
      author='Adam Ewing',
      author_email='adamewing@gmail.com',
      description=("Insertion finder for high throughput sequence data"),
      license='MIT',
      url='https://github.com/adamewing/tebreak',
      packages=['tebreak'],
      install_requires = [
          'pysam>=0.8.1',
          'bx-python>=0.5.0',
          'scipy>=0.14.0',
          'numpy>=1.9.0',
          'align>=0.1',
      ],
      dependency_links = [
          'git+ssh://git@github.com:adamewing/align.git#egg=align-0.1'
      ],
  
  )
  
  
  
subject: add align to setup