old_contents: from setuptools import setup
  
  import species_separator
  
  setup(
      name="species_separator",
      version=species_separator.__version__,
      url='https://github.com/lweasel/species-separator',
      license='MIT License',
      author='TODO',
      author_email='TODO',
      packages=['species_separator'],
      install_requires=[
          'docopt==0.6.2',
          'pysam==0.8.2.1',
          'schema==0.3.1',
      ],
      scripts=[
          'bin/build_star_index',
          'bin/collate_raw_reads',
          'bin/filter_sample_reads',
          'bin/filter_reads',
          'bin/map_reads',
          'bin/sort_reads',
      ]
  )
  
new_contents: from setuptools import setup
  
  import species_separator
  
  setup(
      name="species_separator",
      version=species_separator.__version__,
      url='https://github.com/lweasel/species-separator',
      license='MIT License',
      author='TODO',
      author_email='TODO',
      packages=['species_separator'],
      install_requires=[
          'docopt==0.6.2',
          'pysam==0.8.2.1',
          'schema==0.3.1',
      ],
      scripts=[
          'bin/build_star_index',
          'bin/collate_raw_reads',
          'bin/filter_control',
          'bin/filter_reads',
          'bin/filter_sample_reads',
          'bin/filter_reads_parallel',
          'bin/map_reads',
          'bin/sort_reads',
      ]
  )
  
subject: Add missing scripts to setup.py.