old_contents: from setuptools import setup, find_packages
  
  version = "Unknown"
  for line in open("breakseq2/_version.py"):
      if line.startswith("__version__"):
          version = line.strip().split("=")[1].strip()
  
  print version
  setup(
        name='BreakSeq2',
        version=version,
        description='BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants',
        author='Bina Technologies',
        author_email='rd@bina.com',
        url='https://github.com/bioinform/breakseq2',
        packages = find_packages(),
        install_requires = ["cython", "pysam==0.7.7", "biopython==1.65"],
        scripts=['scripts/run_breakseq2.py'],
        dependency_links = ["https://pypi.python.org/packages/source/p/pysam/pysam-0.7.7.tar.gz"]
        )
  
new_contents: from setuptools import setup, find_packages
  
  version = "Unknown"
  for line in open("breakseq2/_version.py"):
      if line.startswith("__version__"):
          version = line.strip().split("=")[1].strip()
  
  print version
  setup(
        name='BreakSeq2',
        version=version,
        description='BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants',
        author='Bina Technologies',
        author_email='rd@bina.com',
        url='https://github.com/bioinform/breakseq2',
        packages = find_packages(),
        install_requires = ["cython", "pysam==0.7.7", "biopython==1.65"],
        scripts=['scripts/run_breakseq2.py', 'scripts/breakseq2_gen_bplib.py'],
        dependency_links = ["https://pypi.python.org/packages/source/p/pysam/pysam-0.7.7.tar.gz"]
        )
  
subject: add bplib generation script to top-level