from setuptools import setup, find_packages

setup(
      name='MetaSV',
      version='0.1-alpha',
      description='MetaSV: An accurate and integrative structural-variant caller for next generation sequencing',
      author='Bina Technologies',
      author_email='rd@bina.com',
      url='https://github.com/bioinform/metasv',
      packages = find_packages(),
      install_requires = ["cython", "pysam==0.7.7", "pybedtools", "pyvcf"],
      package_data = {"metasv": ["resources/*"]},
      scripts=['scripts/run_metasv.py']
      )

from setuptools import setup, find_packages

setup(
      name='MetaSV',
      version='0.1-alpha',
      description='MetaSV: An accurate and integrative structural-variant caller for next generation sequencing',
      author='Bina Technologies',
      author_email='rd@bina.com',
      url='https://github.com/bioinform/metasv',
      packages = find_packages(),
      install_requires = ["cython", "pysam==0.7.7", "pybedtools", "pyvcf"],
      package_data = {"metasv": ["resources/*"]},
      scripts=['scripts/run_metasv.py', 'scripts/svtool_to_vcf.py'],
      dependency_links = ["https://pypi.python.org/packages/source/p/pysam/pysam-0.7.7.tar.gz"]
      )

Add another script in install and add a dependency link for pysam