setup.py imports

[jjfarrell]

Both cython and pysam are part of the dependency list of required modules to be installed. So are not needed as import statements in the setup.py. An error occurs since they are not installed yet.

from setuptools import setup, find_packages
from Cython.Build import cythonize
import pysam

setup(
    name='svtk',
    version='0.1',
    description='Structural variation toolkit',
    author='Matthew Stone',
    author_email='mstone5@mgh.harvard.edu',
    packages=find_packages(),
    package_data={'svtk': ['data/*_template.vcf']},
    scripts=['scripts/svtk'],
    ext_modules=cythonize('svtk/utils/helpers.pyx'),
    include_dirs=pysam.get_include(),
    install_requires=[
        'numpy',
        'scipy',
        'pysam>=0.11.2.2',
        'pybedtools',
        'cython',
        'natsort',
        'boto3',
        'pandas',
    ]
)