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test_multiplefit.py

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  • setup.py 1.47 KiB
    from setuptools import setup, find_packages
    from glob import glob
    # If you have .pyx things to cythonize
    from distutils.extension import Extension
    from Cython.Build import cythonize
    from pybedtools.helpers import get_includes as pybedtools_get_includes
    from pysam import get_include as pysam_get_include
    
    name = "bam25prime"
    __version__ = "0.1"
    
    # https://github.com/cython/cython/blob/master/docs/src/reference/compilation.rst#configuring-the-c-build
    extensions = [
        Extension(
            "bam25prime.libcollapsesam", ["bam25prime/libcollapsesam.pyx"],
            include_dirs=pysam_get_include()),
        Extension(
            "bam25prime.libcollapsebed", ["bam25prime/libcollapsebed.pyx"],
            include_dirs=glob("/home/bli/src/bedtools2-2.27.1/src/utils/*"),
            #include_dirs=pybedtools_get_includes(),
            language="c++"),
        ]
    
    setup(
        name=name,
        version=__version__,
        description="Library providing utilities to collapse aligned segments"
                    "in a bam file to their 5-prime end.",
        author="Blaise Li",
        author_email="blaise.li@normalesup.org",
        license="MIT",
        packages=find_packages(),
        scripts=["bin/%s" % name],
        ext_modules = cythonize(extensions),
        #ext_modules = cythonize("bam25prime/libbam25prime.pyx", include_path=pysam_get_include()),
        install_requires=["pysam", "pybedtools"])
    # If you have .pyx things to cythonize
        #ext_modules = cythonize("libsmallrna/libsmallrna.pyx"),
        #install_requires=["cytoolz"],
        #zip_safe=False)