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setup_w_cython.py
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setup_w_cython.py
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#!/usr/bin/env python
# Time-stamp: <2018-10-26 14:18:45 Tao Liu>
"""Description:
Setup script for MACS -- Model Based Analysis for ChIP-Seq data
Use this when you need Cython regenerate .c files.
Copyright (c) 2008,2009,2010,2011 Tao Liu <[email protected]>
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD License (see the file COPYING included with
the distribution).
@status: beta
@version: $Revision$
@author: Tao Liu
@contact: [email protected]
"""
import os
import sys
from setuptools import setup, Extension
# Use build_ext from Cython if found
command_classes = {}
try:
import Cython.Distutils
command_classes['build_ext'] = Cython.Distutils.build_ext
from Cython.Build import cythonize
has_cython = True
except:
has_cython = False
try:
from numpy import get_include as numpy_get_include
numpy_include_dir = [numpy_get_include()]
except:
numpy_include_dir = []
def main():
if float(sys.version[:3])<2.7 or float(sys.version[:3])>=2.8:
sys.stderr.write("CRITICAL: Python version must be 2.7!\n")
sys.exit(1)
# I intend to use -Ofast, however if gcc version < 4.6, this option is unavailable so...
extra_c_args = ["-w","-O3","-ffast-math"] # for C, -Ofast implies -O3 and -ffast-math
if has_cython:
ext_modules = [Extension("MACS2.Prob", ["MACS2/Prob.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
Extension("MACS2.IO.Parser",["MACS2/IO/Parser.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
Extension("MACS2.Pileup", ["MACS2/Pileup.pyx","MACS2/cPosValCalculation.pxd","MACS2/cPosValCalculation.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
Extension("MACS2.PeakModel", ["MACS2/PeakModel.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
Extension("MACS2.PeakDetect", ["MACS2/PeakDetect.pyx"], extra_compile_args=extra_c_args),
Extension("MACS2.Signal", ["MACS2/Signal.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
Extension("MACS2.IO.PeakIO", ["MACS2/IO/PeakIO.pyx"], extra_compile_args=extra_c_args),
Extension("MACS2.IO.BedGraphIO", ["MACS2/IO/BedGraphIO.pyx"], extra_compile_args=extra_c_args),
Extension("MACS2.IO.FixWidthTrack", ["MACS2/IO/FixWidthTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
Extension("MACS2.IO.PairedEndTrack", ["MACS2/IO/PairedEndTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
Extension("MACS2.IO.BedGraph", ["MACS2/IO/BedGraph.pyx"], libraries=["m"], extra_compile_args=extra_c_args),
Extension("MACS2.IO.ScoreTrack", ["MACS2/IO/ScoreTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
Extension("MACS2.IO.CallPeakUnit", ["MACS2/IO/CallPeakUnit.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
Extension("MACS2.hashtable", ["MACS2/hashtable.pyx"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=extra_c_args),
Extension("MACS2.Statistics", ["MACS2/Statistics.pyx"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=extra_c_args),
Extension("MACS2.ComputePileups", ["MACS2/ComputePileups.pyx"], extra_compile_args=extra_c_args),#added
Extension("MACS2.IO.PileupUnit", ["MACS2/IO/PileupUnit.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), #added
Extension("MACS2.IO.CallPeakUnitPrecompiled", ["MACS2/IO/CallPeakUnitPrecompiled.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),#added
]
else:
ext_modules = [Extension("MACS2.Prob", ["MACS2/Prob.c"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
Extension("MACS2.IO.Parser",["MACS2/IO/Parser.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
Extension("MACS2.Pileup", ["MACS2/Pileup.c","MACS2/cPosValCalculation.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
Extension("MACS2.PeakModel", ["MACS2/PeakModel.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
Extension("MACS2.PeakDetect", ["MACS2/PeakDetect.c"], extra_compile_args=extra_c_args),
Extension("MACS2.Signal", ["MACS2/Signal.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
Extension("MACS2.IO.PeakIO", ["MACS2/IO/PeakIO.c"], extra_compile_args=extra_c_args),
Extension("MACS2.IO.BedGraphIO", ["MACS2/IO/BedGraphIO.c"], extra_compile_args=extra_c_args),
Extension("MACS2.IO.FixWidthTrack", ["MACS2/IO/FixWidthTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
Extension("MACS2.IO.PairedEndTrack", ["MACS2/IO/PairedEndTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
Extension("MACS2.IO.BedGraph", ["MACS2/IO/BedGraph.c"], libraries=["m"], extra_compile_args=extra_c_args),
Extension("MACS2.IO.ScoreTrack", ["MACS2/IO/ScoreTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
Extension("MACS2.IO.CallPeakUnit", ["MACS2/IO/CallPeakUnit.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
Extension("MACS2.hashtable", ["MACS2/hashtable.c"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=extra_c_args),
Extension("MACS2.Statistics", ["MACS2/Statistics.c", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=extra_c_args),
Extension("MACS2.ComputePileups", ["MACS2/ComputePileups.c"], extra_compile_args=extra_c_args),#added
Extension("MACS2.IO.PileupUnit", ["MACS2/IO/PileupUnit.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), #added
Extension("MACS2.IO.CallPeakUnitPrecompiled", ["MACS2/IO/CallPeakUnitPrecompiled.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), #added
]
with open("README.md", "r") as fh:
long_description = fh.read()
setup(name="MACS2",
version="2.1.3",
description="Model Based Analysis for ChIP-Seq data",
long_description = long_description,
long_description_content_type="text/markdown",
author='Tao Liu',
author_email='[email protected]',
url='http://github.com/taoliu/MACS/',
package_dir={'MACS2' : 'MACS2'},
packages=['MACS2', 'MACS2.IO', 'MACS2.data'],
#package_data={'MACS2': ['data/*.dat']},
scripts=['bin/macs2',
],
classifiers=[
'Development Status :: 5 - Production/Stable',
'Environment :: Console',
'Intended Audience :: Developers',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: BSD License',
'Operating System :: MacOS :: MacOS X',
'Operating System :: POSIX',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'Programming Language :: Python :: 2 :: Only',
'Programming Language :: Cython',
],
install_requires=[
'numpy>=1.15',
'cython>=0.25',
#'scipy',
],
cmdclass = command_classes,
ext_modules = cythonize(ext_modules, language_level="2")
)
if __name__ == '__main__':
main()