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setup_w_cython.py
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#!/usr/bin/env python
# Time-stamp: <2014-10-23 15:48:33 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
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)
if has_cython:
ext_modules = [Extension("MACS2.cProb", ["MACS2/cProb.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
Extension("MACS2.IO.cParser",["MACS2/IO/cParser.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.cPileup", ["MACS2/cPileup.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
Extension("MACS2.cArray", ["MACS2/cArray.pyx"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.cPeakModel", ["MACS2/cPeakModel.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.cPeakDetect", ["MACS2/cPeakDetect.pyx"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.cSignal", ["MACS2/cSignal.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cPeakIO", ["MACS2/IO/cPeakIO.pyx"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cBedGraphIO", ["MACS2/IO/cBedGraphIO.pyx"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cFixWidthTrack", ["MACS2/IO/cFixWidthTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cPairedEndTrack", ["MACS2/IO/cPairedEndTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cBedGraph", ["MACS2/IO/cBedGraph.pyx"], libraries=["m"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cScoreTrack", ["MACS2/IO/cScoreTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
Extension("MACS2.IO.cCallPeakUnit", ["MACS2/IO/cCallPeakUnit.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.hashtable", ["MACS2/hashtable.pyx"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.Statistics", ["MACS2/Statistics.pyx", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-Ofast"]),
]
else:
ext_modules = [Extension("MACS2.cProb", ["MACS2/cProb.c"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
Extension("MACS2.IO.cParser",["MACS2/IO/cParser.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.cPileup", ["MACS2/cPileup.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
Extension("MACS2.cArray", ["MACS2/cArray.c"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.cPeakModel", ["MACS2/cPeakModel.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.cPeakDetect", ["MACS2/cPeakDetect.c"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.cSignal", ["MACS2/cSignal.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cPeakIO", ["MACS2/IO/cPeakIO.c"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cBedGraphIO", ["MACS2/IO/cBedGraphIO.c"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cFixWidthTrack", ["MACS2/IO/cFixWidthTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cPairedEndTrack", ["MACS2/IO/cPairedEndTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cBedGraph", ["MACS2/IO/cBedGraph.c"], libraries=["m"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cScoreTrack", ["MACS2/IO/cScoreTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
Extension("MACS2.IO.cCallPeakUnit", ["MACS2/IO/cCallPeakUnit.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.hashtable", ["MACS2/hashtable.c"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.Statistics", ["MACS2/Statistics.c", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-Ofast"]),
]
setup(name="MACS2",
version="2.1.0.20140616",
description="Model Based Analysis for ChIP-Seq data",
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 :: 4 - Beta',
'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',
],
install_requires=[
'numpy>=1.6',
'cython>=0.18',
#'scipy',
],
cmdclass = command_classes,
ext_modules = ext_modules
)
if __name__ == '__main__':
main()