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setup.py
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#!/usr/bin/python
#Last-modified: 02 Oct 2015 02:42:07 PM
# Module/Scripts Description
#
# Copyright (c) 2008 Yunfei Wang <[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: experimental
# @version: 1.1.0
# @author: Yunfei Wang
# @contact: [email protected]
# ------------------------------------
# python modules
# ------------------------------------
import os,sys
from setuptools import setup, find_packages, Extension
# ------------------------------------
# constants
# ------------------------------------
# ------------------------------------
# Misc functions
# ------------------------------------
# ------------------------------------
# Classes
# ------------------------------------
# ------------------------------------
# Main
# ------------------------------------
if __name__ == '__main__':
if float(sys.version[:3])<2.6 or float(sys.version[:3])>=2.8:
sys.stderr.write("CRITICAL: Python version must be 2.6 or 2.7!\n")
sys.exit(1)
# includepy = "%s/include/python%s" % (sys.prefix, sys.version[:3])
with open("README.rst",'r') as fh:
long_description = fh.read()
# ngslib version
with open('RELEASE','r') as fh:
PROG, VERSION = fh.next().split()[:2]
# Compile Kent lib
if 'clean' in sys.argv:
print >>sys.stderr, "Clean KentLib ..."
os.system('cd external/KentLib && make clean && cd ../..')
print >>sys.stderr, "Clean dist and egg info ..."
os.system('if [ -d dist ]; then rm -rf dist; fi')
os.system('if [ -f ngslib.egg-info ]; then rm ngslib.egg-info; fi')
os.system('if [ -d ngslib.egg-info ]; then rm -rf ngslib.egg-info; fi')
else:
print >>sys.stderr, "Compile KentLib ..."
os.system('cd external/KentLib && make && cd ../..')
# install requirement
install_requires = [ ["numpy >= 1.4.1"],
["pysam >= 0.8.2"]]
# Python 2.6 requires argparse
if float(sys.version[:3]) == 2.6:
install_requires.append(["argparse >= 1.2.1"])
setup(name=PROG,
version=VERSION,
author='Yunfei Wang',
author_email='[email protected]',
url='http://tsznxx.appspot.com',
license="GNU General Public License (GPL)",
keywords = "Python Sequencing Bed BigWig TwoBit",
description = ("Python Modules for Next-Generation Sequencing Data Analysis."),
long_description = long_description,
package_dir={'ngslib':'src'},
packages = ['ngslib'],
scripts=['bin/wSamToWig.py',
'bin/wBedToWig.py',
'bin/wXLSToTXT.py',
'scripts/wBedExtend.py',
'scripts/wBedToFasta.py',
'bin/wSam2Bed.py',
'bin/wWigPlot.py',
'scripts/wGetTSS.py',
'scripts/wlncRNA.py',
'scripts/wGTFToTab.py',
'scripts/wTabToBed.py',
'scripts/wFormatFasta.py',
'scripts/wGCContent.py',
'scripts/wGetSeqByCoordinates.py',
'scripts/wGetSeqByName.py',
'scripts/wRandomBed.py',
'scripts/wFindNearestTwoAnnotation.py',
'scripts/wFindNearestAnnotation.py',
'scripts/wBedAnnotation.py',
'scripts/wBedGetWig.py',
'scripts/wGetIntron.py',
'scripts/wGetExon.py',
'scripts/wMergeSort.py'],
ext_modules=[Extension('wWigIO',['external/KentLib/wWigIO/wWigIO.c'],extra_link_args=['-DMACHTYPE_x86_64','-lz','-lm','external/KentLib/lib/jkweb.a'],extra_compile_args='-w -shared -fPIC -p -Iexternal/KentLib/inc'.split(' ')),
Extension('wTwoBitIO',['external/KentLib/wTwoBitIO/wTwoBitIO.c'],extra_link_args=['-DMACHTYPE_x86_64','-lz','-lm','external/KentLib/lib/jkweb.a'],extra_compile_args='-w -shared -fPIC -p -Iexternal/KentLib/inc'.split(' '))],
classifiers=['Environment :: Console',
'Development Status :: 3 - Alpha',
'Intended Audience :: Developers',
'License :: OSI Approved :: GNU General Public License (GPL)',
'License :: Free for non-commercial use',
'Operating System :: Unix',
'Programming Language :: Python :: 2.7',
'Topic :: Scientific/Engineering :: Bio-Informatics'],
install_requires=install_requires)