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setup.py
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setup.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Copyright (c) 2015 Kwangbom Choi, The Jackson Laboratory
This software was developed by Kwangbom "KB" Choi in Gary Churchill's Lab.
This is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This software is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this software. If not, see <http://www.gnu.org/licenses/>.
"""
import os
try:
from setuptools import setup
except ImportError:
from distutils.core import setup
import emase
with open('README.rst') as readme_file:
readme = readme_file.read()
with open('HISTORY.rst') as history_file:
history = history_file.read().replace('.. :changelog:', '')
# requirements = [
# 'numpy==1.8.2',
# 'numexpr==2.3.1',
# 'scipy==0.13.3',
# 'pysam>=0.6',
# 'cython>=0.13',
# 'tables==3.1.0',
# 'biopython>=1.63'
# ]
requirements = []
on_rtd = os.environ.get('READTHEDOCS', None)
if not on_rtd:
requirements.append('numpy==1.8.2')
requirements.append('numexpr==2.3.1')
requirements.append('scipy==0.13.3')
requirements.append('pysam>=0.6')
requirements.append('cython>=0.13')
requirements.append('tables==3.1.0')
requirements.append('biopython>=1.63')
test_requirements = [
'pytest'
]
setup(
name='emase',
version=emase.__version__,
description="EMASE: Expectation-Maximization algorithm for Allele Specific Expression",
long_description=readme + '\n\n' + history,
author="Kwangbom \"KB\" Choi, Ph. D., The Jackson Laboratory",
author_email='kb.choi@jax.org',
url='https://github.com/churchill-lab/emase',
packages=[
'emase',
],
package_dir={'emase':
'emase'},
include_package_data=True,
scripts=[
'scripts/prepare-emase',
'scripts/create-hybrid',
'scripts/bam-to-emase',
'scripts/combine-emase-files',
'scripts/run-emase',
'scripts/count-alignments',
'scripts/get-common-alignments',
'scripts/pull-out-unique-reads',
'scripts/count-shared-multireads-pairwise',
'scripts/simulate-reads'
],
install_requires=requirements,
license="GPLv3",
zip_safe=False,
keywords='emase',
classifiers=[
'Development Status :: 4 - Beta',
'Intended Audience :: Developers',
'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
'Natural Language :: English',
'Programming Language :: Python :: 2.6',
'Programming Language :: Python :: 2.7',
],
test_suite='tests',
tests_require=test_requirements
)