1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
|
#!/usr/bin/env python
#
# Copyright (c) 2013 Mikkel Schubert <MikkelSch@gmail.com>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
import codecs
import os
import sys
from setuptools import setup, find_packages
def _get_version():
"""Retrieve version from current install directory."""
env = {}
with open(os.path.join("paleomix", "__init__.py")) as handle:
exec(handle.read(), env)
return env["__version__"]
def _get_readme():
"""Retrieves contents of README.rst, forcing UTF-8 encoding."""
with codecs.open("README.rst", encoding="utf-8") as handle:
return handle.read()
setup(
name='paleomix',
version=_get_version(),
description='Bioinformatics pipelines for HTS data',
long_description=_get_readme(),
url='https://github.com/MikkelSchubert/paleomix',
author='Mikkel Schubert',
author_email='MikkelSch@gmail.com',
license='MIT',
classifiers=[
'Development Status :: 5 - Production/Stable',
'Intended Audience :: Science/Research',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'License :: OSI Approved :: MIT License',
'Programming Language :: Python :: 2 :: Only',
'Programming Language :: Python :: 2.7',
],
keywords='pipeline bioinformatics hts phylogeny bam',
packages=find_packages(exclude=['misc', 'tests']),
install_requires=['pysam>=0.10.0',
'setproctitle>=1.1.0'],
# Dependencies set in setup_requires to allow use of 'setup.py nosetests'
# setup_requires=['nose>=1.3.0',
# 'flexmock>=0.9.7',
# 'coverage>=4.0.0'],
test_suite='nose.collector',
entry_points={
'console_scripts': [
'paleomix=paleomix:run',
# Aliases used in previous publications
'bam_pipeline=paleomix:run_bam_pipeline',
'bam_rmdup_collapsed=paleomix:run_rmdup_collapsed',
'conv_gtf_to_bed=paleomix:run_gtf_to_bed',
'phylo_pipeline=paleomix:run_phylo_pipeline',
'trim_pipeline=paleomix:run_trim_pipeline',
],
},
zip_safe=False,
include_package_data=True,
)
|
