forked from CGATOxford/UMI-tools
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathsetup.py
118 lines (102 loc) · 3.46 KB
/
setup.py
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
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
import sys
import os
import glob
try:
import Cython
except ImportError:
raise ImportError(
"UMI-tools requires cython to "
"be installed before running setup.py (pip install cython)")
try:
import pysam
except ImportError:
raise ImportError(
"UMI-tools requires pysam to "
"be installed before running setup.py (pip install pysam)")
########################################################################
########################################################################
# Import setuptools
# Use existing setuptools, otherwise try ez_setup.
try:
import setuptools
except ImportError:
raise ImportError(
"UMI-tools requires setuptools"
"be installed before running setup.py (pip install setuptools)")
from setuptools import setup, find_packages, Extension
from distutils.version import LooseVersion
if LooseVersion(setuptools.__version__) < LooseVersion('1.1'):
print ("Version detected:", LooseVersion(setuptools.__version__))
raise ImportError(
"UMI-tools requires setuptools 1.1 higher")
from Cython.Build import cythonize
########################################################################
########################################################################
# collect umi_tools version
sys.path.insert(0, "umi_tools")
import version
version = version.__version__
###############################################################
###############################################################
# Define dependencies
# Perform a umi_tools Installation
major, minor1, minor2, s, tmp = sys.version_info
if (major == 2 and minor1 < 7) or major < 2:
raise SystemExit("""UMI-tools requires Python 2.7 or later.""")
umi_tools_packages = ["umi_tools"]
umi_tools_package_dirs = {'umi_tools': 'umi_tools'}
# debugging pip installation
#install_requires = []
#for requirement in (
# l.strip() for l in open('requirements.txt') if not l.startswith("#")):
# install_requires.append(requirement)
install_requires = [
"setuptools>=1.1",
"cython>=0.19",
"numpy>=1.7",
"pandas>=0.12.0",
"pysam>=0.8.4",
"future"]
##########################################################
##########################################################
# Classifiers
classifiers = """
Development Status :: 3 - Alpha
Intended Audience :: Science/Research
Intended Audience :: Developers
License :: OSI Approved
Programming Language :: Python
Topic :: Software Development
Topic :: Scientific/Engineering
Operating System :: POSIX
Operating System :: Unix
Operating System :: MacOS
"""
setup(
# package information
name='umi_tools',
version=version,
description='umi-tools: Tools for UMI analyses',
author='Ian Sudbery',
author_email='[email protected]',
license="MIT",
platforms=["any"],
keywords="computational genomics",
long_description='umi-tools: Tools for UMI analyses',
classifiers=list(filter(None, classifiers.split("\n"))),
url="https://github.com/CGATOxford/UMI-tools",
download_url="https://github.com/CGATOxford/UMI-tools/tarball/%s" % version,
# package contents
packages=umi_tools_packages,
package_dir=umi_tools_package_dirs,
include_package_data=True,
# dependencies
install_requires=install_requires,
# extension modules
ext_modules=cythonize("umi_tools/_dedup_umi.pyx"),
entry_points={
'console_scripts': ['umi_tools = umi_tools.umi_tools:main']
},
# other options
zip_safe=False,
)