-
Notifications
You must be signed in to change notification settings - Fork 38
/
setup.py
executable file
·179 lines (150 loc) · 6.22 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
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
#!/usr/bin/env python
# ##########################################################################
# Copyright 2012 Siavash Mirarab, Nam Nguyen, and Tandy Warnow.
# This file is part of SEPP.
#
# SEPP 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.
#
# SEPP 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 SEPP. If not, see <http://www.gnu.org/licenses/>.
# ##########################################################################
import os
import platform
import sys
# from distutils.core import setup
from distribute_setup import use_setuptools
import shutil
from setuptools import find_packages
from distutils.core import setup, Command
use_setuptools(version="0.6.24")
version = "4.5.5"
def get_tools_dir(where):
platform_name = platform.system()
if where is None:
where = os.path.join("bundled", platform_name)
path = os.path.join(os.getcwd(), "tools", where)
if not os.path.exists(path):
raise OSError("SEPP does not bundle tools for '%s' at this time!" %
platform_name)
return path
def get_tool_name(tool, bits):
if platform.system() == "Darwin" or not bits: # MAC doesn't have 32/64
return tool
is_64bits = sys.maxsize > 2**32
return "%s-%s" % (tool, "64" if is_64bits else "32")
class ConfigSepp(Command):
"""setuptools Command"""
description = "Configures Sepp for the current user"
user_options = [(
'contained', 'c',
("Whether SEPP should be installed in a self-contained "
"manner or on user's home"))]
def initopts(self):
self.contained = None
self.configfile = None
self.basepath = None
def initpath(self, name):
if self.contained:
self.configfile = os.path.expanduser(
os.path.abspath(os.path.join(".sepp", name)))
self.basepath = os.path.dirname(self.configfile)
else:
self.configfile = os.path.expanduser("~/.sepp/%s" % name)
self.basepath = os.path.expanduser("~/.sepp")
with open('home.path', 'w') as fo:
fo.write(self.basepath)
fo.close()
def get_tools_dest(self):
return os.path.join(self.basepath, "bundled-v%s" % version)
def copy_tool_to_lib(self, tool, where=None, bits=True):
shutil.copy2(
os.path.join(get_tools_dir(where), get_tool_name(tool, bits)),
os.path.join(self.get_tools_dest(), tool))
def initialize_options(self):
"""init options"""
self.initopts()
def finalize_options(self):
"""finalize options"""
self.initpath("main.config")
print("\nCreating main sepp config file at %s and tools at %s" % (
self.configfile, self.basepath))
def run(self):
def get_tool_name(tool, bits):
# MAC doesn't have 32/64
if platform.system() == "Darwin" or not bits:
return tool
is_64bits = sys.maxsize > 2**32
return "%s-%s" % (tool, "64" if is_64bits else "32")
# Create the default config file
if not os.path.exists(self.basepath):
os.mkdir(self.basepath)
if not os.path.exists(self.get_tools_dest()):
os.mkdir(self.get_tools_dest())
c = open("default.main.config")
d = open(self.configfile, "w")
for l1 in c:
l1 = l1.replace("~", self.get_tools_dest())
d.write(l1)
d.close()
# Copy tools to a bundled directory inside .sepp
self.copy_tool_to_lib("guppy")
self.copy_tool_to_lib("pplacer")
self.copy_tool_to_lib("hmmalign")
self.copy_tool_to_lib("hmmsearch")
self.copy_tool_to_lib("hmmbuild")
# TODO: should we compile and build merge.jar?
self.copy_tool_to_lib("seppJsonMerger.jar", where="merge", bits=False)
class ConfigUPP(ConfigSepp):
"""setuptools Command"""
description = "Configures UPP for the current user"
user_options = [('contained', 'c',
("Whether SEPP should be installed in a self-contained "
"manner or on user's home"))]
def initialize_options(self):
"""init options"""
self.initopts()
def finalize_options(self):
"""finalize options"""
self.initpath("upp.config")
print("\nCreating main UPP config file at %s and tools at %s" % (
self.configfile, self.basepath))
def run(self):
# Create the default config file
c = open("default.main.config")
d = open(self.configfile, "w")
for l2 in c:
l2 = l2.replace("~", self.get_tools_dest())
d.write(l2)
d.write(('\n[pasta]\n'
'path=run_pasta.py\nuser_options= --max-mem-mb=2000'))
d.close()
setup(name="sepp",
version=version,
description="SATe enabled phylogenetic placement.",
packages=find_packages(),
url="https://github.com/smirarab/sepp",
author="Siavash Mirarab and Nam Nguyen",
author_email="smirarab@gmail.com, namphuon@cs.utah.edu",
license="General Public License (GPL)",
install_requires=["dendropy >= 4.6.0"],
provides=["sepp"],
scripts=["run_sepp.py", 'run_upp.py', "split_sequences.py"],
cmdclass={"config": ConfigSepp, "upp": ConfigUPP},
data_files=[('', ['home.path'])],
classifiers=["Environment :: Console",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
("License :: OSI Approved :: GNU General Public "
"License (GPL)"),
"Natural Language :: English",
"Operating System :: OS Independent",
"Programming Language :: Python",
"Topic :: Scientific/Engineering :: Bio-Informatics"])