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comparison ezBAMQC/setup.py @ 0:dfa3745e5fd8

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author youngkim
date Thu, 24 Mar 2016 17:12:52 -0400
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1 #!/usr/bin/env python2.7
2 # Setup for ezBAMQC, utilities for the Sequence Alignment/Map format.
3 #
4 # Copyright (C) 2015 Bioinformatics Shared Resource, CSHL.
5 # Portions copyright (C) 2015 Cold Spring Harbor Laboratory.
6 #
7 # Permission is hereby granted, free of charge, to any person obtaining a copy
8 # of this software and associated documentation files (the "Software"), to deal
9 # in the Software without restriction, including without limitation the rights
10 # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
11 # copies of the Software, and to permit persons to whom the Software is
12 # furnished to do so, subject to the following conditions:
13 #
14 # The above copyright notice and this permission notice shall be included in
15 # all copies or substantial portions of the Software.
16 #
17 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
18 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
19 # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
20 # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
21 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
22 # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
23 # DEALINGS IN THE SOFTWARE.
24
25 import argparse
26 import sys, os, glob, fnmatch
27
28 ## Added 10 Jan 2008
29 from distutils.core import setup, Extension
30 import distutils.command.install_data
31
32 ## Code borrowed from wxPython's setup and config files
33 ## Thanks to Robin Dunn for the suggestion.
34 ## I am not 100% sure what's going on, but it works!
35 def opj(*args):
36 path = os.path.join(*args)
37 return os.path.normpath(path)
38
39 ## Added 10 Jan 2008
40 # Specializations of some distutils command classes
41 class wx_smart_install_data(distutils.command.install_data.install_data):
42 """need to change self.install_dir to the actual library dir"""
43 def run(self):
44 install_cmd = self.get_finalized_command('install')
45 self.install_dir = getattr(install_cmd, 'install_lib')
46 return distutils.command.install_data.install_data.run(self)
47
48 def find_data_files(srcdir, *wildcards, **kw):
49 # get a list of all files under the srcdir matching wildcards,
50 # returned in a format to be used for install_data
51 def walk_helper(arg, dirname, files):
52 if '.svn' in dirname:
53 return
54 names = []
55 lst, wildcards = arg
56 for wc in wildcards:
57 wc_name = opj(dirname, wc)
58 for f in files:
59 filename = opj(dirname, f)
60
61 if fnmatch.fnmatch(filename, wc_name) and not os.path.isdir(filename):
62 names.append(filename)
63 if names:
64 lst.append( (dirname, names ) )
65
66 file_list = []
67 recursive = kw.get('recursive', True)
68 if recursive:
69 os.path.walk(srcdir, walk_helper, (file_list, wildcards))
70 else:
71 walk_helper((file_list, wildcards),
72 srcdir,
73 [os.path.basename(f) for f in glob.glob(opj(srcdir, '*'))])
74 return file_list
75
76 ## This is a list of files to install, and where:
77 ## Make sure the MANIFEST.in file points to all the right
78 ## directories too.
79 files = find_data_files('ezBAMQC/', '*.*')
80
81 from distutils.core import setup
82
83 def readme():
84 with open('README.rst') as f:
85 return f.read()
86
87 if sys.version_info[0] != 2 or sys.version_info[1] < 7:
88 print >> sys.stderr, "ERROR: ezBAMQC requires Python 2.7"
89 sys.exit()
90
91 BAMQC_HEADER = [
92 'src/bamqc/Constants.h',
93 'src/bamqc/Coverage_prof.h',
94 'src/bamqc/GeneFeatures.h',
95 'src/bamqc/InnerDist_prof.h',
96 'src/bamqc/IntervalTree.h',
97 'src/bamqc/Mappability.h',
98 'src/bamqc/parseBAM.h',
99 'src/bamqc/ReadDup_prof.h',
100 'src/bamqc/Results.h',
101 'src/bamqc/rRNA.h'
102 ]
103
104 BAMQC_SOURCE = [
105 'src/bamqc/Coverage_prof.cpp',
106 'src/bamqc/GeneFeatures.cpp',
107 'src/bamqc/InnerDist_prof.cpp',
108 'src/bamqc/IntervalTree.cpp',
109 'src/bamqc/Mappability.cpp',
110 'src/bamqc/parseBAM.cpp',
111 'src/bamqc/ReadDup_prof.cpp',
112 'src/bamqc/Results.cpp',
113 'src/bamqc/rRNA.cpp'
114 ]
115
116 ###TODO HAVE TO SPLIT INTO TWO AND MAKE THE A FILE
117 HTSLIB_PUBLIC_HEADERS = [
118 'src/htslib/bgzf.h',
119 'src/htslib/faidx.h',
120 'src/htslib/hfile.h',
121 'src/htslib/hts.h',
122 'src/htslib/hts_defs.h',
123 'src/htslib/khash.h',
124 'src/htslib/klist.h',
125 'src/htslib/knetfile.h',
126 'src/htslib/kseq.h',
127 'src/htslib/ksort.h',
128 'src/htslib/kstring.h',
129 'src/htslib/regidx.h',
130 'src/htslib/sam.h',
131 'src/htslib/synced_bcf_reader.h',
132 'src/htslib/tbx.h',
133 'src/htslib/vcf.h',
134 'src/htslib/vcf_sweep.h',
135 'src/htslib/vcfutils.h'
136 ]
137
138
139 HTSLIB = [
140 'src/htslib/bgzf.c',
141 'src/htslib/faidx.c',
142 'src/htslib/hfile.c',
143 'src/htslib/hfile_net.c',
144 'src/htslib/hts.c',
145 'src/htslib/kfunc.c',
146 'src/htslib/knetfile.c',
147 'src/htslib/kstring.c',
148 'src/htslib/regidx.c',
149 'src/htslib/sam.c',
150 'src/htslib/synced_bcf_reader.c',
151 'src/htslib/tbx.c',
152 'src/htslib/vcf.c',
153 'src/htslib/vcfutils.c',
154 'src/htslib/cram/cram_codecs.c',
155 'src/htslib/cram/cram_decode.c',
156 'src/htslib/cram/cram_encode.c',
157 'src/htslib/cram/cram_index.c',
158 'src/htslib/cram/cram_io.c',
159 'src/htslib/cram/cram_samtools.c',
160 'src/htslib/cram/cram_stats.c',
161 'src/htslib/cram/files.c',
162 'src/htslib/cram/mFILE.c',
163 'src/htslib/cram/md5.c',
164 'src/htslib/cram/open_trace_file.c',
165 'src/htslib/cram/pooled_alloc.c',
166 'src/htslib/cram/rANS_static.c',
167 'src/htslib/cram/sam_header.c',
168 'src/htslib/cram/string_alloc.c',
169 'src/htslib/cram/thread_pool.c',
170 'src/htslib/cram/vlen.c',
171 'src/htslib/cram/zfio.c'
172 ]
173
174 BAMqc_CFLAGS = ['-fpermissive','-O3','-std=c++11','-Wno-error=declaration-after-statement']
175 BAMqc_DFLAGS = [('_FILE_OFFSET_BITS','64'),('_LARGEFILE64_SOURCE',''),('_CURSES_LIB','1')]
176 BAMqc_INCLUDES = ['./src/htslib']
177 BAMqc_HEADERS = ['./src/bamqc']
178 BAMqc_EXTRA = ['build/lib.linux-x86_64-2.7/htslib.so']
179
180 htslib_CFLAGS = ['-Wno-error=declaration-after-statement']
181 htslib_HEADERS = ['./src/htslib','./src/htslib/htslib','./src/htslib/cram']
182 htslib_DFLAGS = [('_FILE_OFFSET_BITS','64'),('_USE_KNETFILE','')]
183
184 setup(name = "ezBAMQC",
185 version = "0.6.5",
186 description = 'Quality control tools for NGS alignment file',
187 keywords = 'Quality control BAM file',
188 # make sure to add all the nessacary requires
189 dependency_links=['https://gcc.gnu.org/gcc-4.8/','https://www.r-project.org/','https://cran.r-project.org/web/packages/corrplot/'],
190 cmdclass = { 'install_data': wx_smart_install_data },
191 scripts = ["ezBAMQC"],
192 author = "Ying Jin",
193 author_email ="yjin@cshl.edu",
194 license='GPLv3',
195 platforms = ['Linux'],
196 url='http://hammelllab.labsites.cshl.edu/software#BAMqc',
197 long_description=readme(),
198 classifiers=[
199 'Development Status :: 4 - Beta',
200 'Natural Language :: English',
201 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
202 'Topic :: Scientific/Engineering :: Bio-Informatics',
203 'Intended Audience :: Science/Research',
204 'Programming Language :: Python :: 2.7',
205 'Programming Language :: C++',
206 'Operating System :: Unix',
207 ],
208 zip_safe = False,
209 include_package_data=True,
210 ext_modules = [
211 Extension('htslib',
212 sources = HTSLIB,
213 include_dirs = htslib_HEADERS,
214 extra_compile_args = htslib_CFLAGS,
215 define_macros = htslib_DFLAGS,
216 libraries=['z']
217 ),
218 Extension('libBAMqc',
219 sources = BAMQC_SOURCE,
220 extra_compile_args = BAMqc_CFLAGS,
221 include_dirs = BAMqc_HEADERS + htslib_HEADERS,
222 extra_objects = BAMqc_EXTRA,
223 define_macros = BAMqc_DFLAGS
224 )
225 ]
226 )