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comparison ezBAMQC/setup.py @ 9:6610eedd9fae

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Uploaded
author cshl-bsr
date Wed, 30 Mar 2016 12:11:46 -0400
parents dfa3745e5fd8
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8:82bb8c455761 9:6610eedd9fae
87 if sys.version_info[0] != 2 or sys.version_info[1] < 7: 87 if sys.version_info[0] != 2 or sys.version_info[1] < 7:
88 print >> sys.stderr, "ERROR: ezBAMQC requires Python 2.7" 88 print >> sys.stderr, "ERROR: ezBAMQC requires Python 2.7"
89 sys.exit() 89 sys.exit()
90 90
91 BAMQC_HEADER = [ 91 BAMQC_HEADER = [
92 'src/bamqc/Constants.h', 92 'src/ezBAMQC/Constants.h',
93 'src/bamqc/Coverage_prof.h', 93 'src/ezBAMQC/Coverage_prof.h',
94 'src/bamqc/GeneFeatures.h', 94 'src/ezBAMQC/GeneFeatures.h',
95 'src/bamqc/InnerDist_prof.h', 95 'src/ezBAMQC/InnerDist_prof.h',
96 'src/bamqc/IntervalTree.h', 96 'src/ezBAMQC/IntervalTree.h',
97 'src/bamqc/Mappability.h', 97 'src/ezBAMQC/Mappability.h',
98 'src/bamqc/parseBAM.h', 98 'src/ezBAMQC/parseBAM.h',
99 'src/bamqc/ReadDup_prof.h', 99 'src/ezBAMQC/ReadDup_prof.h',
100 'src/bamqc/Results.h', 100 'src/ezBAMQC/Results.h',
101 'src/bamqc/rRNA.h' 101 'src/ezBAMQC/rRNA.h'
102 ] 102 ]
103 103
104 BAMQC_SOURCE = [ 104 BAMQC_SOURCE = [
105 'src/bamqc/Coverage_prof.cpp', 105 'src/ezBAMQC/Coverage_prof.cpp',
106 'src/bamqc/GeneFeatures.cpp', 106 'src/ezBAMQC/GeneFeatures.cpp',
107 'src/bamqc/InnerDist_prof.cpp', 107 'src/ezBAMQC/InnerDist_prof.cpp',
108 'src/bamqc/IntervalTree.cpp', 108 'src/ezBAMQC/IntervalTree.cpp',
109 'src/bamqc/Mappability.cpp', 109 'src/ezBAMQC/Mappability.cpp',
110 'src/bamqc/parseBAM.cpp', 110 'src/ezBAMQC/parseBAM.cpp',
111 'src/bamqc/ReadDup_prof.cpp', 111 'src/ezBAMQC/ReadDup_prof.cpp',
112 'src/bamqc/Results.cpp', 112 'src/ezBAMQC/Results.cpp',
113 'src/bamqc/rRNA.cpp' 113 'src/ezBAMQC/rRNA.cpp'
114 ] 114 ]
115 115
116 ###TODO HAVE TO SPLIT INTO TWO AND MAKE THE A FILE 116 ###TODO HAVE TO SPLIT INTO TWO AND MAKE THE A FILE
117 HTSLIB_PUBLIC_HEADERS = [ 117 HTSLIB_PUBLIC_HEADERS = [
118 'src/htslib/bgzf.h', 118 'src/htslib/bgzf.h',
172 ] 172 ]
173 173
174 BAMqc_CFLAGS = ['-fpermissive','-O3','-std=c++11','-Wno-error=declaration-after-statement'] 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')] 175 BAMqc_DFLAGS = [('_FILE_OFFSET_BITS','64'),('_LARGEFILE64_SOURCE',''),('_CURSES_LIB','1')]
176 BAMqc_INCLUDES = ['./src/htslib'] 176 BAMqc_INCLUDES = ['./src/htslib']
177 BAMqc_HEADERS = ['./src/bamqc'] 177 BAMqc_HEADERS = ['./src/ezBAMQC']
178 BAMqc_EXTRA = ['build/lib.linux-x86_64-2.7/htslib.so'] 178 BAMqc_EXTRA = ['build/lib.linux-x86_64-2.7/htslib.so']
179 179
180 htslib_CFLAGS = ['-Wno-error=declaration-after-statement'] 180 htslib_CFLAGS = ['-Wno-error=declaration-after-statement']
181 htslib_HEADERS = ['./src/htslib','./src/htslib/htslib','./src/htslib/cram'] 181 htslib_HEADERS = ['./src/htslib','./src/htslib/htslib','./src/htslib/cram']
182 htslib_DFLAGS = [('_FILE_OFFSET_BITS','64'),('_USE_KNETFILE','')] 182 htslib_DFLAGS = [('_FILE_OFFSET_BITS','64'),('_USE_KNETFILE','')]
183 183
184 setup(name = "ezBAMQC", 184 setup(name = "ezBAMQC",
185 version = "0.6.5", 185 version = "0.6.7",
186 description = 'Quality control tools for NGS alignment file', 186 description = 'Quality control tools for NGS alignment file',
187 keywords = 'Quality control BAM file', 187 keywords = 'Quality control BAM file',
188 # make sure to add all the nessacary requires 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/'], 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 }, 190 cmdclass = { 'install_data': wx_smart_install_data },