from distutils.core import setup, Extension import distutils.ccompiler import glob import os import sys ## Test for functions, with a hack to suppress compiler warnings. cc = distutils.ccompiler.new_compiler() defines = [] if cc.has_function('rintf(1.0);rand', includes=['math.h', 'stdlib.h'], libraries=['m']): defines.append(('HAVE_RINTF', '1')) if cc.has_function('finite(1.0);rand', includes=['math.h', 'stdlib.h']): defines.append(('HAVE_FINITE', '1')) if cc.has_function('expm1(1.0);rand', includes=['math.h', 'stdlib.h'], libraries=['m']): defines.append(('HAVE_EXPM1', '1')) if cc.has_function('rint(1.0);rand', includes=['math.h', 'stdlib.h'], libraries=['m']): defines.append(('HAVE_RINT', '1')) if cc.has_function('double log2(double) ; log2(1.0);rand', includes=['math.h', 'stdlib.h'], libraries=['m']): defines.append(('HAVE_LOG2', '1')) if cc.has_function('logbl(1.0);rand', includes=['math.h', 'stdlib.h'], libraries=['m']): defines.append(('HAVE_LOGBL', '1')) if cc.has_function('snprintf(0, 0, "");rand', includes=['stdio.h', 'stdlib.h']): defines.append(('HAVE_SNPRINTF', '1')) if cc.has_function('log1p(1.0);rand', includes=['math.h', 'stdlib.h'], libraries=['m']): defines.append(('HAVE_LOG1P', '1')) if cc.has_function('double round(double) ; round(1.0);rand', includes=['math.h', 'stdlib.h'], libraries=['m']): defines.append(('HAVE_ROUND', '1')) if cc.has_function('double fmin(double, double); fmin(1.0,0.0);rand', includes=['math.h', 'stdlib.h'], libraries=['m']): defines.append(('HAVE_FMIN', '1')) # prefix directory for pysplicing module pysplicing_dir = 'pysplicing' splicingsources = glob.glob(os.path.join(pysplicing_dir, 'src', '*.c')) lapacksources = glob.glob(os.path.join(pysplicing_dir, 'src', 'lapack', '*.c')) f2csources = glob.glob(os.path.join(pysplicing_dir, 'src', 'f2c', '*.c')) sources = splicingsources + lapacksources + f2csources include_dirs = [os.path.join(pysplicing_dir, 'include'), os.path.join(pysplicing_dir, 'src', 'lapack'), os.path.join(pysplicing_dir, 'src', 'f2c')] splicing_extension = Extension('pysplicing.pysplicing', sources, include_dirs=include_dirs, define_macros=defines) # Extract long description of MISO from README long_description = open('README').read() #if sys.version_info > (3, 0): # options["use_2to3"] = True # This forces distutils to place the data files # in the directory where the Py packages are installed # (usually 'site-packages'). This is unfortunately # required since there's no good way to retrieve # data_files= from setup() in a platform independent # way. from distutils.command.install import INSTALL_SCHEMES for scheme in INSTALL_SCHEMES.values(): scheme['data'] = scheme['purelib'] ## ## Definition of the current version. This is defined here ## and then gets written to __init__.py in misopy. ## MISO_VERSION = "0.5.3" ## ## Generate a __version__.py attribute ## for the module ## with open("./misopy/__init__.py", "w") as version_out: version_out.write("__version__ = \"%s\"\n" %(MISO_VERSION)) setup(name = 'misopy', ## ## CRITICAL: When changing version, remember ## to change version in __version__.py ## version = MISO_VERSION, description = "Mixture of Isoforms model (MISO) " \ "for isoform quantitation using RNA-Seq", long_description = long_description, author = 'Yarden Katz,Gabor Csardi', author_email = 'yarden@mit.edu,gcsardi@stat.harvard.edu', maintainer = 'Yarden Katz', maintainer_email = 'yarden@mit.edu', url = 'http://genes.mit.edu/burgelab/miso/', ext_modules = [splicing_extension], # Tell distutils to look for pysplicing in the right directory package_dir = {'pysplicing': 'pysplicing/pysplicing'}, packages = ['misopy', 'misopy.sashimi_plot', 'misopy.sashimi_plot.plot_utils', 'pysplicing'], entry_points={ 'console_scripts': [ 'module_availability = misopy.module_availability:main', 'sam_to_bam = misopy.sam_to_bam:main', 'run_events_analysis.py = misopy.run_events_analysis:main', 'run_miso.py = misopy.run_miso:main', 'exon_utils = misopy.exon_utils:main', 'pe_utils = misopy.pe_utils:main', 'filter_events = misopy.filter_events:main', 'test_miso = misopy.test_miso:main', 'miso_zip = misopy.miso_zip:main', 'miso = misopy.miso:main', 'compare_miso = misopy.compare_miso:main', 'summarize_miso = misopy.summarize_miso:main', 'index_gff = misopy.index_gff:main', 'miso_pack = misopy.miso_pack:main', # sashimi_plot scripts 'plot.py = misopy.sashimi_plot.plot:main', 'sashimi_plot = misopy.sashimi_plot.sashimi_plot:main' ], }, data_files = [('misopy/settings', ['misopy/settings/miso_settings.txt', 'misopy/sashimi_plot/settings/sashimi_plot_settings.txt']), ('misopy/test-data/sam-data', ['misopy/test-data/sam-data/c2c12.Atp2b1.sam']), ('misopy/gff-events/mm9', ['misopy/gff-events/mm9/SE.mm9.gff']), ('misopy/gff-events/mm9/genes', ['misopy/gff-events/mm9/genes/Atp2b1.mm9.gff']), ('misopy/sashimi_plot/test-data', ['misopy/sashimi_plot/test-data/events.gff']), ('misopy/sashimi_plot/test-data/miso-data', ['misopy/sashimi_plot/test-data/miso-data/heartKOa/chr17/chr17:45816186:45816265:-@chr17:45815912:45815950:-@chr17:45814875:45814965:-.miso', 'misopy/sashimi_plot/test-data/miso-data/heartKOb/chr17/chr17:45816186:45816265:-@chr17:45815912:45815950:-@chr17:45814875:45814965:-.miso', 'misopy/sashimi_plot/test-data/miso-data/heartWT1/chr17/chr17:45816186:45816265:-@chr17:45815912:45815950:-@chr17:45814875:45814965:-.miso', 'misopy/sashimi_plot/test-data/miso-data/heartWT2/chr17/chr17:45816186:45816265:-@chr17:45815912:45815950:-@chr17:45814875:45814965:-.miso']), ('misopy/sashimi_plot/test-data/bam-data', ['misopy/sashimi_plot/test-data/bam-data/heartKOa.bam.bai', 'misopy/sashimi_plot/test-data/bam-data/heartKOa.sorted.bam', 'misopy/sashimi_plot/test-data/bam-data/heartKOa.sorted.bam.bai', 'misopy/sashimi_plot/test-data/bam-data/heartKOb.sorted.bam', 'misopy/sashimi_plot/test-data/bam-data/heartKOb.sorted.bam.bai', 'misopy/sashimi_plot/test-data/bam-data/heartWT1.sorted.bam', 'misopy/sashimi_plot/test-data/bam-data/heartWT1.sorted.bam.bai', 'misopy/sashimi_plot/test-data/bam-data/heartWT2.sorted.bam', 'misopy/sashimi_plot/test-data/bam-data/heartWT2.sorted.bam.bai'])], # Required modules install_requires = [ "matplotlib", "numpy >= 1.5.0", "scipy >= 0.9.0", "pysam >= 0.6.0" ], platforms = 'ALL', keywords = ['bioinformatics', 'sequence analysis', 'alternative splicing', 'RNA-Seq', 'probabilistic models', 'bayesian'], classifiers = [ 'Development Status :: 4 - Beta', 'Intended Audience :: Science/Research', 'Programming Language :: C', 'Programming Language :: Python', 'Topic :: Scientific/Engineering :: Bio-Informatics' ] )