def _gen_freeze_scheme(): """ Generate scheme to freeze distribution. """ freeze_scheme = {} for key in SCHEME_KEYS: paths = [] for scheme_name, install_scheme in INSTALL_SCHEMES.iteritems(): val = install_scheme[key] if scheme_name == 'unix_home': val = val.replace('$base', '$home', 1) else: val = val.replace('$base', '$prefix', 1) val = val.replace('$platbase', '$exec_prefix', 1) paths.append(val) freeze_scheme[key] = paths return freeze_scheme
('gimmemotifs/score_dists', ['score_dists/total_wic_mean_score_dist.txt']), ('gimmemotifs/genes', ['genes/hg18.bed', 'genes/hg19.bed', 'genes/xenTro2.bed', 'genes/mm9.bed']), ('gimmemotifs/bg', ['bg/hg19.MotifSampler.bg', 'bg/hg18.MotifSampler.bg', 'bg/mm9.MotifSampler.bg', 'bg/xenTro2.MotifSampler.bg']), ('gimmemotifs/motif_databases', [ 'motif_databases/JASPAR2010_vertebrate.pwm', 'motif_databases/vertebrate_motifs.pwm', 'motif_databases/vertebrate_clusters.pwm', ]), # ('gimmemotifs/doc', ['doc/gimmemotifs_manual.pdf','doc/gimmemotifs_manual.html']), ('gimmemotifs/examples', ['examples/TAp73alpha.bed','examples/TAp73alpha.fa']), ('gimmemotifs/genome_index', ['genome_index/README.txt']) ] # Fix for install_data, add share to prefix (borrowed from Dan Christiansen) for platform, scheme in INSTALL_SCHEMES.iteritems(): if platform.startswith('unix_'): if scheme['data'][0] == '$' and '/' not in scheme['data']: scheme['data'] = os.path.join(scheme['data'], 'share') class build_tools(Command): description = "compile all included motif prediction tools" def initialize_options(self): self.build_base = None self.plat_name = None self.build_tools_dir = None self.machine = None def finalize_options(self): if self.plat_name is None:
]), ('gimmemotifs/score_dists', ['score_dists/total_wic_mean_score_dist.txt']), ('gimmemotifs/genes', ['genes/hg18.bed', 'genes/mm9.bed', 'genes/xenTro2.bed']), ('gimmemotifs/bg', [ 'bg/hg18.MotifSampler.bg', 'bg/mm9.MotifSampler.bg', 'bg/xenTro2.MotifSampler.bg' ]), ('gimmemotifs/motif_databases', ['motif_databases/jaspar.pfm']), ('gimmemotifs/doc', ['doc/gimmemotifs_manual.pdf', 'doc/gimmemotifs_manual.html']), ('gimmemotifs/examples', ['examples/TAp73alpha.bed', 'examples/TAp73alpha.fa']), ('gimmemotifs/genome_index', ['genome_index/README.txt'])] # Fix for install_data, add share to prefix (borrowed from Dan Christiansen) for platform, scheme in INSTALL_SCHEMES.iteritems(): if platform.startswith('unix_'): if scheme['data'][0] == '$' and '/' not in scheme['data']: scheme['data'] = os.path.join(scheme['data'], 'share') dlog.info("checking dependencies") try: import pp import matplotlib import kid import scipy import numpy except ImportError, inst: print "Error: required dependency not found!" print inst sys.exit()