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()
