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setup.py
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setup.py
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from distutils.core import setup
import sys
from subprocess import check_call
from os.path import join, abspath, exists
from os import chdir, getcwd, rename, remove
xtra_opts = {"--with-libcfu-inc":"libcfu headers at this location",
"--with-libcfu-lib":"libcfu library at this location",
"--with-libhts-inc":"htslib headers at this location",
"--with-libhts-lib":"htslib library at this location"}
if '-help' not in sys.argv and \
'-h' not in sys.argv and \
'--help' not in sys.argv and \
'--h' not in sys.argv:
if 'sdist' not in sys.argv:
# grab extra configuration arguments
configure_args = []
for opt in xtra_opts.keys():
try:
opt_idx = sys.argv.index(opt)
configure_args.append(opt+"="+abspath(sys.argv[opt_idx+1]))
del sys.argv[opt_idx+1]
sys.argv.remove(opt)
except ValueError:
pass
# configure and make the c portion of the program
cur_dir = getcwd()
chdir(join(cur_dir, 'c'))
check_call([join(getcwd(), "configure")] + configure_args)
check_call(['make','clean'])
check_call(['make'])
chdir(cur_dir)
# move the compiled library into the bamm folder so it's
# picked up by distutils
rename(join('c', 'libBamM.a'), join('bamm', 'libBamM.a'))
else:
print
print "Embedded C options (for building libPMBam.a) USE: --OPTION<space>PATH"
for opt in xtra_opts.keys():
print " %s %s"%(opt,xtra_opts[opt])
print
exec(open('bamm/version.py').read()) # loads __version__
# return to regular viewing
setup(
name='BamM',
version=__version__,
author='Michael Imelfort',
author_email='mike@mikeimelfort.com',
packages=['bamm'],
scripts=['bin/bamm', 'bin/bamFlags'],
license='LGPLv3',
description='BamM - working with the BAM',
long_description=open('README.md').read(),
install_requires=["numpy >= 1.6.1"],
package_data={'bamm' : ['libBamM.a']},
)
# remove the library
#to_remove = join('bamm', 'libBamM.a')
#if exists(to_remove):
# remove(to_remove)