def discosnp_install():
print(_os.listdir('.'))
_subprocess.call(['bash', './compile_discoSnp++.sh'])
# ensure VCF generation works if system default python is version 3
# VCF code is python 2 only
fixed = open('run_VCF_creator.sh').read().replace('python ', 'python2 ')
open('run_VCF_creator.sh', 'w').write(fixed)
def discosnp_install():
print(_os.listdir('.'))
_subprocess.call(['bash','./compile_discoSnp++.sh'])
# ensure VCF generation works if system default python is version 3
# VCF code is python 2 only
fixed = open('run_VCF_creator.sh').read().replace('python ','python2 ')
open('run_VCF_creator.sh','w').write(fixed)
def pysam_install():
_subprocess.call([_sys.executable, 'setup.py', 'build'])
for f in _os.listdir('build/lib.linux-x86_64-2.7/pysam'):
if f[-3:] == '.so':
#print(f)
_shutil.copy('build/lib.linux-x86_64-2.7/pysam/{}'.format(f), 'pysam/{}'.format(f))
try:
_shutil.rmtree('../pysam')
except OSError:
pass
_os.rename('pysam', '../pysam')
def pysam_install():
_subprocess.call([_sys.executable, 'setup.py', 'build'])
for f in _os.listdir('build/lib.linux-x86_64-2.7/pysam'):
if f[-3:] == '.so':
#print(f)
_shutil.copy('build/lib.linux-x86_64-2.7/pysam/{}'.format(f),
'pysam/{}'.format(f))
try:
_shutil.rmtree('../pysam')
except OSError:
pass
_os.rename('pysam', '../pysam')