Ejemplo n.º 1
0
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)
Ejemplo n.º 2
0
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)
Ejemplo n.º 3
0
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')
Ejemplo n.º 4
0
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')