bcl.py 文件源码

def get_bcl2fastq_v2(hostname):
    try:
        subprocess.check_call(["which", "bcl2fastq"])
        # Restore the LD_LIBRARY_PATH set aside by sourceme.bash/shell10x.
        # Required for some installations of bcl2fastq.
        new_environ = dict(os.environ)
        new_environ['LD_LIBRARY_PATH'] = os.environ.get('_TENX_LD_LIBRARY_PATH', '')
        output = subprocess.check_output(["bcl2fastq", "--version"], env=new_environ, stderr=subprocess.STDOUT)
        match = None
        for l in output.split("\n"):
            match = re.match("bcl2fastq v([0-9.]+)", l)
            if match is not None:
                return (match.groups()[0], None)

        return (None, "bcl2fastq version not recognized -- please check the output of bcl2fastq --version")
    except subprocess.CalledProcessError:
        msg = "On machine: %s, bcl2fastq not found on PATH." % hostname
        return (None, msg)