Ejemplos de get_datadir en Python

Ejemplo n.º 1

Archivo: test_automated_analysis.py Proyecto: hammer/bcbio-nextgen

def get_post_process_yaml(data_dir, workdir):
    try:
        from bcbiovm.docker.defaults import get_datadir
        datadir = get_datadir()
        system = os.path.join(datadir, "galaxy", "bcbio_system.yaml") if datadir else None
    except ImportError:
        system = None
    if system is None or not os.path.exists(system):
        try:
            _, system = load_system_config("bcbio_system.yaml")
        except ValueError:
            system = None
    sample = os.path.join(data_dir, "post_process-sample.yaml")
    std = os.path.join(data_dir, "post_process.yaml")
    if os.path.exists(std):
        return std
    elif system and os.path.exists(system):
        # create local config pointing to reduced genomes
        test_system = os.path.join(workdir, os.path.basename(system))
        with open(system) as in_handle:
            config = yaml.load(in_handle)
            config["galaxy_config"] = os.path.join(data_dir, "universe_wsgi.ini")
            with open(test_system, "w") as out_handle:
                yaml.dump(config, out_handle)
        return test_system
    else:
        return sample

Ejemplo n.º 2

def get_post_process_yaml(data_dir, workdir):
    try:
        from bcbiovm.docker.defaults import get_datadir
        datadir = get_datadir()
        system = os.path.join(datadir, "galaxy",
                              "bcbio_system.yaml") if datadir else None
    except ImportError:
        system = None
    if system is None or not os.path.exists(system):
        try:
            _, system = load_system_config("bcbio_system.yaml")
        except ValueError:
            system = None
    sample = os.path.join(data_dir, "post_process-sample.yaml")
    std = os.path.join(data_dir, "post_process.yaml")
    if os.path.exists(std):
        return std
    elif system and os.path.exists(system):
        # create local config pointing to reduced genomes
        test_system = os.path.join(workdir, os.path.basename(system))
        with open(system) as in_handle:
            config = yaml.load(in_handle)
            config["galaxy_config"] = os.path.join(data_dir,
                                                   "universe_wsgi.ini")
            with open(test_system, "w") as out_handle:
                yaml.dump(config, out_handle)
        return test_system
    else:
        return sample

Ejemplo n.º 3

def get_post_process_yaml(data_dir, workdir):
    """Prepare a bcbio_system YAML file pointing to test data.
    """
    try:
        from bcbiovm.docker.defaults import get_datadir
        datadir = data_dir or get_datadir()
        sys_conf_file = os.path.join(datadir, "galaxy", "bcbio_system.yaml")
        system = sys_conf_file if datadir else None
    except ImportError:
        system = None
    if system is None or not os.path.exists(system):
        try:
            _, system = load_system_config(config_file="bcbio_system.yaml",
                                           work_dir=workdir)
        except ValueError:
            system = None
    if system is None or not os.path.exists(system):
        system = os.path.join(data_dir, "post_process-sample.yaml")
    # create local config pointing to reduced genomes
    test_system = os.path.join(workdir, "bcbio_system.yaml")
    with open(system) as in_handle:
        config = yaml.load(in_handle)
        config["galaxy_config"] = os.path.join(data_dir, "universe_wsgi.ini")
        with open(test_system, "w") as out_handle:
            yaml.dump(config, out_handle)
    return test_system

Ejemplo n.º 4

Archivo: conftest.py Proyecto: chapmanb/bcbio-nextgen

def get_post_process_yaml(data_dir, workdir):
    """Prepare a bcbio_system YAML file pointing to test data.
    """
    try:
        from bcbiovm.docker.defaults import get_datadir

        datadir = data_dir or get_datadir()
        sys_conf_file = os.path.join(datadir, "galaxy", "bcbio_system.yaml")
        system = sys_conf_file if datadir else None
    except ImportError:
        system = None
    if system is None or not os.path.exists(system):
        try:
            _, system = load_system_config(config_file="bcbio_system.yaml", work_dir=workdir)
        except ValueError:
            system = None
    if system is None or not os.path.exists(system):
        system = os.path.join(data_dir, "post_process-sample.yaml")
    # create local config pointing to reduced genomes
    test_system = os.path.join(workdir, "bcbio_system.yaml")
    with open(system) as in_handle:
        config = yaml.load(in_handle)
        config["galaxy_config"] = os.path.join(data_dir, "universe_wsgi.ini")
        with open(test_system, "w") as out_handle:
            yaml.dump(config, out_handle)
    return test_system

Ejemplo n.º 5

Archivo: conftest.py Proyecto: limbus-medtec/bcbio-nextgen-1

def _get_bcbiovm_config(data_dir):
    try:
        from bcbiovm.docker.defaults import get_datadir
        datadir = data_dir or get_datadir()
        sys_conf_file = os.path.join(datadir, "galaxy", "bcbio_system.yaml")
        system = sys_conf_file if datadir else None
    except ImportError:
        system = None
    return system

Ejemplo n.º 6

Archivo: conftest.py Proyecto: chapmanb/bcbio-nextgen

def _get_bcbiovm_config(data_dir):
    try:
        from bcbiovm.docker.defaults import get_datadir
        datadir = data_dir or get_datadir()
        sys_conf_file = os.path.join(datadir, "galaxy", "bcbio_system.yaml")
        system = sys_conf_file if datadir else None
    except ImportError:
        system = None
    return system