How to use yacman - 5 common examples

To help you get started, we’ve selected a few yacman examples, based on popular ways it is used in public projects.

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github databio / pypiper / pypiper / manager.py View on Github external
if config_to_load is not None:
                    pass
                    # TODO: Switch this message to a debug message using _LOGGER
                    self.debug("\nUsing custom config file: {}".format(config_to_load))
            else:
                # No custom config file specified. Check for default
                default_config = default_pipeline_config(sys.argv[0])
                if os.path.isfile(default_config):
                    config_to_load = default_config
                    self.debug("Using default pipeline config file: {}".
                          format(config_to_load))

        # Finally load the config we found.
        if config_to_load is not None:
            self.debug("\nLoading config file: {}\n".format(config_to_load))
            self.config = AttMapEcho(load_yaml(config_to_load))
        else:
            self.debug("No config file")
            self.config = None
github databio / pypiper / pypiper / ngstk.py View on Github external
def __init__(self, config_file=None, pm=None):
        # parse yaml into the project's attributes
        # self.add_entries(**config)
        super(NGSTk, self).__init__(
            None if config_file is None else load_yaml(config_file))

        # Keep a link to the pipeline manager, if one is provided.
        # if None is provided, instantiate "tools" and "parameters" with empty AttMaps
        # this allows the usage of the same code for a command with and without using a pipeline manager
        if pm is not None:
            self.pm = pm
            if hasattr(pm.config, "tools"):
                self.tools = self.pm.config.tools
            else:
                self.tools = AttMapEcho()
            if hasattr(pm.config, "parameters"):
                self.parameters = self.pm.config.parameters
            else:
                self.parameters = AttMapEcho()
        else:
            self.tools = AttMapEcho()
github pepkit / peppy / peppy / project2.py View on Github external
def _read_schema(schema):
    """
    Safely read schema from YAML-formatted file.

    :param str | Mapping schema: path to the schema file
        or schema in a dict form
    :return dict: read schema
    :raise TypeError: if the schema arg is neither a Mapping nor a file path
    """
    if isinstance(schema, str):
        return _load_yaml(schema)
    elif isinstance(schema, dict):
        return schema
    raise TypeError("schema has to be either a dict, URL to remote schema "
                    "or a path to an existing file")
github pepkit / peppy / peppy / utils.py View on Github external
def read_schema(schema):
    """
    Safely read schema from YAML-formatted file.

    :param str | Mapping schema: path to the schema file
        or schema in a dict form
    :return dict: read schema
    :raise TypeError: if the schema arg is neither a Mapping nor a file path
    """
    if isinstance(schema, str):
        return _load_yaml(schema)
    elif isinstance(schema, dict):
        return schema
    raise TypeError("schema has to be either a dict, URL to remote schema "
                    "or a path to an existing file")
github databio / refgenie / refgenie / add_assets_igenome.py View on Github external
def main():
    """ main workflow """
    parser = build_argparser()
    args, remaining_args = parser.parse_known_args()
    cfg = select_config(args.config, refgenconf.CFG_ENV_VARS, check_exist=True, strict_env=True)
    if not cfg:
        raise MissingGenomeConfigError(args.config)
    rgc = refgenconf.RefGenConf(filepath=cfg, writable=True)
    pths = [args.path, mkabs(args.path, rgc.genome_folder)]
    if not untar_or_copy(pths[0], os.path.join(rgc.genome_folder, args.genome)) \
            and not untar_or_copy(pths[1], os.path.join(rgc.genome_folder, args.genome)):
        rgc.unlock()
        raise OSError("Path '{}' does not exist. Tried: {}".format(args.path, " and ".join(pths)))
    path_components = [rgc.genome_folder] + [args.genome] + ["*"] * 3 + ["Sequence"]
    assets_paths = glob(os.path.join(*path_components))
    assert len(assets_paths) > 0, OSError("Your iGenomes directory is corrupted, more than one directory matched by {}."
                                          "\nMatched dirs: {}".format(os.path.join(*path_components),
                                                                      ", ".join(assets_paths)))
    assets_path = assets_paths[0]
    asset_names = [d for d in os.listdir(assets_path) if os.path.isdir(assets_path)]
    processed = []

yacman

A standardized configuration object for reference genome assemblies

BSD-2-Clause
Latest version published 5 months ago

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Popular yacman functions