build: replace pyliftover with agct to improve performance

[korikuzma]

close #263

[jsstevenson]

@korikuzma are these still used? agct should just be pulling them via wags-tails

[korikuzma]

Ooooh, I think we need to provide support to agct to allow env vars to be passed for the chain files. I plan on storing these files in EFS and pointing to that mounted location

[jsstevenson]

You should be able to set WAGS_TAILS_DIR to a parent directory, if that helps. Alternatively, we can have agct pass along a data_dir argument to the CustomData class from wags-tails.

[korikuzma]

@jsstevenson What if we want to bypass wags-tails all together?

[korikuzma]

@jsstevenson This is what I would propose:

Current:

    def __init__(self, from_db: Genome, to_db: Genome) -> None:
        ....
        data_handler = CustomData(
            f"chainfile_{from_db.value}_to_{to_db.value}",
            "chain",
            lambda: "",
            self._download_function_builder(from_db, to_db),
            data_dir=get_data_dir() / "ucsc-chainfile",
        )
        file, _ = data_handler.get_latest()

Suggested change:

    def __init__(self, from_db: Genome, to_db: Genome, file: Optional[Path] = None) -> None:
        ...
        if not file:
            data_handler = CustomData(
                f"chainfile_{from_db.value}_to_{to_db.value}",
                "chain",
                lambda: "",
                self._download_function_builder(from_db, to_db),
                data_dir=get_data_dir() / "ucsc-chainfile",
            )
            file, _ = data_handler.get_latest()

[jsstevenson]

yeah, I think so -- make a PR?

[korikuzma]

Cool, wanted to make sure I wasn't missing something before making changes.