.. _`bio/vep/cache`:

VEP DOWNLOAD CACHE
==================


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/vep/cache?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/vep/cache

Download VEP cache for given species, build and release.

**URL**: http://www.ensembl.org/info/docs/tools/vep/index.html

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule get_vep_cache:
        output:
            directory("resources/vep/cache"),
        params:
            species="saccharomyces_cerevisiae",
            build="R64-1-1",
            release="98",
        log:
            "logs/vep/cache.log",
        cache: "omit-software"  # save space and time with between workflow caching (see docs)
        wrapper:
            "v3.0.4/bio/vep/cache"

Note that input, output and log file paths can be chosen freely.

When running with

.. code-block:: bash

    snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.


Software dependencies
---------------------

* ``python=3.12.0``
* ``ensembl-vep=110.1``




Authors
-------

* Johannes Köster


Code
----

.. code-block:: python

    __author__ = "Johannes Köster"
    __copyright__ = "Copyright 2023, Johannes Köster"
    __email__ = "johannes.koester@uni-due.de"
    __license__ = "MIT"

    import tempfile
    from pathlib import Path
    from snakemake.shell import shell


    extra = snakemake.params.get("extra", "")

    try:
        release = int(snakemake.params.release)
    except ValueError:
        raise ValueError("The parameter release is supposed to be an integer.")

    with tempfile.TemporaryDirectory() as tmpdir:
        # We download the cache tarball manually because vep_install does not consider proxy settings (in contrast to curl).
        # See https://github.com/bcbio/bcbio-nextgen/issues/1080
        vep_dir = "vep" if release >= 97 else "VEP"
        cache_tarball = (
            f"{snakemake.params.species}_vep_{release}_{snakemake.params.build}.tar.gz"
        )
        log = snakemake.log_fmt_shell(stdout=True, stderr=True)
        shell(
            "curl -L ftp://ftp.ensembl.org/pub/release-{snakemake.params.release}/"
            "variation/{vep_dir}/{cache_tarball} "
            "-o {tmpdir}/{cache_tarball} {log}"
        )

        log = snakemake.log_fmt_shell(stdout=True, stderr=True, append=True)
        shell(
            "vep_install --AUTO c "
            "--SPECIES {snakemake.params.species} "
            "--ASSEMBLY {snakemake.params.build} "
            "--CACHE_VERSION {release} "
            "--CACHEURL {tmpdir} "
            "--CACHEDIR {snakemake.output} "
            "--CONVERT "
            "--NO_UPDATE "
            "{extra} {log}"
        )


.. |nl| raw:: html

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