VEP DOWNLOAD 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:

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:
        "v3.8.0-49-g6f33607/bio/vep/cache"

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

When running with

snakemake --use-conda

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

Software dependencies

• python=3.12.2

• ensembl-vep=111.0

Authors

• Johannes Köster

Code

__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}"
    )