recipe snpeff

Genetic variant annotation and effect prediction toolbox

Homepage:

http://snpeff.sourceforge.net/

License:

LGPLv3

Recipe:

/snpeff/meta.yaml

Links:

biotools: snpeff

package snpeff

(downloads) docker_snpeff

versions:
5.2-1,  5.2-0,  5.1-2,  5.1-1,  5.1-0,  5.1d-0,  5.0-1,  5.0-0,  4.5covid19-2, 

5.2-1,  5.2-0,  5.1-2,  5.1-1,  5.1-0,  5.1d-0,  5.0-1,  5.0-0,  4.5covid19-2,  4.5covid19-1,  4.5covid19-0,  4.3.1t-5,  4.3.1t-4,  4.3.1t-3,  4.3.1t-2,  4.3.1t-1,  4.3.1t-0,  4.3.1r-0,  4.3.1q-0,  4.3.1p-1,  4.3.1p-0,  4.3.1o-0,  4.3.1m-0,  4.3.1k-0,  4.3-3,  4.3-2,  4.3-1,  4.3-0,  4.3k-0,  4.3i-0,  4.3g-0,  4.3b-0,  4.2-0,  4.1l-8,  4.1l-7,  4.1l-6,  4.1l-5,  4.1l-4,  4.1l-3,  4.1l-2,  4.1l-1,  4.1l-0,  3_6-0

depends openjdk:

>=11

depends python:

depends zlib:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install snpeff

and update with::

   mamba update snpeff

To create a new environment, run:

mamba create --name myenvname snpeff

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/snpeff:<tag>

(see `snpeff/tags`_ for valid values for ``<tag>``)

Notes

The tool is available as command `snpEff`. Note that the package version is slightly different from upstream, this is to make sure conda will order the package versions correctly.

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