recipe gatk-framework

The core MIT-licensed Genome Analysis Toolkit (GATK) framework, free for all uses

Homepage:

https://github.com/chapmanb/gatk

License:

MIT

Recipe:

/gatk-framework/meta.yaml

package gatk-framework

(downloads) docker_gatk-framework

versions:
3.6.24-6,  3.6.24-5,  3.6.24-4,  3.6.24-3,  3.6.24-2,  3.6.24-1,  3.6.24-0,  3.5.21-0,  3.4.46-3, 

3.6.24-6,  3.6.24-5,  3.6.24-4,  3.6.24-3,  3.6.24-2,  3.6.24-1,  3.6.24-0,  3.5.21-0,  3.4.46-3,  3.4.46-2,  3.4.46-1,  3.4.46-0

depends openjdk:

>=8,<9

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 gatk-framework

and update with::

   mamba update gatk-framework

To create a new environment, run:

mamba create --name myenvname gatk-framework

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/gatk-framework:<tag>

(see `gatk-framework/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/gatk-framework/README.html)