recipe gatk

The full Genome Analysis Toolkit (GATK) framework, v3

Homepage:

https://www.broadinstitute.org/gatk/

License:

BSD

Recipe:

/gatk/meta.yaml

Links:

biotools: gatk

package gatk

(downloads) docker_gatk

versions:
3.8-11,  3.8-10,  3.8-9,  3.8-8,  3.8-7,  3.8-5,  3.8-4,  3.8-3,  3.8-2, 

3.8-11,  3.8-10,  3.8-9,  3.8-8,  3.8-7,  3.8-5,  3.8-4,  3.8-3,  3.8-2,  3.8-1,  3.8-0,  3.7-1,  3.7-0,  3.6-11,  3.6-10,  3.6-9,  3.6-8,  3.6-7,  3.6-6,  3.6-5,  3.6-4,  3.6-3,  3.6-2,  3.6-1,  3.5-11,  3.5-10,  3.5-6,  3.5-5

depends openjdk:

>=8,<9

depends python:

depends r-ggplot2:

depends r-gplots:

depends r-gsalib:

depends r-reshape:

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

and update with::

   mamba update gatk

To create a new environment, run:

mamba create --name myenvname gatk

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:<tag>

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

Download stats

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/README.html)