gatk

downloads

The full Genome Analysis Toolkit (GATK) framework, license restricted.

Home https://www.broadinstitute.org/gatk/
Versions 3.5, 3.6, 3.7, 3.8
License https://www.broadinstitute.org/gatk/about/#licensing
Recipe https://github.com/bioconda/bioconda-recipes/tree/master/recipes/gatk
Links biotools: gatk

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install gatk

and update with:

conda update gatk

Notes

Due to license restrictions, this recipe cannot distribute and install GATK directly. To fully install GATK, you must download a licensed copy of GATK from the Broad Institute (https://www.broadinstitute.org/gatk/download/), install this package, and call “gatk3-register /path/to/GenomeAnalysisTK[-$PKG_VERSION.tar.bz2|.jar]”, which will copy GATK into your conda environment. The main run script has been renamed to gatk3 to allow compatibility with the new GATK 4 launch script (which is now gatk).

docker

A Docker container is available at https://quay.io/repository/biocontainers/gatk.