recipe gatk

The Genome Analysis Toolkit (GATK) v3, license restricted.

Homepage

https://software.broadinstitute.org/gatk/download/archive

License

https://software.broadinstitute.org/gatk/download/licensing

Recipe

/gatk/meta.yaml

Links

biotools: gatk

package gatk

(downloads) docker_gatk

Versions

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, 3.6-6, 3.6-5, 3.6-4, 3.6-3, 3.6-2, 3.6-1, 3.5-6, 3.5-5

Depends
Required By

Installation

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

conda install gatk

and update with:

conda update gatk

or use the docker container:

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

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

Notes

Due to license restrictions, this recipe cannot distribute and install GATK v3 directly. To fully install GATK, you must download a licensed copy of GATK from the Broad Institute (https://software.broadinstitute.org/gatk/download/archive), 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”).