gatk

Versions: [4.2.0.0, 4.2.2.0]

gatk

Download        : docker pull ghcr.io/autamus/gatk
Compressed Size : 655MB

Description

Genome Analysis Toolkit Variant Discovery in High-Throughput Sequencing Data

Usage

Pull (Download)

To download the latest version of gatk run,

docker pull ghcr.io/autamus/gatk:latest

or to download a specific version of gatk run,

docker pull ghcr.io/autamus/gatk:4.2.0.0

Run

To run the container as an application run,

docker run --rm ghcr.io/autamus/gatk gatk --version

or to run the container in an interactive session run,

docker run -it --rm ghcr.io/autamus/gatk bash

Mounting volumes between the container and your machine

To access files from your machine within the gatk container you’ll have to mount them using the -v external/path:internal/path option.

For example,

docker run -v ~/Documents/Data:/Data ghcr.io/autamus/gatk gatk /Data/myData.csv

which will mount the ~/Documents/Data directory on your computer to the /Data directory within the container.

HPC

If you’re looking to use this container in an HPC environment we recommend using Singularity-HPC to use the container just as any other module on the cluster. Check out the SHPC gatk container here.