gatk
Download : docker pull ghcr.io/autamus/gatk
Compressed Size : 747MB
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.