How to convert a Docker container to an Apptainer container
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General
Docker provides a convenient way of running software from within a preset environment with all the dependencies setup by the developers on any other Linux system. However, due to technical limitations Docker is not supported and not available on ARC.
Instead an alternative container technology based on Apptainer (former Singularity) can be used. Apptainer is another container technology with its own container format and specifications, but it also can use Docker containers as a source and convert them in its native Apptainer format.
Converting a GATK Docker image
GATK is a popular bioinformatics toolbox. To find a container for the latest version of we have to go to its home page at