Apptainer cache validity

I was recently asked whether Apptainer (forked from the Singularity project) will definitely update its cache of Apptainer images created from OCI/Docker images if a tagged image changes on a remote repo. Let’s find out: Let’s start by creating a v. simple image that just sends a message to stdout when executed. After creating the image we tag it so we have an identifier to push to a remote image registry.

Running job arrays on HPC using Singularity and a Docker image

I thought I’d share a little success story. A researcher recently approached me to say he’d been having difficulty getting his bioinformatics workflow (based on this) working on the University of Sheffield’s ShARC HPC cluster and had an urgent need to get it running to meet a pending deadline. He’s primarily using the GATK ‘genome analysis toolkit’. He appealed for help on the GATK forum, members of which suggested that the issue may be due to the way in which GATK was installed.

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