Apptainer

Apptainer is a software for creating and running containers.

Installation

This guide describes how to install Apptainer using Pixi. Before proceeding, ensure that you have followed the Pixi installation guide. Once Pixi is installed in your environment, you can install Apptainer globally by running:

pixi global install apptainer

mkdir $HOME/images
apptainer pull $HOME/images/samtools.sif "docker://quay.io/biocontainers/samtools:1.22.1--h96c455f_0"
apptainer --silent exec "$HOME/images/samtools.sif" samtools --help

samtools() {
    apptainer --silent exec "$HOME/images/samtools.sif" samtools "$@"
}

apptainer cache clean --force