Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud
Marius van den Beek,
Ralf JM Weber,
Reza M Salek,
Posted 07 Dec 2018
bioRxiv DOI: 10.1101/488643
Posted 07 Dec 2018
Summary: Making reproducible, auditable and scalable data-processing analysis workflows is an important challenge in the field of bioinformatics. Recently, software containers and cloud computing introduced a novel solution to address these challenges. They simplify software installation, management and reproducibility by packaging tools and their dependencies. In this work we implemented a cloud provider agnostic and scalable container orchestration setup for the popular Galaxy workflow environment. This solution enables Galaxy to run on and offload jobs to most cloud providers (e.g. Amazon Web Services, Google Cloud or OpenStack, among others) through the Kubernetes container orchestrator. Availability: All code has been contributed to the Galaxy Project and is available (since Galaxy 17.05) at https://github.com/galaxyproject/ in the galaxy and galaxy-kubernetes repositories. https://public.phenomenal-h2020.eu/ is an example deployment.
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