Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud [article]

Pablo Moreno, Luca Pireddu, Pierrick Roger, Nuwan Goonasekera, Enis Afgan, Marius van den Beek, Sijin He, Anders Larsson, Christoph Ruttkies, Daniel Schober, David Johnson, Philippe Rocca-Serra (+8 others)
2018 bioRxiv   pre-print
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
more » ... ment. 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.
doi:10.1101/488643 fatcat:4covzekbrnbxrlqb43gmvrlhkq