Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud

Moreno, P.; Pireddu, L.; Roger, P.; Goonasekera, N.; Afgan, E.; van den Beek, M.; He, S.; Larsson, A.; Ruttkies, C.; Schober, D.; Johnson, D.; Rocca-Serra, P.; Weber, R. J. M.; Gruening, B.; Salek, R.; Kale, N.; Perez-Riverol, Y.; Papatheodorou, I.; Spjuth, O.; Neumann, S.

doi:10.1101/488643

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bioRxiv · 10.1101/488643

Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud

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Abstract

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. AvailabilityAll 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. Suppl. InformationSupplementary Files are available online. Contactpmoreno@ebi.ac.uk, European Molecular Biology Laboratory, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK, Tel: +44-1223-494267, Fax: +44-1223-484696.

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Moreno, P., Pireddu, L., Roger, P., Goonasekera, N., Afgan, E., van den Beek, M., He, S., Larsson, A., Ruttkies, C., Schober, D., Johnson, D., Rocca-Serra, P., Weber, R. J. M., Gruening, B., Salek, R., Kale, N., Perez-Riverol, Y., Papatheodorou, I., Spjuth, O., Neumann, S.. 2018-12-07. Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud. https://doi.org/10.1101/488643

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