Abstract

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.

Footnotes

* Author emails, add PDF versions of supplementary materials and URLs.

* https://github.com/galaxyproject/galaxy-kubernetes/

Details

Title
Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud
Author
Moreno, Pablo; Pireddu, Luca; Pierrick Roger; Goonasekera, Nuwan; Afgan, Enis; Van Den Beek, Marius; He, Sijin; Larsson, Anders; Ruttkies, Christoph; Schober, Daniel; Johnson, David; Rocca-Serra, Philippe; Weber, Ralf Jm; Gruening, Bjoern; Salek, Reza; Kale, Namrata; Perez-Riverol, Yasset; Papatheodorou, Irene; Spjuth, Ola; Neumann, Steffen
University/institution
Cold Spring Harbor Laboratory Press
Section
New Results
Publication year
2019
Publication date
Feb 12, 2019
Publisher
Cold Spring Harbor Laboratory Press
ISSN
2692-8205
Source type
Working Paper
Language of publication
English
DOI
https://doi.org/10.1101/488643
ProQuest document ID
2178838310
Copyright
© 2019. This article is published under http://creativecommons.org/licenses/by/4.0/ (“the License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.