BioContainers: an open-source and community-driven framework for software standardization

Felipe da Veiga Leprevost(University of Michigan), Björn Grüning(University of Freiburg), Saulo Aflitos, Hannes Röst(Stanford University), Julian Uszkoreit(Ruhr University Bochum), Harald Barsnes(University of Bergen), Marc Vaudel(Haukeland University Hospital), Pablo Moreno(European Bioinformatics Institute), Laurent Gatto(University of Cambridge), Jonas Weber(University of Freiburg), Mingze Bai(European Bioinformatics Institute), Rafael C. Jiménez(European Bioinformatics Institute), Timo Sachsenberg(University of Tübingen), Julianus Pfeuffer(University of Tübingen), Roberto Vera Alvarez(National Institutes of Health), Johannes Griss(European Bioinformatics Institute), Alexey I. Nesvizhskii(University of Michigan), Yasset Pérez‐Riverol(European Bioinformatics Institute)
Bioinformatics
March 29, 2017
10.1093/bioinformatics/btx192
Cited by 837Open Access
Full Text

Abstract

MOTIVATION: BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters). AVAILABILITY AND IMPLEMENTATION: The software is freely available at github.com/BioContainers/. CONTACT: yperez@ebi.ac.uk.

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