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The impact of Docker containers on the performance of genomic pipelines

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dc.contributor.author Di Tommaso, Paolo
dc.contributor.author Palumbo, Emilio
dc.contributor.author Chatzou, Maria, 1985-
dc.contributor.author Prieto Barja, Pablo, 1986-
dc.contributor.author Heuer, Michael L.
dc.contributor.author Notredame, Cedric
dc.date.accessioned 2015-11-18T13:46:03Z
dc.date.available 2015-11-18T13:46:03Z
dc.date.issued 2015
dc.identifier.citation Di Tommaso P, Palumbo E, Chatzou M, Prieto P, Heuer ML, Notredame C. The impact of Docker containers on the performance of genomic pipelines. PeerJ. 2015;3:e1273. DOI: 10.7717/peerj.1273
dc.identifier.issn 2167-8359
dc.identifier.uri http://hdl.handle.net/10230/25137
dc.description.abstract Genomic pipelines consist of several pieces of third party software and, because of their experimental nature, frequent changes and updates are commonly necessary thus raising serious deployment and reproducibility issues. Docker containers are emerging as a possible solution for many of these problems, as they allow the packaging of pipelines in an isolated and self-contained manner. This makes it easy to distribute and execute pipelines in a portable manner across a wide range of computing platforms. Thus, the question that arises is to what extent the use of Docker containers might affect the performance of these pipelines. Here we address this question and conclude that Docker containers have only a minor impact on the performance of common genomic pipelines, which is negligible when the executed jobs are long in terms of computational time.
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher PeerJ Inc.
dc.relation.ispartof PeerJ. 2015;3:e1273
dc.rights © 2015 Di Tommaso et al. Distributed under Creative Commons CC-BY 4.0
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.subject.other Biologia computacional
dc.subject.other Bioinformàtica
dc.title The impact of Docker containers on the performance of genomic pipelines
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.7717/peerj.1273
dc.subject.keyword Workflow
dc.subject.keyword Pipelines
dc.subject.keyword Docker
dc.subject.keyword Virtualisation
dc.subject.keyword Bioinformatics
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/acceptedVersion


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