The impact of Docker containers on the performance of genomic pipelines
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- dc.contributor.author Di Tommaso, Paoloca
- dc.contributor.author Palumbo, Emilioca
- dc.contributor.author Chatzou, Maria, 1985-ca
- dc.contributor.author Prieto Barja, Pablo, 1986-ca
- dc.contributor.author Heuer, Michael L.ca
- dc.contributor.author Notredame, Cedricca
- dc.date.accessioned 2015-11-18T13:46:03Z
- dc.date.available 2015-11-18T13:46:03Z
- dc.date.issued 2015
- 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.ca
- dc.format.mimetype application/pdfca
- 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.1273ca
- dc.identifier.doi http://dx.doi.org/10.7717/peerj.1273
- dc.identifier.issn 2167-8359
- dc.identifier.uri http://hdl.handle.net/10230/25137
- dc.language.iso engca
- dc.publisher PeerJ Inc.ca
- dc.relation.ispartof PeerJ. 2015;3:e1273
- dc.rights © 2015 Di Tommaso et al. Distributed under Creative Commons CC-BY 4.0ca
- dc.rights.accessRights info:eu-repo/semantics/openAccessca
- dc.rights.uri http://creativecommons.org/licenses/by/4.0/ca
- dc.subject.keyword Workflow
- dc.subject.keyword Pipelines
- dc.subject.keyword Docker
- dc.subject.keyword Virtualisation
- dc.subject.keyword Bioinformatics
- dc.subject.other Biologia computacional
- dc.subject.other Bioinformàtica
- dc.title The impact of Docker containers on the performance of genomic pipelinesca
- dc.type info:eu-repo/semantics/articleca
- dc.type.version info:eu-repo/semantics/acceptedVersionca