The impact of Docker containers on the performance of genomic pipelines

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 probl...

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Main Authors:	Di Tommaso, Paolo, Palumbo, Emilio, Chatzou, Maria, Prieto, Pablo, Heuer, Michael L., Notredame, Cedric
Format:	Online
Language:	English
Published:	PeerJ Inc. 2015
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4586803/

id	pubmed-4586803
recordtype	oai_dc
spelling	pubmed-45868032015-09-29 The impact of Docker containers on the performance of genomic pipelines Di Tommaso, Paolo Palumbo, Emilio Chatzou, Maria Prieto, Pablo Heuer, Michael L. Notredame, Cedric Bioinformatics 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. PeerJ Inc. 2015-09-24 /pmc/articles/PMC4586803/ /pubmed/26421241 http://dx.doi.org/10.7717/peerj.1273 Text en © 2015 Di Tommaso et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Di Tommaso, Paolo Palumbo, Emilio Chatzou, Maria Prieto, Pablo Heuer, Michael L. Notredame, Cedric
spellingShingle	Di Tommaso, Paolo Palumbo, Emilio Chatzou, Maria Prieto, Pablo Heuer, Michael L. Notredame, Cedric The impact of Docker containers on the performance of genomic pipelines
author_facet	Di Tommaso, Paolo Palumbo, Emilio Chatzou, Maria Prieto, Pablo Heuer, Michael L. Notredame, Cedric
author_sort	Di Tommaso, Paolo
title	The impact of Docker containers on the performance of genomic pipelines
title_short	The impact of Docker containers on the performance of genomic pipelines
title_full	The impact of Docker containers on the performance of genomic pipelines
title_fullStr	The impact of Docker containers on the performance of genomic pipelines
title_full_unstemmed	The impact of Docker containers on the performance of genomic pipelines
title_sort	impact of docker containers on the performance of genomic pipelines
description	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.
publisher	PeerJ Inc.
publishDate	2015
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4586803/
_version_	1613481385683582976

The impact of Docker containers on the performance of genomic pipelines

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