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...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
PeerJ Inc.
2015-09-01
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| Series: | PeerJ |
| Subjects: | |
| Online Access: | https://peerj.com/articles/1273.pdf |
| _version_ | 1797424300949504000 |
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| author | Paolo Di Tommaso Emilio Palumbo Maria Chatzou Pablo Prieto Michael L. Heuer Cedric Notredame |
| author_facet | Paolo Di Tommaso Emilio Palumbo Maria Chatzou Pablo Prieto Michael L. Heuer Cedric Notredame |
| author_sort | Paolo Di Tommaso |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-09T08:00:14Z |
| format | Article |
| id | doaj.art-0e8cf15c6a164b10b92cabc7f498a043 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T08:00:14Z |
| publishDate | 2015-09-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-0e8cf15c6a164b10b92cabc7f498a0432023-12-03T00:46:56ZengPeerJ Inc.PeerJ2167-83592015-09-013e127310.7717/peerj.1273The impact of Docker containers on the performance of genomic pipelinesPaolo Di Tommaso0Emilio Palumbo1Maria Chatzou2Pablo Prieto3Michael L. Heuer4Cedric Notredame5Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Barcelona, SpainBioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Barcelona, SpainBioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Barcelona, SpainBioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Barcelona, SpainDepartment of Bioinformatics Research, National Marrow Donor Program, Minneapolis, MN, United StatesBioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Barcelona, SpainGenomic 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.https://peerj.com/articles/1273.pdfWorkflowPipelinesDockerVirtualisationBioinformatics |
| spellingShingle | Paolo Di Tommaso Emilio Palumbo Maria Chatzou Pablo Prieto Michael L. Heuer Cedric Notredame The impact of Docker containers on the performance of genomic pipelines PeerJ Workflow Pipelines Docker Virtualisation Bioinformatics |
| title | 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_short | The impact of Docker containers on the performance of genomic pipelines |
| title_sort | impact of docker containers on the performance of genomic pipelines |
| topic | Workflow Pipelines Docker Virtualisation Bioinformatics |
| url | https://peerj.com/articles/1273.pdf |
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