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Conference papers

A curated Domain centric shared Docker registry linked to the Galaxy toolshed

Abstract : Nowadays, Docker containers are used to ease application deployment, from command lines tools to cluster management1. This technology has a strong impact in bioinformatics where specialized software can often require multiple dependencies. It is a long term preservation solution for legacy and unmaintained tools and it enables a better process isolation in a multi-user environment. Docker as a way to quickly integrate new tools is already used with Galaxy. We have setup a functional prototype of a web registry of Docker images, BioShaDock,2 dedicated to bioinformatics tools and utilities. We created a set of tools descriptors based on Docker images available in our toolshed3. Even if a general purpose registry can be used to hold shared Docker containers, we think that a domain centric registry, e.g. for the French life science community through a registry linked to the cloud of the French Institute of Bioinformatics (IFB8), would have a significant impact on bioinformatician productivity and help to spread best practices. With a clear open source and domain orientation, it could federate container providers4,5 more easily. It would also be able to include validation and curation to eliminate redundant tools, organize versioning and standardize documentation. Future works will concern advanced searching capabilities, possible referencing within the ELIXIR Tools and Data Services Registry6 and in the IFB one (as the ELIXIR French node). We want also to contribute to standardize containers7 and evaluate if benchmarks5 could be produced from a meta-data enriched, Docker registry. References: 1 Google Kubernetes, Docker container cluster management : kubernetes.io 2 BioShaDock, a Bioinformatics Shared Docker registry : http://docker-ui.genouest.org 3 GUGGO Galaxy Tooshed : http://toolshed.genouest.org 4 Hexabio Docker repository : http://biodocker.github.io 5 Nucleotid.es, continuous, objective and reproducible evaluation of genome assemblers using docker containers : http://nucleotid.es 6 ELIXIR Tools and Data Services Registry : https://elixir-registry.cbs.dtu.dk 7 Bioboxes, a standard for creating interchangable bioinformatics software containers : http://bioboxes.org 8 IFB academic Cloud : http://www.france-bioinformatique.fr/?q=en/core/e-infrastructure-team/ifb-cloud
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Contributor : Francois Moreews Connect in order to contact the contributor
Submitted on : Friday, June 5, 2020 - 6:03:42 PM
Last modification on : Tuesday, May 17, 2022 - 2:30:05 PM


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  • HAL Id : hal-01160514, version 1
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François Moreews, Olivier Sallou, Yvan Le Bras, Grosjean Marie, Cyril Monjeaud, et al.. A curated Domain centric shared Docker registry linked to the Galaxy toolshed. Galaxy Community Conference 2015, Jul 2015, Norwich, United Kingdom. ⟨hal-01160514⟩



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