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Gigascience. 2017 Jun 1;6(6):1-4. doi: 10.1093/gigascience/gix022.

ReGaTE: Registration of Galaxy Tools in Elixir.

Author information

1
Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 Institut Pasteur et CNRS), 25 rue du Docteur Roux, Paris, France.
2
Computational Biology Unit, Department of Informatics, University of Bergen, Thormøhlensgate 55, Bergen, Norway.
3
Earlham Institute, Norwich Research Park, NR4 7UG Norwich, United Kingdom.
4
Institut de Biologie Paris-Seine, Université Pierre et Marie Curie, Paris, France.
5
Department of Computer Science, Albert-Ludwigs-University,Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany.
6
Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, 2800 Kongens, Lyngby, Denmark.

Abstract

Bioinformaticians routinely use multiple software tools and data sources in their day-to-day work and have been guided in their choices by a number of cataloguing initiatives. The ELIXIR Tools and Data Services Registry (bio.tools) aims to provide a central information point, independent of any specific scientific scope within bioinformatics or technological implementation. Meanwhile, efforts to integrate bioinformatics software in workbench and workflow environments have accelerated to enable the design, automation, and reproducibility of bioinformatics experiments. One such popular environment is the Galaxy framework, with currently more than 80 publicly available Galaxy servers around the world. In the context of a generic registry for bioinformatics software, such as bio.tools, Galaxy instances constitute a major source of valuable content. Yet there has been, to date, no convenient mechanism to register such services en masse. We present ReGaTE (Registration of Galaxy Tools in Elixir), a software utility that automates the process of registering the services available in a Galaxy instance. This utility uses the BioBlend application program interface to extract service metadata from a Galaxy server, enhance the metadata with the scientific information required by bio.tools, and push it to the registry. ReGaTE provides a fast and convenient way to publish Galaxy services in bio.tools. By doing so, service providers may increase the visibility of their services while enriching the software discovery function that bio.tools provides for its users. The source code of ReGaTE is freely available on Github at https://github.com/C3BI-pasteur-fr/ReGaTE .

KEYWORDS:

Galaxy; bio.tools; bioinformatics services

PMID:
28402416
PMCID:
PMC5530318
DOI:
10.1093/gigascience/gix022
[Indexed for MEDLINE]
Free PMC Article

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