ReGaTE: Registration of Galaxy Tools in Elixir.
ReGaTE: Registration of Galaxy Tools in Elixir.
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DOI：
10.1093/gigascience/gix022
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发表时间：
2017-06-01
期刊：
影响因子：
9.2
通讯作者：
Menager, Herve
中科院分区：
文献类型：
--
作者：
Doppelt-Azeroual, Olivia;Mareuil, Fabien;Menager, Herve
背景：生物信息学家在他们的日常工作中经常使用多种软件工具和数据源，他们的选择受到一些编目倡议的指导。灵丹妙药工具和数据服务注册处(Bio.Tools)旨在提供一个中央信息点，独立于生物信息学或技术实施中的任何具体科学范围。与此同时，在工作台和工作流程环境中集成生物信息学软件的努力已经加快，以实现生物信息学实验的设计、自动化和重复性。Galaxy框架就是这样一个流行的环境，目前在世界各地有80多个公开可用的Galaxy服务器。在生物信息学软件的通用登记处，如Bio.Tools，Galaxy实例构成了有价值内容的主要来源。然而，到目前为止，还没有一种方便的机制来集体注册这类服务。我们介绍了ReGaTE(在Elixir中注册Galaxy Tools)，这是一个软件实用程序，可以自动注册Galaxy实例中可用的服务。该实用程序使用BioBlend应用程序接口从Galaxy服务器提取服务元数据，使用Bio.Tools所需的科学信息增强元数据，并将其推送到注册表。ReGate提供了一种在Bio.Tools中发布Galaxy服务的快捷方式。通过这样做，服务提供商可以提高他们服务的可见度，同时丰富Bio.Tools为其用户提供的软件发现功能。ReGate的源代码可以在https://github.com/C3BI-pasteur-fr/ReGaTE的Github上免费获得。
Background: 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 .