Wrangling Galaxy's reference data
Wrangling Galaxy's reference data
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DOI：
10.1093/bioinformatics/btu119
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发表时间：
2014-07-01
期刊：
影响因子：
5.8
通讯作者：
Nekrutenko, Anton
中科院分区：
文献类型：
--
作者：
Blankenberg, Daniel;Johnson, James E.;Nekrutenko, Anton
Galaxy平台已经发展成为一个功能齐全的协作工作台，其目标是从本质上捕获出处，以实现可重复的数据分析，并使其直接运行自己的服务器。然而，银河平台的许多工具依赖于比对指数等参考数据的存在才能有效运作。到目前为止，为Galaxy构建这种数据缓存一直是一个容易出错的手动过程，缺乏可重复性和出处。银河数据管理器框架是一项改进，将银河内置数据缓存的管理从手动程序改为自动图形用户界面驱动的过程，其中包含与银河分析工具相同的开放性，可重复性和出处。数据管理器工具允许银河系统管理员为任何类型的参考数据真实的实时下载、创建和安装额外的数据集。可用性和实施：Galaxy Data Manager框架是用Python实现的，并已集成为核心Galaxy平台的一部分。单个数据管理器工具可以在本地定义或从ToolShed安装，允许Galaxy社区根据需要定义其他数据管理器工具，并提供完整的版本控制和依赖支持。
The Galaxy platform has developed into a fully featured collaborative workbench, with goals of inherently capturing provenance to enable reproducible data analysis, and of making it straightforward to run one's own server. However, many Galaxy platform tools rely on the presence of reference data, such as alignment indexes, to function efficiently. Until now, the building of this cache of data for Galaxy has been an error-prone manual process lacking reproducibility and provenance. The Galaxy Data Manager framework is an enhancement that changes the management of Galaxy's built-in data cache from a manual procedure to an automated graphical user interface (GUI) driven process, which contains the same openness, reproducibility and provenance that is afforded to Galaxy's analysis tools. Data Manager tools allow the Galaxy administrator to download, create and install additional datasets for any type of reference data in real time. Availability and implementation: The Galaxy Data Manager framework is implemented in Python and has been integrated as part of the core Galaxy platform. Individual Data Manager tools can be defined locally or installed from a ToolShed, allowing the Galaxy community to define additional Data Manager tools as needed, with full versioning and dependency support.