VijayKrishna Nagampalli, Joshi Jayadev, Coraor Nate, Hillman-Jackson Jennifer, Bouvier Dave, van den Beek Marius, Eguinoa Ignacio, Coppens Frederik, Davis John, Stolarczyk Michał, Sheffield Nathan C, Gladman Simon, Cuccuru Gianmauro, Grüning Björn, Soranzo Nicola, Rasche Helena, Langhorst Bradley W, Bernt Matthias, Fornika Dan, de Lima Morais David Anderson, Barrette Michel, van Heusden Peter, Petrillo Mauro, Puertas-Gallardo Antonio, Patak Alex, Hotz Hans-Rudolf, Blankenberg Daniel
Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA.
Bioinform Adv. 2022 Apr 29;2(1):vbac030. doi: 10.1093/bioadv/vbac030. eCollection 2022.
Properly and effectively managing reference datasets is an important task for many bioinformatics analyses. Refgenie is a reference asset management system that allows users to easily organize, retrieve and share such datasets. Here, we describe the integration of refgenie into the Galaxy platform. Server administrators are able to configure Galaxy to make use of reference datasets made available on a refgenie instance. In addition, a Galaxy Data Manager tool has been developed to provide a graphical interface to refgenie's remote reference retrieval functionality. A large collection of reference datasets has also been made available using the CVMFS (CernVM File System) repository from GalaxyProject.org, with mirrors across the USA, Canada, Europe and Australia, enabling easy use outside of Galaxy.
The ability of Galaxy to use refgenie assets was added to the core Galaxy framework in version 22.01, which is available from https://github.com/galaxyproject/galaxy under the Academic Free License version 3.0. The refgenie Data Manager tool can be installed via the Galaxy ToolShed, with source code managed at https://github.com/BlankenbergLab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull and released using an MIT license. Access to existing data is also available through CVMFS, with instructions at https://galaxyproject.org/admin/reference-data-repo/. No new data were generated or analyzed in support of this research.
正确有效地管理参考数据集是许多生物信息学分析的一项重要任务。Refgenie是一个参考资产管理系统，可让用户轻松组织、检索和共享此类数据集。在此，我们描述了将Refgenie集成到Galaxy平台的过程。服务器管理员能够配置Galaxy，以利用在Refgenie实例上提供的参考数据集。此外，还开发了一个Galaxy数据管理器工具，为Refgenie的远程参考检索功能提供图形界面。还使用来自GalaxyProject.org的CVMFS（CernVM文件系统）存储库提供了大量参考数据集，并在美国、加拿大、欧洲和澳大利亚设有镜像，便于在Galaxy之外使用。
Galaxy使用Refgenie资产的功能已添加到22.01版的核心Galaxy框架中，可从https://github.com/galaxyproject/galaxy获取，遵循学术自由许可证3.0版。Refgenie数据管理器工具可通过Galaxy工具库安装，其源代码托管在https://github.com/BlankenbergLab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull，并根据MIT许可证发布。也可通过CVMFS访问现有数据，相关说明见https://galaxyproject.org/admin/reference-data-repo/。本研究未生成或分析新的数据以提供支持。
