Wrangling Galaxy's reference data

Daniel Blankenberg; James E Johnson; Galaxy Team; James Taylor; Anton Nekrutenko

doi:10.1093/bioinformatics/btu119

Wrangling Galaxy's reference data

Bioinformatics. 2014 Jul 1;30(13):1917-9. doi: 10.1093/bioinformatics/btu119. Epub 2014 Feb 28.

Authors

Daniel Blankenberg¹, James E Johnson²; Galaxy Team; James Taylor³, Anton Nekrutenko¹

Affiliations

¹ Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA, http://www.galaxyproject.org, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA, Department of Biology and Department of Mathematics and Computer Science, Emory University, Atlanta, GA 30322, USADepartment of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA, http://www.galaxyproject.org, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA, Department of Biology and Department of Mathematics and Computer Science, Emory University, Atlanta, GA 30322, USA.
² Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA, http://www.galaxyproject.org, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA, Department of Biology and Department of Mathematics and Computer Science, Emory University, Atlanta, GA 30322, USA.
³ Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA, http://www.galaxyproject.org, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA, Department of Biology and Department of Mathematics and Computer Science, Emory University, Atlanta, GA 30322, USADepartment of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA, http://www.galaxyproject.org, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA, Department of Biology and Department of Mathematics and Computer Science, Emory University, Atlanta, GA 30322, USADepartment of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA, http://www.galaxyproject.org, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA, Department of Biology and Department of Mathematics and Computer Science, Emory University, Atlanta, GA 30322, USA.

Abstract

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.

Wrangling Galaxy's reference data

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