Expanding the Galaxy's reference data

Nagampalli VijayKrishna; Jayadev Joshi; Nate Coraor; Jennifer Hillman-Jackson; Dave Bouvier; Marius van den Beek; Ignacio Eguinoa; Frederik Coppens; John Davis; Michał Stolarczyk; Nathan C Sheffield; Simon Gladman; Gianmauro Cuccuru; Björn Grüning; Nicola Soranzo; Helena Rasche; Bradley W Langhorst; Matthias Bernt; Dan Fornika; David Anderson de Lima Morais; Michel Barrette; Peter van Heusden; Mauro Petrillo; Antonio Puertas-Gallardo; Alex Patak; Hans-Rudolf Hotz; Daniel Blankenberg

doi:10.1093/bioadv/vbac030

Expanding the Galaxy's reference data

Bioinform Adv. 2022 Apr 29;2(1):vbac030. doi: 10.1093/bioadv/vbac030. eCollection 2022.

Authors

Nagampalli VijayKrishna¹, Jayadev Joshi¹, Nate Coraor², Jennifer Hillman-Jackson², Dave Bouvier², Marius van den Beek², Ignacio Eguinoa^{3

4}, Frederik Coppens^{3

4}, John Davis⁵, Michał Stolarczyk⁶, Nathan C Sheffield⁶, Simon Gladman⁷, Gianmauro Cuccuru⁸, Björn Grüning⁸, Nicola Soranzo⁹, Helena Rasche¹⁰, Bradley W Langhorst¹¹, Matthias Bernt¹², Dan Fornika¹³, David Anderson de Lima Morais¹⁴, Michel Barrette¹⁴, Peter van Heusden¹⁵, Mauro Petrillo¹⁶, Antonio Puertas-Gallardo¹⁶, Alex Patak¹⁶, Hans-Rudolf Hotz^{17

18}, Daniel Blankenberg^{1

19}

Affiliations

¹ Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
² Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA.
³ VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
⁴ Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
⁵ Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
⁶ Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA.
⁷ University of Melbourne, Melbourne, VIC, Australia.
⁸ University of Freiburg, Freiburg im Breisgau, Germany.
⁹ Earlham Institute, Norwich Research Park, Norwich, UK.
¹⁰ Clinical Bioinformatics Group, Department of Pathology, Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands.
¹¹ New England Biolabs, Ipswich, MA 01938, USA.
¹² Department Computational Biology, Helmholtz Centre for Environmental Research, UFZ, 04318 Leipzig, Germany.
¹³ BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada.
¹⁴ Centre de Calcul Scientifique, Université de Sherbrooke, Sherbrooke, QC, Canada.
¹⁵ South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.
¹⁶ European Commission, Joint Research Centre (JRC), Ispra, Italy.
¹⁷ Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
¹⁸ SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
¹⁹ Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA.

Abstract

Summary: 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.

Availability and implementation: 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.

Abstract

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