Expanding the Galaxy's reference data

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.

PMID: 35669346
PMCID: PMC9155181
DOI: 10.1093/bioadv/vbac030

Expanding the Galaxy's reference data

Nagampalli VijayKrishna et al. Bioinform Adv. 2022.

. 2022 Apr 29;2(1):vbac030.

doi: 10.1093/bioadv/vbac030. eCollection 2022.

Authors

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.

PMID: 35669346
PMCID: PMC9155181
DOI: 10.1093/bioadv/vbac030

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.

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Figures

**Fig. 1.**
Extending Galaxy’s reference data with refgenie. (A) Setting the value of ‘refgenie_config_file’ to the previously chosen genome configuration file path within the primary Galaxy configuration file (e.g. ‘galaxy.yml’). (B) Example data table mapping between refgenie assets and Galaxy data tables for the BWA tool. Cheetah templating language is used to specify mappings between values, with several pre-populated refgenie variables available as shown. (C) refgenie assets are available for users to select and use in the Galaxy BWA tool. In this example, the user is mapping a set of paired-end sequencing reads against the hg38 genome. (D) A dynamically generated list of available remote refgenie assets are listed for an administrator to select in the ‘refgenie pull’ Galaxy Data Manager tool

See this image and copyright information in PMC

References

1. Blankenberg D. et al.; Galaxy Team. (2014a) Dissemination of scientific software with Galaxy ToolShed. Genome Biol., 15, 403. - PMC - PubMed
1. Blankenberg D. et al.; Galaxy Team. (2014b) Wrangling Galaxy’s reference data. Bioinformatics, 30, 1917–1919. - PMC - PubMed
1. Blomer J. et al. (2011) Distributing LHC application software and conditions databases using the CernVM file system. J. Phys: Conf. Ser., 331, 042003.
1. Dobin A. et al. (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29, 15–21. - PMC - PubMed
1. Giardine B. et al. (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res., 15, 1451–1455. - PMC - PubMed

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Expanding the Galaxy's reference data

Affiliations

Expanding the Galaxy's reference data

Authors

Affiliations

Abstract

Figures

References

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