Expanding the Galaxy’s reference data

Author:

VijayKrishna Nagampalli1,Joshi Jayadev1,Coraor Nate2,Hillman-Jackson Jennifer2,Bouvier Dave2,van den Beek Marius2,Eguinoa Ignacio34,Coppens Frederik34,Davis John5,Stolarczyk Michał6,Sheffield Nathan C6,Gladman Simon7,Cuccuru Gianmauro8,Grüning Björn8ORCID,Soranzo Nicola9ORCID,Rasche Helena10,Langhorst Bradley W11,Bernt Matthias12ORCID,Fornika Dan13,de Lima Morais David Anderson14,Barrette Michel14,van Heusden Peter15ORCID,Petrillo Mauro16,Puertas-Gallardo Antonio16ORCID,Patak Alex16ORCID,Hotz Hans-Rudolf1718ORCID,Blankenberg Daniel119ORCID

Affiliation:

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

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.

Funder

National Institutes of Health

Publisher

Oxford University Press (OUP)

Subject

Cell Biology,Developmental Biology,Embryology,Anatomy

Reference12 articles.

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