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