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Expanding the Galaxy's reference data.
VijayKrishna, Nagampalli; Joshi, Jayadev; Coraor, Nate; Hillman-Jackson, Jennifer; Bouvier, Dave; van den Beek, Marius; Eguinoa, Ignacio; Coppens, Frederik; Davis, John; Stolarczyk, Michal; Sheffield, Nathan C; Gladman, Simon; Cuccuru, Gianmauro; Grüning, Björn; Soranzo, Nicola; Rasche, Helena; Langhorst, Bradley W; Bernt, Matthias; Fornika, Dan; de Lima Morais, David Anderson; Barrette, Michel; van Heusden, Peter; Petrillo, Mauro; Puertas-Gallardo, Antonio; Patak, Alex; Hotz, Hans-Rudolf; Blankenberg, Daniel.
Affiliation
  • VijayKrishna N; Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
  • Joshi J; Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
  • Coraor N; Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA.
  • Hillman-Jackson J; Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA.
  • Bouvier D; Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA.
  • van den Beek M; Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA.
  • Eguinoa I; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
  • Coppens F; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
  • Davis J; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
  • Stolarczyk M; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
  • Sheffield NC; Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
  • Gladman S; Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA.
  • Cuccuru G; Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA.
  • Grüning B; University of Melbourne, Melbourne, VIC, Australia.
  • Soranzo N; University of Freiburg, Freiburg im Breisgau, Germany.
  • Rasche H; University of Freiburg, Freiburg im Breisgau, Germany.
  • Langhorst BW; Earlham Institute, Norwich Research Park, Norwich, UK.
  • Bernt M; Clinical Bioinformatics Group, Department of Pathology, Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands.
  • Fornika D; New England Biolabs, Ipswich, MA 01938, USA.
  • de Lima Morais DA; Department Computational Biology, Helmholtz Centre for Environmental Research, UFZ, 04318 Leipzig, Germany.
  • Barrette M; BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada.
  • van Heusden P; Centre de Calcul Scientifique, Université de Sherbrooke, Sherbrooke, QC, Canada.
  • Petrillo M; Centre de Calcul Scientifique, Université de Sherbrooke, Sherbrooke, QC, Canada.
  • Puertas-Gallardo A; South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.
  • Patak A; European Commission, Joint Research Centre (JRC), Ispra, Italy.
  • Hotz HR; European Commission, Joint Research Centre (JRC), Ispra, Italy.
  • Blankenberg D; European Commission, Joint Research Centre (JRC), Ispra, Italy.
Bioinform Adv ; 2(1): vbac030, 2022.
Article in En | MEDLINE | ID: mdl-35669346
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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Full text: 1 Collection: 01-internacional Database: MEDLINE Language: En Journal: Bioinform Adv Year: 2022 Type: Article Affiliation country: United States
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Full text: 1 Collection: 01-internacional Database: MEDLINE Language: En Journal: Bioinform Adv Year: 2022 Type: Article Affiliation country: United States