@article{VijayKrishna_Joshi_Coraor-Expan_the_Galax-2022,
author = {VijayKrishna, Nagampalli and Joshi, Jayadev and Coraor, 
          Nate and Hillman-Jackson, Jennifer and Bouvier, Dave and van 
          den Beek, Marius and Eguinoa, Ignacio and Coppens, Frederik 
          and Davis, John and Stolarczyk, Michal and Sheffield, Nathan 
          C. and Gladman, Simon and Cuccuru, Gianmauro and Grüning, 
          Björn and Soranzo, Nicola and Rasche, Helena and Langhorst, 
          Bradley W. and Bernt, Matthias and Fornika, Dan and de Lima 
          Morais, David Anderson and Barrette, Michel and van Heusden, 
          Peter and Petrillo, Mauro and Puertas-Gallardo, Antonio and 
          Patak, Alex and Hotz, Hans-Rudolf and Blankenberg, Daniel},
title = {Expanding the {Galaxy}'s reference data},
journal = {Bioinform Adv},
year = {2022},
doi = {10.1093/bioadv/vbac030},
volume = {2},
user = {backofen},
pmid = {35669346},
pages = {vbac030},
number = {1},
issn = {2635-0041},
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.}
}