@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 Gruning, 
                  Bjorn 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},
  volume =	 {2},
  number =	 {1},
  pages =	 {vbac030},
  user =	 {backofen},
  pmid =	 {35669346},
  doi = 	 {10.1093/bioadv/vbac030},
  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.}
}