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  1. IGB
  2. IGBF-4112

2025 Update Galaxy dbkey values in IGB synonyms.txt

        Details

        • Type: Task
        • Status: To-Do (View Workflow)
        • Priority: Major
        • Resolution: Unresolved
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          Situation: usegalaxy.org website is used frequently by IGB users. When a user views data from Galaxy in IGB we attempt to load the appropriate genome in IGB. Many of the genomes line up with and use the same nomenclature as Galaxy, but there are now many more genomes in Galaxy.

          Task: Update the IGB synonyms.txt with any missing Galaxy synonyms. See IGBF-1879 for additional details.

          Galaxy genome API: https://usegalaxy.org/api/genomes
          Galaxy Europe genome API: https://usegalaxy.eu/api/genomes
          UCSC genome API (for comparison, this should be up to date in IGB already): https://api.genome.ucsc.edu/list/ucscGenomes

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              Improvement - An improvement or enhancement to an existing feature or task. IGBF-1879 Ensure Galaxy default dbkey values are in synonyms.txt

              • Major - Major loss of function.
              • Closed

                Activity

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                nfreese Nowlan Freese created issue -
                nfreese Nowlan Freese made changes -
                Field Original Value New Value
                Epic Link IGBF-1880 [ 17970 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-1879 [ IGBF-1879 ]
                nfreese Nowlan Freese made changes -
                Description Situation: usegalaxy.org website is used frequently by IGB users. When a user views data from Galaxy in IGB we attempt to load the appropriate genome in IGB. Many of the genomes line up with and use the same nomenclature as Galaxy, but there are now many more genomes in Galaxy.

                Task: Update the IGB synonyms.txt with any missing Galaxy synonyms.

                Galaxy genome API: https://usegalaxy.org/api/genomes
                Galaxy Europe genome API: https://usegalaxy.eu/api/genomes
                UCSC genome API (for comparison, this should be up to date in IGB already): https://api.genome.ucsc.edu/list/ucscGenomes                 		Situation: usegalaxy.org website is used frequently by IGB users. When a user views data from Galaxy in IGB we attempt to load the appropriate genome in IGB. Many of the genomes line up with and use the same nomenclature as Galaxy, but there are now many more genomes in Galaxy.

                Task: Update the IGB synonyms.txt with any missing Galaxy synonyms. See IGBF-1879 for additional details.

                Galaxy genome API: https://usegalaxy.org/api/genomes
                Galaxy Europe genome API: https://usegalaxy.eu/api/genomes
                UCSC genome API (for comparison, this should be up to date in IGB already): https://api.genome.ucsc.edu/list/ucscGenomes
                pkulzer Paige Kulzer made changes -
                Assignee Paige Kulzer [ pkulzer ]
                pkulzer Paige Kulzer made changes -
                Sprint Spring 3 [ 212 ] Spring 4 [ 213 ]

                  People

                  • Assignee:
                    pkulzer Paige Kulzer
                    Reporter:
                    nfreese Nowlan Freese
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                    Dates

                    • Created:
                      Updated: