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  1. IGB
  2. IGBF-1883

Find Daphnia genome and annotation

        Details

        • Type: New Feature
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
        • Story Points:
          1
        • Epic Link:
        • Sprint:
          Summer 2019 Sprint 10, Summer 2019 Sprint 11

          Description

          Find the Daphnia magna and Daphnia Pulex genomes and annotations so that they can be added to the IGB Quickload.

            Attachments

              Issue Links

              relates to

              New Feature - A new feature of the product, which has yet to be developed. HELP-323 Support Daphnia Genome in IGB

              • Major - Major loss of function.
              • Closed

              New Feature - A new feature of the product, which has yet to be developed. IGBF-1915 Add Daphnia magna and pulex genomes to IGB

              • Major - Major loss of function.
              • Closed

                Activity

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                8 older comments
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                ann.loraine Ann Loraine added a comment - - edited

                Please allow your computer to mirror "Data Management for Quickload" Dropbox folder.
                Once it is mirrored on your machine, please add the new folders to the checked-out svn repository there - it is in the folder "genomes"
                Edit the contents.txt file you see there to include the new genome versions.
                Once everything is there, I will be able to commit it to the repository.

                Show
                ann.loraine Ann Loraine added a comment - - edited Please allow your computer to mirror "Data Management for Quickload" Dropbox folder. Once it is mirrored on your machine, please add the new folders to the checked-out svn repository there - it is in the folder "genomes" Edit the contents.txt file you see there to include the new genome versions. Once everything is there, I will be able to commit it to the repository.
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                ann.loraine Ann Loraine added a comment - - edited

                Regarding the species.txt file:

                • Please edit the corresponding files in the IGB code base so that when we do a new release of IGB, the new version will pick up the new genome version synonyms.
                Show
                ann.loraine Ann Loraine added a comment - - edited Regarding the species.txt file: Please edit the corresponding files in the IGB code base so that when we do a new release of IGB, the new version will pick up the new genome version synonyms.
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                ann.loraine Ann Loraine added a comment -

                Sorry, I forgot this request:

                • Please update .htaccess in Quickload as well
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                ann.loraine Ann Loraine added a comment - Sorry, I forgot this request: Please update .htaccess in Quickload as well
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                nfreese Nowlan Freese added a comment -

                Added the four Daphnia assemblies and annotations to "Data Management for Quickload" Dropbox folder. Updated contents.txt. I modified the .htaccess.

                I did not modify the species.txt or synonyms.txt in the dropbox folder. I created the pull request IGBF-1883-AddDaphnia with modifications to the IGB codebase species.txt and synonyms.txt (core/synonym-lookup/src/main/resources/species.txt and core/synonym-lookup/src/main/resources/synonyms.txt). Tested in IGB and the species/synonyms appeared to be working correctly.

                Show
                nfreese Nowlan Freese added a comment - Added the four Daphnia assemblies and annotations to "Data Management for Quickload" Dropbox folder. Updated contents.txt. I modified the .htaccess. I did not modify the species.txt or synonyms.txt in the dropbox folder. I created the pull request IGBF-1883-AddDaphnia with modifications to the IGB codebase species.txt and synonyms.txt (core/synonym-lookup/src/main/resources/species.txt and core/synonym-lookup/src/main/resources/synonyms.txt). Tested in IGB and the species/synonyms appeared to be working correctly.
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                ann.loraine Ann Loraine added a comment -

                PR merged.

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                ann.loraine Ann Loraine added a comment - PR merged.

                  People

                  • Assignee:
                    nfreese Nowlan Freese
                    Reporter:
                    nfreese Nowlan Freese
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                    Dates

                    • Created:
                      Updated:
                      Resolved: