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  1. IGB
  2. IGBF-3330

Add mm39 (GRCm39) mouse genome to IGB

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          2
        • Epic Link:
        • Sprint:
          Summer 2 2023 May 29, Summer 3 2023 June 12, Summer 4 2023 June 26

          Description

          Situation: A user has asked if we have the GRCm39 (mm39) mouse genome in IGB. We do not support it through Quickloads, but it is available through the UCSC DAS data source.

          Task: Add the GRCm39 (mm39) genome and annotation to IGB.

            Attachments

              Issue Links

              relates to

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              • Minor - Minor loss of function, or other problem where easy workaround is present.
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              Updated Genome - After a genome has been updated and committed to SVN IGBF-753 Add new zebrafish genome

              • Major - Major loss of function.
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              Updated Genome - After a genome has been updated and committed to SVN IGBF-2952 Add UCSC dm6 fruit fly genome and annotation to IGB

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                Activity

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                4 older comments
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                Mdavis4290 Molly Davis added a comment - - edited

                Review: I was able to get through each step of the instructions and ran into no errors. The following is an image of my screen after finishing.

                IGB_Mus-musculus.pdf

                If the image is correct than the ticket is ready to move forward!

                Show
                Mdavis4290 Molly Davis added a comment - - edited Review : I was able to get through each step of the instructions and ran into no errors. The following is an image of my screen after finishing. IGB_Mus-musculus.pdf If the image is correct than the ticket is ready to move forward!
                Hide
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                nfreese Nowlan Freese added a comment - - edited

                Notes from pushing changes to subversion repository: https://svn.bioviz.org/viewvc/genomes/quickload/M_musculus_Jun_2020/

                Comment for subversion update
                IGBF-3330: Add Mus musculus Jun 2020 genome;Jun 29, 2023

                Need to update the following files:
                contents.txt -> M_musculus_Jun_2020 Mus musculus (Jun 2020) mouse (GRCm39/mm39)
                .htaccess -> AddDescription "Mus musculus (Jun 2020) mouse (GRCm39/mm39)" M_musculus_Jun_2020

                Basic steps to checking in files and adding new rat folder with files:

                1. Modify the contents.txt and .htaccess files
                2. Drag the mouse folder into the quickload folder
                  then: 
                  svn status
svn ci -m "IGBF-3330: Add Mus musculus Jun 2020 genome;Jun 29, 2023" quickload/.htaccess
svn ci -m "IGBF-3330: Add Mus musculus Jun 2020 genome;Jun 29, 2023" quickload/contents.txt
svn add quickload/M_musculus_Jun_2020
svn ci -m "IGBF-3330: Add Mus musculus Jun 2020 genome;Jun 29, 2023"
                Show
                nfreese Nowlan Freese added a comment - - edited Notes from pushing changes to subversion repository: https://svn.bioviz.org/viewvc/genomes/quickload/M_musculus_Jun_2020/ Comment for subversion update IGBF-3330 : Add Mus musculus Jun 2020 genome;Jun 29, 2023 Need to update the following files: contents.txt -> M_musculus_Jun_2020 Mus musculus (Jun 2020) mouse (GRCm39/mm39) .htaccess -> AddDescription "Mus musculus (Jun 2020) mouse (GRCm39/mm39)" M_musculus_Jun_2020 Basic steps to checking in files and adding new rat folder with files: Modify the contents.txt and .htaccess files Drag the mouse folder into the quickload folder then: svn status svn ci -m "IGBF-3330: Add Mus musculus Jun 2020 genome;Jun 29, 2023" quickload/.htaccess svn ci -m "IGBF-3330: Add Mus musculus Jun 2020 genome;Jun 29, 2023" quickload/contents.txt svn add quickload/M_musculus_Jun_2020 svn ci -m "IGBF-3330: Add Mus musculus Jun 2020 genome;Jun 29, 2023"
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                nfreese Nowlan Freese added a comment -

                New mouse genome has been added to subversion repository.

                Next step, deploy to quickload site.

                Show
                nfreese Nowlan Freese added a comment - New mouse genome has been added to subversion repository. Next step, deploy to quickload site.
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                ann.loraine Ann Loraine added a comment - - edited

                Data are deployed. For details on where the data are deployed, and how to test, see
                linked ticket titled "Add rn7 rat genome to IGB".

                Show
                ann.loraine Ann Loraine added a comment - - edited Data are deployed. For details on where the data are deployed, and how to test, see linked ticket titled " Add rn7 rat genome to IGB ".
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                nfreese Nowlan Freese added a comment -

                Tested on Mac on IGB release (9.1.10).
                Able to load all data (RefGene, NCBI RefSeq, mRNA, EST, sequence file) on scidas and igbquickload.org

                Closing ticket.

                Show
                nfreese Nowlan Freese added a comment - Tested on Mac on IGB release (9.1.10). Able to load all data (RefGene, NCBI RefSeq, mRNA, EST, sequence file) on scidas and igbquickload.org Closing ticket.

                  People

                  • Assignee:
                    nfreese Nowlan Freese
                    Reporter:
                    nfreese Nowlan Freese
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: