Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-3534

Update deployment strategy to distribute JDK 21 IGB and early access installers

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          1
        • Epic Link:
        • Sprint:
          Fall 8, Spring 1, Spring 2, Spring 3, Spring 4, Spring 5

          Description

          For this task:

          • Update deployment code to deploy new versions of IGB better
          • Distribute new IGB installers on bioviz.org "early access" page.

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              relates to

              Task - A task that needs to be done. IGBF-3634 Fix IGB Bookmark server_url logic

              • Minor - Minor loss of function, or other problem where easy workaround is present.
              • To-Do

                Activity

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                17 older comments
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                ann.loraine Ann Loraine added a comment -

                Dr. Freese: Could you provide a link to instructions needed to test that the "bar" feature is working as expected?

                cc: Nowlan Freese

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                ann.loraine Ann Loraine added a comment - Dr. Freese: Could you provide a link to instructions needed to test that the "bar" feature is working as expected? cc: Nowlan Freese
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                nfreese Nowlan Freese added a comment - - edited

                To test the BAR feature in IGB:

                1. Start IGB 10.0.0
                2. In a web browser, navigate to https://bar.utoronto.ca/eFP-Seq_Browser/?locus=AT2G24270&dataset=cgi-bin/data/bamdata_araport11.xml
                3. Look for the sample: E-MTAB-1668:24hCS-RNA
                4. Click Alignments in IGB
                5. A webpage should open (https://bioviz.org/bar.html)
                6. IGB should change to the Arabidopsis genome, move to the appropriate gene (AT2G24270) and load the selected data
                • Check that the track name is listed as: ERR274310 Aerial part of long-day-grown 4-leaf-stage seedling with mock (NaCl) treatment
                • Check that the foreground color of the track is green
                • Check that there are no errors in the IGB log
                Show
                nfreese Nowlan Freese added a comment - - edited To test the BAR feature in IGB: Start IGB 10.0.0 In a web browser, navigate to https://bar.utoronto.ca/eFP-Seq_Browser/?locus=AT2G24270&dataset=cgi-bin/data/bamdata_araport11.xml Look for the sample: E-MTAB-1668:24hCS-RNA Click Alignments in IGB A webpage should open ( https://bioviz.org/bar.html ) IGB should change to the Arabidopsis genome, move to the appropriate gene (AT2G24270) and load the selected data Check that the track name is listed as: ERR274310 Aerial part of long-day-grown 4-leaf-stage seedling with mock (NaCl) treatment Check that the foreground color of the track is green Check that there are no errors in the IGB log
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                nfreese Nowlan Freese added a comment - - edited

                Ann Loraine - The IGB bitbucket docker file lists the old JREs. I know we switched to using the new JRE (21.0.2) as part of IGBF-3588 but am unsure if we also need to update the docker file. Were these changes done locally and not pushed to the repo?

                Show
                nfreese Nowlan Freese added a comment - - edited Ann Loraine - The IGB bitbucket docker file lists the old JREs. I know we switched to using the new JRE (21.0.2) as part of IGBF-3588 but am unsure if we also need to update the docker file. Were these changes done locally and not pushed to the repo?
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                ann.loraine Ann Loraine added a comment -

                Need to commit the new Dockerfile to the git repo.

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                ann.loraine Ann Loraine added a comment - Need to commit the new Dockerfile to the git repo.
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                nfreese Nowlan Freese added a comment - - edited

                Commit to update the docker file to use JRE 21.0.2: https://bitbucket.org/lorainelab/integrated-genome-browser-docker/commits/e1ee5b69243dc725cf8b6e2e3313940781a589bb

                I have also tested BAR using the IGB 10.0.0 release installer, it is working correctly.

                Closing ticket.

                Show
                nfreese Nowlan Freese added a comment - - edited Commit to update the docker file to use JRE 21.0.2: https://bitbucket.org/lorainelab/integrated-genome-browser-docker/commits/e1ee5b69243dc725cf8b6e2e3313940781a589bb I have also tested BAR using the IGB 10.0.0 release installer, it is working correctly. Closing ticket.

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    ann.loraine Ann Loraine
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                    Dates

                    • Created:
                      Updated:
                      Resolved: