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  1. IGB
  2. IGBF-4105

Create hub.txt file and genomes.txt file for quickload to track hub conversion

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Minor
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          As part of quickload to trackhub conversion, we need to generate hub.txt file.
          Sample hub.txt :
          hub IGBQuickLoad
          shortLabel IGB QUICK LOAD
          longLabel Generated from IGB QuickLoad
          genomesFile genomes.txt
          email myEmail@address

          api : https://api.bitbucket.org/2.0/repositories/lorainelab_udaya/testquickload/src/main/trackHub2/hub.txt

          Sample genome.txt:
          genome tair9
          trackDb tair9/trackDb.txt
          organism araTha
          defaultPos Chr1:0-30427671
          twoBitPath http://igbquickload.org/quickload/A_thaliana_Jun_2009/A_thaliana_Jun_2009.2bit

          api : https://api.bitbucket.org/2.0/repositories/lorainelab_udaya/testquickload/src/main/trackHub2/genomes.txt

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-4162 Make required changes in front end for quickload to trackhub conversion

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

              New Feature - A new feature of the product, which has yet to be developed. IGBF-4090 Investigate IGB Quickload to UCSC track hub converter

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-4104 Create a POC for track hub converter

              • Major - Major loss of function.
              • Closed

                Activity

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                ann.loraine Ann Loraine added a comment -

                Latest PR is merged and new code is deployed to translate.bioviz.org as per usual.
                Ready for testing.

                Show
                ann.loraine Ann Loraine added a comment - Latest PR is merged and new code is deployed to translate.bioviz.org as per usual. Ready for testing.
                Hide
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                nfreese Nowlan Freese added a comment -

                Testing on Chrome:
                The hub.txt appears correct: https://translate.bioviz.org/api/igbTrackHubs?quickLoadUrl=https://api.bitbucket.org/2.0/repositories/lorainelab_udaya/testquickload/src/main/quickload1&filePath=/hub.txt
                The genomes.txt appears correct: https://translate.bioviz.org/api/igbTrackHubs?quickLoadUrl=https://api.bitbucket.org/2.0/repositories/lorainelab_udaya/testquickload/src/main/quickload1&filePath=/genomes.txt

                However, this does not work when I add it as a UCSC Track Hub. I have created IGBF-4192 to further test this.

                As the hub.txt and genomes.txt are being returned, closing ticket.

                Show
                nfreese Nowlan Freese added a comment - Testing on Chrome: The hub.txt appears correct: https://translate.bioviz.org/api/igbTrackHubs?quickLoadUrl=https://api.bitbucket.org/2.0/repositories/lorainelab_udaya/testquickload/src/main/quickload1&filePath=/hub.txt The genomes.txt appears correct: https://translate.bioviz.org/api/igbTrackHubs?quickLoadUrl=https://api.bitbucket.org/2.0/repositories/lorainelab_udaya/testquickload/src/main/quickload1&filePath=/genomes.txt However, this does not work when I add it as a UCSC Track Hub. I have created IGBF-4192 to further test this. As the hub.txt and genomes.txt are being returned, closing ticket.
                Hide
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                ann.loraine Ann Loraine added a comment -

                PR is merged and new code is deployed to translate.bioviz.org. Ready for testing.

                Show
                ann.loraine Ann Loraine added a comment - PR is merged and new code is deployed to translate.bioviz.org. Ready for testing.
                Hide
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                uchinta Udaya Chinta (Inactive) added a comment -

                PR: https://bitbucket.org/lorainelab/hub-facade/pull-requests/40/overview
                Dr. Ann Loraine, Please review and merge the PR. This ticket can be tested only after deployment.

                Show
                uchinta Udaya Chinta (Inactive) added a comment - PR: https://bitbucket.org/lorainelab/hub-facade/pull-requests/40/overview Dr. Ann Loraine , Please review and merge the PR. This ticket can be tested only after deployment.
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                jsirigin Jaya Sravani Sirigineedi (Inactive) added a comment -

                Reviewed the latest code chagnes, everyhting looks good.

                Show
                jsirigin Jaya Sravani Sirigineedi (Inactive) added a comment - Reviewed the latest code chagnes, everyhting looks good.
                7 older comments

                  People

                  • Assignee:
                    uchinta Udaya Chinta (Inactive)
                    Reporter:
                    uchinta Udaya Chinta (Inactive)
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                    4 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: