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  1. IGB
  2. IGBF-2581

Fix: Bundle description not getting added to repository.xml for soft clips operator

        Details

        • Type: Bug
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
        • Story Points:
          0.5
        • Epic Link:
        • Sprint:
          Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8

          Description

          We now have a new IGB App that creates graphs from BAM files using only the soft clips.

          The repository is here:
          https://bitbucket.org/lorainelab/softclip_track_operation/src/master/

          The POM.xml is configured to ensure that when you build the project, the file AppDescription.md gets base64-encoded and included in the repository.xml file.

          This is required so that the information contained in the file gets shown to the user when they click on the app in the App Manager window within IGB.

          However, this encoding is not happening for some reason.

          Investigate why not.

          For an example of this correctly working, see the other Apps in the IGB Apps Project.

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              8 older comments
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              ssegu Sai Supreeth Segu (Inactive) added a comment - - edited

              Everything works fine. But I am not sure if this is how the soft-clip option should appear if I select operations for a BAM file.

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              ssegu Sai Supreeth Segu (Inactive) added a comment - - edited Everything works fine. But I am not sure if this is how the soft-clip option should appear if I select operations for a BAM file.
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              ann.loraine Ann Loraine added a comment -

              Please submit PR when ready.

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              ann.loraine Ann Loraine added a comment - Please submit PR when ready.
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              inaylor Irvin Naylor (Inactive) added a comment -

              Pull request: https://bitbucket.org/lorainelab/softclip_track_operation/pull-requests/2/igbf-2581-fix-bundle-description-not

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              inaylor Irvin Naylor (Inactive) added a comment - Pull request: https://bitbucket.org/lorainelab/softclip_track_operation/pull-requests/2/igbf-2581-fix-bundle-description-not
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              ann.loraine Ann Loraine added a comment - - edited

              For testing, try loading the App from team repo downloads section:
              https://bitbucket.org/lorainelab/softclip_track_operation/downloads/

              To do this:

              • Add the above link as a new App Repository (Tools > App Manager > Manage Repositories)
              • The soft clip app should appear in the list of available apps within App Manager
              • When you select the soft clip app, you should see the description of the app shown in the App manager

              If the above occurs, move to Done.

              Show
              ann.loraine Ann Loraine added a comment - - edited For testing, try loading the App from team repo downloads section: https://bitbucket.org/lorainelab/softclip_track_operation/downloads/ To do this: Add the above link as a new App Repository (Tools > App Manager > Manage Repositories) The soft clip app should appear in the list of available apps within App Manager When you select the soft clip app, you should see the description of the app shown in the App manager If the above occurs, move to Done.
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              cdias1 Chester Dias (Inactive) added a comment -

              The softclip app appears as `Graph Soft Clips` application in the list of available apps and shows the description in the app manager
              The soft Clip app installs as expected... There are no errors in the logs.
              Tested on Mac OS Catalina 10.15.7

              Show
              cdias1 Chester Dias (Inactive) added a comment - The softclip app appears as `Graph Soft Clips` application in the list of available apps and shows the description in the app manager The soft Clip app installs as expected... There are no errors in the logs. Tested on Mac OS Catalina 10.15.7

                People

                • Assignee:
                  Unassigned
                  Reporter:
                  ann.loraine Ann Loraine
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                  • Created:
                    Updated:
                    Resolved: