IGB Release Documentation
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General Function Checklist


Open the App Repositories tab in Preferences.

  • The App Repositories table matches the image below (both servers should be enabled).

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  1. Click the Add... button.
    1. Name: MergeAnnot
    2. URL: https://bitbucket.org/lorainelab/merge-annotation-operator/downloads/ (This URL contains an App jar file and OBR index file which makes this a valid App repository) 
  2. Click Submit.
  • The MergeAnnot app repository has been added to the App Repositories table with the Name and URL displayed exactly as you entered them.

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Close Preferences. Select the Plug-ins tab at the bottom of IGB.

  • There is a Launch App Manager button.

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Click Launch App Manager.

  • The IGB App Manager opens and contains apps similar to those shown below.
    • Note: Before selecting any of the plugins at the left, the area at the right is blank. The letter/color for any plugins that are present in both the default set and the test repository will change. By default it is a B for BioViz. If you name the test repository "Test" then they all change to a "T". (UPDATE IMAGE)

 

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Select Manage Repositories…

  • The App Repositories tab in Preferences opens.

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  1. Select the checked checkbox in the Enabled column to disable the MergeAnnot app repository.
  2. Ensure the BioViz app repository is enabled, and then click Done.
  3. Select the Plug-ins tab at the bottom of IGB and launch the IGB App Manager again.
  • The available BioViz apps are listed and the color of the "Merge Annotation Track Operator" app's icon changes to indicate that the MergeAnnot app repository isn't being used (UPDATE IMAGE):

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Install the Geometric Mean app by selecting it from the list and clicking Install.

  • The Install button toggled to read Uninstall and there is a green dot next to the Geometric Mean app to indicate an installed status.

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  1. Close the IGB App Manager.
  2. View the Log by selecting Help > Show Log.
  • A logging statement confirms that the Geometric Mean app was installed correctly.



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  1. Launch the IGB App Manager again.
  2. Uninstall the Geometric Mean app by clicking the Uninstall button.
  • The Uninstall button now reads Install and the green dot next to the Geometric Mean app is now gone.

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Close the IGB App Manager and open the Log.

  • A logging statement confirms that the Geometric Mean app was uninstalled correctly.

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Launch the IGB App Manager again and install the ProtAnnot app.

  • The Install button toggled to read Uninstall and there is a green dot next to the ProtAnnot app in the list to indicate an installed status.

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Close the IGB App Manager and click Tools.

  • A new Start ProtAnnot option appears in the Tools menu.



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  1. Launch the IGB App Manager again.
  2. Uninstall the ProtAnnot app.
  3. Close the IGB App Manager.
  4. Click Tools.
  • The Start ProtAnnot option has disappeared from the Tools menu.

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Click Open App Manager in the Tools menu.

  • The IGB App Manager opened.

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Select the Command Socket app from the list.

  • The Command Socket app contains content in the App Manager that provides additional details about the app (this ensures that the IGB App Manager is using the README files appropriately).



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  1. Install the Command Socket app.
  2. Click Manage Repositories... and remove checks from the checkboxes for all of the app repositories.
  • The Command Socket app is still installed (indicated with a green dot next to the app) and the letter next to the app's name has changed to an "L" (indicating that the app is now installed locally, not from a repository).

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  • The IGB App Manager only lists installed apps.
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Click Manage Repositories... and remove all of the app repositories from the App Repositories table by selecting the repository and clicking Remove. Click Done.

  • The IGB App Manager still only displays the Command Socket app.

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Finally, uninstall the Command Socket app by selecting it and clicking Uninstall.

  • The IGB App Manager appears empty.

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