General Function Checklist
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Open the App Repositories
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tab in Preferences.
- The App Repositories table matches the image below
- It is possible to add an additional apprepository to the repository listimage below (both servers should be enabled).
- Mac
- Windows
- Linux
- Click the Add...
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- button.
- Name: MergeAnnot
- URL: https://
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...
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- Click Submit
- Observation: confirm the repository is added to the repository table
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- /lorainelab/merge-annotation-operator/downloads/ (This URL contains an App jar file and OBR index file which makes this a valid App repository)
- 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.
- Mac
- Windows
- Linux
Close Preferences. Select the Plug-ins tab at the bottom of IGB.
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- There is a
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- Launch App Manager
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- button.
- Mac
- Windows
- Linux
Click Launch App Manager.
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- The IGB App Manager
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- Select the Manage Repositories… button (top-right corner of App manager).
- Observation: The App Repositories tab of IGB Preferences opens (see below).
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- Select the empty checkbox under the Enabled column to enable the Bioviz development repo 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)
- Mac
- Windows
- Linux
Select Manage Repositories…
- The App Repositories tab in Preferences opens.
- Mac
- Windows
- Linux
- Select the checked checkbox in the Enabled column to disable the MergeAnnot app repository.
- Ensure the BioViz app repository is enabled, and then click Done.
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- Select the Plug-ins tab at the bottom of IGB and launch the IGB App Manager
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- again.
- The available BioViz apps are listed and the color of the "Merge Annotation Track Operator" app's icon changes to indicate that
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- View the IGB Console by selecting Help > Show Console and then install the the MergeAnnot app repository isn't being used (UPDATE IMAGE):
- Mac
- Windows
- Linux
Install the Geometric Mean app by selecting it from the list
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and clicking
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Install
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.
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- The Install button
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- toggled to read Uninstall
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- and there is a green dot next to the Geometric Mean app
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- to indicate an installed status
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- .
- Mac
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- Windows
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- Observation: The IGB Console will show a logging statement when the app is installed (see below)Linux
- Close the IGB App Manager.
- View the Log by selecting Help > Show Log.
- A logging statement confirms that the Geometric Mean app was installed correctly.
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- Mac
- Windows
- Linux
- Launch the IGB App Manager again.
- Uninstall the Geometric Mean app by clicking the Uninstall button
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- .
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- The Uninstall button
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- now reads Install and the green dot next to the
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- Geometric Mean app is now gone.
- Observation: The IGB console will show a logging statement when the app is uninstalled (see below)Mac
- Windows
- Linux
Close the IGB App Manager and open the Log.
- A logging statement confirms that the Geometric Mean app was uninstalled correctly.
- Mac
- Windows
- Linux
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Launch the IGB App Manager
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again and install the ProtAnnot app.
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- The Install button
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- toggled to read Uninstall
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- and there is a green dot next to
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- the ProtAnnot app in the list to indicate an installed status
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- .
- Observation: When the app is installed, a new Find Annotations tab appears at the bottom of IGB (see below).
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- Uninstall the Find Annotations app using the IGB App Manager.
- Observation: When the app is uninstalled, the Find Annotations tab disappears from IGB (see below).
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- Close the IGB App Manager and reopen it by selecting Tools > Open App Manager (as seen below).
- Observation: The IGB App Manager should open.
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- Mac
- Windows
- Linux
Close the IGB App Manager and click Tools.
- A new Start ProtAnnot option appears in the Tools menu.
- Mac
- Windows
- Linux
- Launch the IGB App Manager again.
- Uninstall the ProtAnnot app.
- Close the IGB App Manager.
- Click Tools.
- The Start ProtAnnot option has disappeared from the Tools menu.
- Mac
- Windows
- Linux
Click Open App Manager in the Tools menu.
- The IGB App Manager opened.
- Mac
- Windows
- Linux
Select the Command Socket app from the list
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.
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- The Command Socket app contains content in the App Manager that provides additional details about the app
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- (this ensures that the IGB App Manager is using the README files appropriately).
- Mac
- Windows
- Linux
- Install the Command Socket app.
- Click
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- Manage Repositories
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- ... and remove
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- checks from the
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- checkboxes for all of the
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- app repositories.
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- The
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- Command Socket app
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- is still
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- installed (indicated with a green dot next to the app)
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- and the letter next to the app's name
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- has changed to an "L"
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- (indicating that the app is now installed locally, not from a
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- repository).
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- Mac
- Windows
- Linux
- The IGB App Manager only lists installed apps.
- Mac
- Windows
- Linux
Click Manage Repositories... and remove all of the app
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repositories from the App Repositories table by selecting the
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repository and clicking Remove. Click Done.
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- The IGB App Manager
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- still only displays the Command Socket app
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- .
- Mac
- Windows
- Linux
Finally, uninstall the Command Socket app by selecting it and clicking Uninstall.
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- The IGB App Manager appears empty
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- .
- Mac
- Windows
- Linux