General Function Checklist
...
Open the App Repositories
...
tab in Preferences.
- The App Repositories table matches the
...
- It is possible to add an additional app repository to the repository listimage below (both servers should be enabled).
- Mac
- Windows
- Linux
- Click the Add...
...
- button.
- Name: MergeAnnot
- 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
...
- )
- 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.
...
- There is a
...
- Launch App Manager
...
- button
...
- .
- Mac
- Windows
- Linux
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)
- 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.
...
- 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):
...
- Mac
- Windows
- Linux
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
...
- .
...
- Mac
- Windows
...
- 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.
...
- Mac
- Windows
- Linux
- Launch the IGB App Manager again.
- 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.
- 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
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
...
- .
- Observation: When the app is installed, a 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
...
.
...
- 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).
- Mac
- Windows
- Linux
- Install the Command Socket app.
- 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).
...
- Mac
- Windows
- Linux
- The IGB App Manager only lists installed apps.
- Mac
- Windows
- Linux
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
...
- .
- Mac
- Windows
- Linux
Finally, uninstall the Command Socket app by selecting it and clicking Uninstall.
...
- The IGB App Manager appears empty
...
- .
- Mac
- Windows
- Linux