Skip to content

Install a Sample Cytoscape App

Fred Eisele edited this page Apr 5, 2019 · 2 revisions

Install the app

When the build has finished the target folder contains the App jar file. The target folder is located in the project folder alongside the pom.xml file. The App jar file for the example is the file sample-create-network-view-1.0.jar. To install the App you will place this App jar file in the CytoscapeConfiguration folder.

You will need to have run Cytoscape at least once beforehand.

If you're on a... Do this to open CytoscapeConfiguration
Mac Go to the Finder, then in the Go menu choose Home. You will find the CytoscapeConfiguration folder inside your home folder.
Windows In Windows Explorer, go to C:\Users\Your-User-Name. You will find the CytoscapeConfiguration directory inside there.
Linux GNOME 3 In the GNOME Files application, click on the Home tab on the left. You will find CytoscapeConfiguration inside there.

Now that you have the CytoscapeConfiguration open, open 3, then open apps. You will find the installed folder there. Copy your jar file to the installed folder by dragging it from Eclipse while holding the option/alt key.

{i} The CytoscapeConfiguration/3/apps/installed directory is where all active Cytoscape apps reside.

Installing using a symbolic link

If you are using MacOS or Linux then you can avoid having to copy the jar file every time your app is rebuilt. This is done by creating a symbolic link from the Cytoscape apps folder to the App jar file in the Eclipse workspace. This only has to be done once.

  • Open a terminal window
  • Navigate to the CytoscapeConfiguration/3/apps/installed folder. For example type the command cd /home/user/CytoscapeConfiguration/3/apps/installed (where /home/user is replaced by the location of your CytoscapeConfiguration folder).
  • Type the command ln -s /path/to/my_app.jar my_app.jar (where /path/to/my_app.jar is the full path to the App jar file).

To find the full path to the App jar file select the jar file in Eclipse and press Alt + Enter. The Resource Properties dialog will open and the full system path to the file is shown as the first entry in the dialog.

Installing using the Cytoscape UI

It is also possible to load the sample App from the Cytoscape UI. This is the way end-users install from the App Store.

Run your app

  • Open Cytoscape. In the Apps menu, go to Samples, then choose Create Network View.
  • Your App will create a network view and a new node.
  • You just ran your App in Cytoscape.
You can’t perform that action at this time.