Cytoscape Installation and Setup
================================

Cytoscape is required for network visualization in the application. Ensure that Cytoscape is installed and running **before launching the application**. Follow the steps below to install Cytoscape on your operating system.

Installing Cytoscape
--------------------

Linux
~~~~~
1. **Prerequisites**:
   - Ensure Java 17 is installed:
     .. code-block:: bash

        sudo apt update
        sudo apt install openjdk-17-jdk
        java -version

2. **Download Cytoscape**:
   - Visit the `Cytoscape Downloads page <https://cytoscape.org/download.html>`_ and download the latest `.sh` installer.

3. **Install Cytoscape**:
   - Open a terminal and navigate to the folder containing the downloaded file.
   - Run the installer:
     .. code-block:: bash

        sh Cytoscape_<version>_unix.sh

   - Follow the on-screen instructions to complete the installation.

4. **Launch Cytoscape**:
   - After installation, run:
     .. code-block:: bash

        cytoscape

5. **Troubleshooting**:
   - If you encounter a Java error, ensure the correct Java version is set:
     .. code-block:: bash

        export INSTALL4J_JAVA_HOME=/usr/lib/jvm/java-17-openjdk-amd64

Windows
~~~~~~~
1. **Download Cytoscape**:
   - Visit the `Cytoscape Downloads page <https://cytoscape.org/download.html>`_ and download the `.exe` installer.

2. **Install Cytoscape**:
   - Double-click the downloaded `.exe` file to start the installation.
   - Follow the on-screen instructions, choosing the default installation options.

3. **Launch Cytoscape**:
   - Search for "Cytoscape" in the Start Menu and open it.

macOS
~~~~~
1. **Download Cytoscape**:
   - Visit the `Cytoscape Downloads page <https://cytoscape.org/download.html>`_ and download the `.dmg` file.

2. **Install Cytoscape**:
   - Open the downloaded file and drag the Cytoscape icon into the `Applications` folder.

3. **Launch Cytoscape**:
   - Open Cytoscape from the Applications folder.
   - If you encounter a security warning, go to `System Preferences > Security & Privacy` and allow Cytoscape to run.

Verifying Cytoscape Installation
---------------------------------
1. Launch Cytoscape and ensure it opens without errors.
2. You should see the Cytoscape interface where you can load and manipulate networks.

Testing the Cytoscape Connection
---------------------------------
To verify that the application can communicate with Cytoscape, run the following commands in R:

.. code-block:: R

   library(RCy3)
   cytoscapePing()

If Cytoscape is running, you should see a message confirming the connection.

Important Notes
---------------
1. **Run Cytoscape Before the Application**:
   - Ensure Cytoscape is open and running before starting the application.
2. **Supported Versions**:
   - Use Cytoscape version **3.10.x or higher**.