Recent updates of Mac OS have caused the OpenCL based Cytoscape Apps to fail on some machines. If this is the case, you can disable OpenCL with the following method:
Download the disable-opencl.dummy file to your
CytoscapeConfiguration directory. You can browse to this directory from the Home location on your Mac. After you have downloaded it, your folder should look similar to the screenshot below.
Alternatively, if you are comfortable using terminals, you can create this file using the following command:
First, follow the steps outlined in our Troubleshooting page
If you’ve run the System Checker script on that page, please include the output from it in any bug reports or help requests. It will contain important information about your configuration that can help diagnose the problem.
Sometimes, additional log info can be needed to diagnose Cytoscape problems. There are two sources of log information that can be further analyzed.
This is console output from running Cytoscape. You will need to open a terminal in your operating system and copy any output you see produced.
This is a log file generated automatically by running Cytoscape. It is normally located in the following places.
Locate your Java installation directory
If you didn't change the path during installation, it'll be something like
You can also type
where java at the command prompt.
Do one of the following:
My Computerand select
Properties > Advanced
Control Panel > System > Advanced System Settings
Environment Variablesthen select
Edit the system environment variables
Environment Variables button.
System Variables, click
Variable Namefield, enter
Variable Value field, enter your JDK or JRE installation path.
*Note for Windows users on 64-bit systems:
Apply Changesas prompted
You'll need to close and re-open any command windows that were open before you made these changes, as there's no way to reload environment variables from an active command prompt. If the changes don't take effect after reopening the command window, restart Windows.
If you would prefer to set the JAVA_HOME (or JRE_HOME) variable via the command line:
Run as administratorso you're able to add a system environment variable).
Set the value of the environment variable to your JDK (or JRE) installation path as follows:
setx -m JAVA_HOME "C:\Progra~1\Java\jdk1.8.0_XX"
If the path contains spaces, use the shortened path name.
Restart Command Prompt to reload the environment variables then use the following command to check the it's been added correctly.
You should see the path to your JDK (or JRE) installation.
which java. It should show something like
JAVA_HOME is essentially the full path of the directory that contains a
bin, which contains the JVM. It generally looks like this:
JAVA_HOME to this path using this command:
echo $JAVA_HOMEto confirm the path
This only sets
JAVA_HOME for the current session. To persistently set it, follow these
emacs .profileto edit your profile.
Add this to the end of the .profile file:
Open a new Terminal window and type:
You should see something like the following:
openjdk version "11.0.9" 2020-10-20
OpenJDK Runtime Environment AdoptOpenJDK (build 11.0.9+11)
OpenJDK 64-Bit Server VM AdoptOpenJDK (build 11.0.9+11, mixed mode)
Cytoscape may not scale well on High DPI monitors. If this is the case and you are running on a Linux
machine, you can add the following line to the
This works on Ubuntu 18.04 with GNOME/Cinnamon. However, scaling is not respected if one starts the application via the Cytoscape.desktop application shortcut, only if launched from the terminal.