Query regarding cytoscape installation and uninstallation in ubuntu

Question

[microorganism_001]

I installed Cytoscape in my Ubuntu system but I can not run it now it will be okay if I can install it or uninstall it perfectly for your kind information I have Java installed in my system. In my scenario, two copies of the icon of Cytoscape got installed, and both cannot be opened. Here is the following error when I run the Cytoscape command in my system -

(base) omic@omic-world-001:~$ Cytoscape
Unrecognized option: -Xdock:icon=./framework/cytoscape_logo_512.png
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.

Answer 1

[Scooter]

Hi there,

Yes, this is a bug in the 3.10 installer. Rather than running "Cytoscape", run "cytoscape.sh" and things should be good, provided you have JAVA_HOME set to your jdk17 installation. I pretty much always run cytoscape.sh on Linux systems anyways (which is how this got missed).

-- scooter

[microorganism_001]

Thank you scooter sir for your response. but following command not worked showing output like this-

cytoscape.sh: command not found

[Manuela]

Same issue. Already checked JAVA_HOME is set correctly.