Question

Query regarding cytoscape installation and uninstallation in ubuntu

0

Entering edit mode

16 months ago

microorganism_001 ▴ 30

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.

Cytoscape ubuntu • 1.7k views

ADD COMMENT • link updated 15 months ago by Manuela • 0 • written 16 months ago by microorganism_001 ▴ 30

score 0 · Answer 1 · 2023-07-13

0

Entering edit mode

15 months ago

Scooter ▴ 280

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

ADD COMMENT • link 15 months ago by Scooter ▴ 280

0

Entering edit mode

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

cytoscape.sh: command not found

ADD REPLY • link 15 months ago by microorganism_001 ▴ 30

0

Entering edit mode

Same issue. Already checked JAVA_HOME is set correctly.

ADD REPLY • link 15 months ago by Manuela • 0