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I am trying to install Cytoscape 3.9 for my Ubuntu system (22.04). I have installed Java 17 through OpenJDK as well as through the Adoptium link given on the installation page. Neither works. When I installed Cytoscape, I had no errors and went through the wizard without any issues. Here is the output I get when I run the system requirements checker:

##### Cytoscape System Requirements Checker for Linux #####

 - Target Cytoscape version: 3.9.0
 - Your Shell: bash

===== Checking Distribution =====

 - Linux Distribution: Ubuntu
 - Version: 22.04
 - Target Platform: x86_64

 - Pass: Distribution = Ubuntu
Fail: This Ubuntu version is not supported: 22.04
Supported versions are:
 - 14.04
 - 14.10
 - 15.04
 - 15.10
 - 16.04
 - 16.10
 - 17 04
 - 17 10
 - 18.04
 - 18.10
 - 20.04
 - 21.04

===== Checking Java Version =====

Error: "java" command is not available
You need to set PATH to $JAVA_HOME/bin.

Your current $PATH:

/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/jvm/java-8-openjdk/bin:/usr/lib/jvm/java-11-openjdk/bin:/usr/lib/jvm/java-17-openjdk/bin:/usr/lib/jvm/java-17-openjdk-amd64/bin/java/bin:/usr/lib/jvm/java-17-openjdk-amd64/bin

===== Checking $JAVA_HOME =====

 - Pass: JAVA_HOME found: /usr/lib/jvm/java-17-openjdk-amd64

===== Checking Connection to Cytoscape App Store =====

 - Checking connection to Cytoscape App Store...

apps.cytoscape.org has address xx.xx.xxx.xxx
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0 50642    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

 - Result: 200
 - Success!


----------------------------------------

Your system still has some issues.
Please fix those and re-run this script again.

When I try to run Cytoscape, the desktop application does nothing. When I try to run through terminal, this is the output:

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.

The requirements checker states that my Ubuntu version isn’t compatible, however, I’m using Cytoscape 3.10.0 and the version checker is for version 3.9.0, which should explain this.

Edit: running java -version gives me the correct output. So I know java is installed correctly.

2

Answers


  1. Chosen as BEST ANSWER

    No matter what combination of Java I used with Cytoscape, nothing seemed to fix this issue. The solution for me ended up being that I needed to downgrade to Cytoscape 3.9.1 with Java 11. This version of the application runs perfectly.


  2. What you run through the terminal, you should use cytoscape.sh. You do need Java 17 for 3.10. The -Xdock stuff will be fixed in 3.10.1.

    — scooter

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