Troubleshooting

Cannot run Cytoscape? Please read this page first.

System Checker Script

Cytoscape is a Java application and it requires some third-party software packages to run properly. To test your system, please download the following script first.

Scripts for Other Platforms

How to Test Your System: Linux and Mac

Open Terminal

Go into download directory

This depends on where you saved the script above.

Make the script executable

You need to change permission to make it runnable.

Test your system

After few seconds, it should desplay the test results.

How to Test Your System: Windows

Open directory where you saved "windows.bat"

This is probably either "Downloads" or Desktop

Double click on "windows.bat" to test your system

After few seconds, it should desplay the test results.

If your system passes all tests, you are ready to use Cytoscape.

Still Have Problems?

How to Report Issues

If the checker shows your machine is ready, and still unable to run Cytoscape, it can be a bug. Please report them from:

Help → Report a bug...

Or, you can directly report it from Report a bug link on the navigation bar.

Ask Questions

If you get error message from system checker script, and cannot solve the issue by yourself, please send your question to out mailing list. Cytoscape-helpdesk is the best place to send this type of questions.

cytoscape-helpdesk

Known Issues

There are several known issues for this release. Please read the release notes to check those issues.

Release Notes: Known Issues

Don't forget to copy-and-paste outputs from the system checker script!

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