Cytoscape 3 Interactive Shell

Cytoscape comes with an interactive shell for managing its runtime bundle configuration. You can add, remove, and update bundles using this interface. Cytoscape will look for bundles to install in your local Maven repository, if you have one. Failing that, it will consult the Nexus on

Working with Bundles

If you want to install a bundle, you can use the following command in the Cytoscape shell:

Cytoscape 3.0> install mvn:groupId/artifactId/version

...where "/version" is optional. For example:

Cytoscape 3.0> install mvn:org.example/myplugin/1.0
Bundle ID: 200

Once your bundle is installed, the shell will give you a bundle id (e.g. 200). Now you need to activate it:

Cytoscape 3.0> start 200

If you make changes to myplugin and it happens to be a Maven project, all you need to do is mvn install it, then run the following in the Cytoscape shell:

Cytoscape 3.0> update 200

That will reload your plugin without having to restart Cytoscape.

You can get a listing of all the loaded bundles using the following command:

Cytoscape 3.0> list
START LEVEL 100 , List Threshold: 99
   ID   State         Blueprint      Level  Name
[ 200] [Installed  ] [            ] [  100] org.example.myplugin (1.0)

By default, the list command will not show system-level bundles. If you would like to see these, set a start-level threshold like so:

Cytoscape 3.0> list -t 0
START LEVEL 100 , List Threshold: 0
   ID   State         Blueprint      Level  Name
[   0] [Active     ] [            ] [    0] System Bundle (3.0.9)
[   1] [Active     ] [            ] [    5] OPS4J Pax Url - wrap: (1.2.8)
[   2] [Active     ] [            ] [    5] OPS4J Pax Url - mvn: (1.2.8)

You can also put bundles in the framework/deploy directory. These bundles will be automatically installed and started.

Reverting to a Clean State

The bundle configuration at runtime persists between executions. If you shutdown Cytoscape and start it back up, it will restore your bundle configuration from when you shut down the platform. If you want to start clean, run:


Cytoscape_3/Interactive_Shell (last edited 2011-10-25 20:05:32 by 192)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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