Cytoscape plugin for Gaggle Integration
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README.md

CyGoose - Cytoscape Gaggle Plugin

This is a Cytoscape plugin that integrates with the Gaggle communication framework.

The current version was tested with Cytoscape 2.8.0 and 2.7.0 and was adapted to account for the changes made starting in 2.7.0. The original CyGoose was written by

  • Sarah Killcoyne and Dan Tenenbaum, Institute for Systems Biology
  • John Lin, Kevin Drew and Richard Bonneau, NYU Bonneau Lab

Build Requirements

JDK >= 1.5 Maven >= 2.x Cytoscape >= 2.7.0

Note: Institute for Systems Biology provides the Maven repository for Gaggle dependencies, due to licensing/packaging, a separate Cytoscape download is required to compile the project.

Build Instructions

For practical reasons, we do not reference the cytoscape.jar file directly - it is about 45 MB in size ! Instead, the dependency was added via a systemPath setting, which means it is expected that the developer has downloaded the Cytoscape application and provides the setting either through a profile in a settings.xml or via the command line.

  1. Profile in settings.xml

In your ~/.m2/settings.xml, add the following section

...
<profiles>
	...
	<profile>
		<id>cytoscape</id>
		<properties>
			<cytoscape.home>/path/to/cytoscape.jar/directory</cytoscape.home>
  			</properties>
	</profile>
	...
</profiles>
...

Invoke

mvn assembly:assembly -P cytoscape
  1. Specifying the location directly

invoke

mvn assembly:assembly -Dcytoscape.home=/path/to/cytoscape.jar/directory

The project will build a jar file including the necessary dependencies.

-- Wei-ju Wu, January 7th, 2011