How to Build an OSGi-Based Cytoscape 3 Plugin on Eclipse

Introduction

This section is a step-by-step instruction for building Cytoscape 3 plugin based on OSGi framework. By following this document, you can create your plugin for Cytoscape 3.

Background

In an OSGi system, everything is a plugin. This means, Cytoscape 3 running on OSGi framework is a collection of plugins called bundle. In this tutorial, you are going to create a very simple plugin (bundle) running with Cytoscape 3.

The main difference between Cytoscape 2.x plugin and 3.x plugin is that you do not have to implement CytoscapePlugin interface in Cytoscape 3. Instead, you need to build your plugin with a metadata file for OSGi. However, this process will be handled by a tool called PAX-Construct and it is automatic.

Requirements

To understand each steps in this document, it is better to understand following before building your plugin:

Tools

The following tools should be installed on your machine before starting this tutorial:

Eclipse Plugins

Procedure

  1. Open a terminal. Execute the following script: 
  2. Move to the root directory of your plugin project. Now you can see the files like the following: 
  3. Convert this plugin project to Eclipse project 
       mvn pax:provision


Command Line Tools




Pax-Construct


To generate eclipse project files from projects generated by Pax-Construct, type: 
mvn pax:eclipse









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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