## page was renamed from Cytoscape_3/PluginDeveloper/SettingUpAnIDE/Eclipse
## page was renamed from Cytoscape_3.0/PluginDeveloper/SettingUpAnIDE/Eclipse
## page was renamed from RFC Template
||'''Setting up an IDE''' : Eclipse ||'''Editor(s)''': KeiichiroOno PietMolenaar ||'''Date''': July 5, 2012 ||'''Status''': Updated for Eclipse Juno ||


<<TableOfContents>>

== Introduction ==
This is an introduction to Cytoscape 3 App development for Eclipse users.  

=== Prerequisites ===
You need to know basics of Eclipse and [[http://maven.apache.org/|Maven]].

== Install JDK ==
To develop Cytoscape 3, you need Java 6 or 7.  If you find problems on Java 7, [[http://groups.google.com/group/cytoscape-helpdesk|please let us know]].

== Setting up Eclipse ==
This procedure had been tested with latest version of Eclipse, ''Juno (4.2)''.  You can use [[http://www.eclipse.org/downloads/|any version of Eclipse distribution]], but we recommend to use '''Eclipse for RCP and RAP Developers''' or '''Eclipse IDE for Java Developers'''.

{{{#!wiki caution
'''Use JDK, not JRE'''

Make sure eclipse is running in the JDK virtual machine; on Windows this is not default. To use JDK's VM, create a shortcut and edit the shortcut's property:  eclipse.exe -vm "c:\your_path_to_JDK\bin\javaw.exe"
}}}

=== Installing Eclipse Plugins From Eclipse Marketplace ===
Eclipse Indigo and later include a feature called the '''''[[http://marketplace.eclipse.org/|Eclipse Marketplace]]'''''.  All of the following plugins are available from the Marketplace.  To install an Eclipse plugin, open the Marketplace dialog ('''Help &rarr; Eclipse Marketplace'''), type the plugin name in the search box, and click ''Install''.

{{attachment:marketplace2.png}}

Usually, you will be asked to restart Eclipse after installing plugins.


=== Eclipse Plugins to Install ===
You need to install some Eclipse plugins to develop Cytoscape 3 apps.  All of the following are required to develop Cytoscape 3 (or any Java applications using Maven and Spring).

==== EGit ====

EGit provides Eclipse with Git integration.  It is included with most Eclipse distributions, but in case yours doesn't, you'll need to install it to get the source code from our GitHub repositories.

==== m2eclipse ====
!M2Eclipse is an Eclipse plugin to integrate Maven.  Now it is a part of Eclipse foundation, and it is a part of Eclipse distribution.  You do not have to install this plugin in Juno.

[[http://www.eclipse.org/m2e/|Many useful documents]] are available from the project and we recommend to read them.

----

== Checkout Cytoscape 3 App Developer's Template Project ==

 1. In the menu, select '''''File &rarr; Import &rarr; Git &rarr; Projects from Git &rarr; URI'''''.
 1. Under '''''URI''''', paste {{{https://github.com/cytoscape/cytoscape-app-developer.git}}}.  Eclipse will fill in the other fields for you automatically:
   {{attachment:git-settings.png}}
 1. Under '''''Initial branch''''' select:
   * '''''master''''' if you want to develop an app using the latest stable release of Cytoscape, or
   * '''''develop''''' if you want to develop an app using the latest Cytoscape sources in the repository.
 1. Click '''''Next'''''.
 1. Select '''''Import as general project'''''.
 1. Click '''''Next'''''.
 1. Click '''''Finish'''''.
 1. Now you should have a project in Eclipse called {{{cytoscape-app-developer}}}.
 1. Right click on the project and select '''''Configure &rarr; Convert to Maven Project'''''.
 1. You should end up with a project that looks like this:
  
  {{attachment:plugin-template0.png}}

== Build App Developer's Template Project ==
 1. Right-click ''cytoscape'' project top folder
 1. Select '''''Run As &rarr; Maven Build'''''
 1. Type '''''clean install''''' in the '''''Goals''''' text box
 1. Click '''''Run''''' button

Now you can see the following directory structure under ''target'' directory (if you cannot see ''target'', press f5 to refresh your workspace):

{{attachment:plugin-template1.png}}


== Run Cytoscape 3 ==
 1. Open command-line terminal.
 1. Go into '''''target''''' directory you've just created with m2eclipse plugin
 1. Execute ''cytoscape.sh'' (for unix/mac) or ''cytoscape.bat'' (windows)

If you can run Cytoscape, now you are ready to code your app. 

== Create the App ==
There are two types of apps for Cytoscape 3 and you can use Eclipse for both of them.

=== Simple App ===
 1. Select '''''New &rarr; Java Project'''''
 1. Enter project name.  This can be anything.  In this example, we use '''''Cy3SimpleApp''''' as a sample app name.
 1. Add '''cytoscape-app-api''' jar file as a library
 1. Right-click src folder and create a class file '''''HelloWorldApp'''''.  Use ''org.cytoscape.sample'' as its package name
 1. Create Manifest file.  It's just a text file named ''MANIFEST.MF''.  The only entry you need to write in this file is the following:
  {{{
Manifest-Version: 1.0
Cytoscape-App: org.cytoscape.sample.HelloWorldApp

  }}}
  This is your App's main class name. ''Be sure to include a return at the end of the last line or it may be excluded upon export!''


 1. Your project directory looks like this:
 
  {{attachment:simple-plugin1.png}}
 
 1. Write App main class:
  {{{#!java
package org.cytoscape.sample;

import org.cytoscape.app.AbstractCyApp;
import org.cytoscape.app.CyAppAdapter;

public class HelloWorldApp extends AbstractCyApp {

	public HelloWorldApp(CyAppAdapter adapter) {
		super(adapter);
		
		System.out.println("Hello Cytoscape 3!");
	}
}
  }}} 
 1. Select '''''File>Export'''''
 1. Select ''JAR FIle'' and click ''Next''
 1. Uncheck ''MANIFEST.MF'' file.  Otherwise, two manifest files will be created in the JAR!

    {{attachment:export1.png}}

 1. Type app jar file name and click ''Next''
 1. Leave all settings as-is and click ''Next''
 1. Select '''''Use existing manifest from workspace''''' and specify the one you've just created
  
  {{attachment:simple-plugin2.png}}
  
 1. Click ''Finish''.  Make sure the app jar file exists in the directory you specified above.

==== Test your app ====
 1. Run Cytoscape from command-line
 1. Select '''''Apps>App Manager'''''
 1. Select '''''Import Local App''''' tab
 1. Click '''''Select''''' button and select the app jar file you've created
 1. You can see ''Hello Cytoscape 3!'' in the console

For more realistic example, please try this tutorial:

[[http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Creating_a_Simple_Cytoscape_3_App|Tutorial:Creating a Simple Cytoscape 3 App]]


=== Cytoscape 3 Bundle App ===
If you want to create ''Cytoscape 3 Native'' bundle app, please try the following tutorial:

[[http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Creating_an_OSGi_Bundle_Cytoscape_3_App|Tutorial:Creating an OSGi Bundle Cytoscape 3 App]]

== Questions? ==
If you find problems or have questions, [[http://groups.google.com/group/cytoscape-discuss|please let us know]].