• Lab Infrastructure Tips & Tricks
• EclipseJava

Eclipse for Java Developement

Current Install

• Installed version: Eclipse for RCP/Plug-in Developers (Ganymede-SR1)
• On which machines: i386 desktops

Set proxy in Eclipse

In Window -> Preferences: General -> Network Connections:

• check Manual proxy configuration and specify:

  • HTTP proxy: cache.pasteur.fr
  • Port: 8080

• check Use this proxy server for SSL

How to run and develop Cytoscape 3 with Eclipse PDE and other Eclipse plugins

We assume here you want to work with Eclipse, and keep all your files in $HOME/CytoscapeDevel/

   mkdir -p ~/CytoscapeDevel/workspace/

Dependencies

• Java JDK 1.6, which is installed in /usr/local/Java/jdk

In Eclipse

• Start Eclipse

  •   mathias@cumin:~$ eclipse 
      

    and specify ~/CytoscapeDevel/workspace as usual workspace.

• Replace Maven Executable Used in Eclipse

  • Go To Window -> Preferences

  • Select Maven -> Installations

  • Click Add...

  • Specify your local installation of Maven. Note: this is not the bin directory, the root of Maven installation

  • Unselect Embedded

  • Select External ...

    • (don't worry about potential errors, here)

      

    • Click OK
• Checkout and Create Cytoscape 3 Eclipse Project

  • Select Window > Show View > Other > SVN > SVN Repository. SVN Repository viewer will be displayed.

  • Right-click on the white background, and do New -> Repository Location

  • Add http://chianti.ucsd.edu/svn and click Finish

  • Once you specify the repository location, you can see the entire repository tree. The Cytoscape 3 repository is cytoscape3/trunk.

  • Right-click on cytoscape3/trunk, and select Check out as Maven project...

    • 

  • Click Next
  • If you're ok with the default Workspace location, click Finish
• Build Project and Run Cytoscape 3
  • Select core project on the workspace.

  • Right click and select Run As > Maven install. This command builds and install Cytoscape 3 bundles to your local maven repository and it takes several minutes to complete (depends on your machine power).

  • if THIS FAILS!: Workaround:
    • Select Run → Run Configurations
    • Create new Maven Build and name it (Click Maven Build -- New_configuration)
    • Set the Base directory to core bundle

      

    • Right-click on core -> run as... -> Maven Build