Cytoscape_3/CoreDevelopment/GettingStarted

Purpose

This document covers how to fetch the Cytoscape 3 source code from our repository, how to build using Maven, and how to get Cytoscape 3 running. In addition, it covers how to make your first changes to the core code and then rebuild and run.

Check out, build and run

1. If you are using Eclipse, please look at this page first.

2. Clone the git repositories.

3. Go to gui-distribution/assembly/target/cytoscape, then run cytoscape.sh if you're on Mac or Linux or cytoscape.bat if you're on Windows.

Modifying a bundle

• For isolated changes, at a minimum, you need to...
  1. Rebuild the bundles you modify, e.g.,

     • mvn -pl impl/work-impl clean install

  2. Then update the bundle via the Cytoscape console:

     • update [bundle id]

     • Note: you can get the bundle id with list|grep [part of bundle name] (more commands)

  3. Depending on the bundle and its dependencies you may need to restart the Cytoscape Application.
• For more extensive changes and prior to committing changes, you should...
  1. Rebuild the bundles you modify and all dependencies, with tests, e.g.,

     • mvn -amd -pl api/work-api,impl/work-impl clean install

     • Note: use a comma between projects

  2. Remove the karaf_data cache and restart Cytoscape:

     • rm -rf ~/CytoscapeConfiguration/3/karaf_data