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. Clone the git repositories.

2. 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