|| '''Cytoscape 3 Documentation''' : Getting Started|| '''Editor(s)''': SamadLotia || '''Date''': December 5th 2011 ||'''Status''': First version ||

<<TableOfContents(2)>>

== 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. [[https://github.com/cytoscape/cytoscape#readme|Clone the git repositories and build the core]].
 1. 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}}}
  1. 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]}}} ''([[http://wiki.cytoscape.org/Cytoscape_3/Interactive_Shell|more commands]])''
  1. 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''
  1. Remove the karaf_data cache and restart Cytoscape:
     {{{rm -rf ~/CytoscapeConfiguration/3/karaf_data}}}