Cytoscape_3/CoreDevelopment/GettingStarted

Purpose

This document covers how to check the cy3 trunk, 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. Check out Cytoscape with Subversion at this URL:

   • svn+ssh://grenache.ucsd.edu/cellar/common/svn/core3/cy3

   • If it's been a while since you last checked anything out, make sure you can ssh into grenache.ucsd.edu before doing a check out to make sure your password has not expired.

   • When using the command line to do a check out:

     • If your local machine's user name differs from your user name on grenache, Subversion may incorrectly switch from using your grenache user name to your local machine's user name, preventing you from completing a check out. To fix this, open ~/.subversion/config and under the [tunnels] section, add this line:

       • ssh = $SVN_SSH ssh -l  user-name

       • The above line forces Subversion to call ssh with the -l parameter whenever it does ssh tunneling. Note that you will have to comment out this line if you have to work with another Subversion repository that uses ssh tunneling with a different user name.

     • If you don't want ssh to repeatedly ask for your password, see this: http://oreilly.com/pub/h/66

2. Do mvn install in cy3/gui-distribution.

3. Go to cy3/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

1. Find the bundle you want to modify in either the cy3/api or cy3/impl.

2. After making a change to the source code, run mvn install.

3. Go back to cy3/gui-distribution and do mvn clean install.

   • If you don't want to recompile all of every time a bundle is modified, go to and copy your newly compiled bundle to the appropriate location. follows the conventions of a local Maven repository.

4. Now running Cytoscape in cy3/gui-distribution/assembly/target/cytoscape should pick up your newly compiled bundle.