Getting started with Cytoscape 3

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

       • 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. Go to cy3/gui-distribution, then do a mvn install.

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.