Cytoscape_3/CoreDevelopment/GettingStarted

Purpose

This document covers how to check out the cytoscape 3 source code form cy3 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 development environment, please look at this page first.

2. Check out Cytoscape with Subversion:

   1. Public Access (no account required; read-only)

      • svn co http://chianti.ucsd.edu/svn/core3/cy3 cy3

      • This will take a few seconds to start, then will sequentially fetch each subfolder. The entire checkout will take many minutes to complete.

   2. Private Access (you must be a Cytoscape developer and have account at grenache.ucsd.edu; read-write access)

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

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

4. 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 within cy3/api or cy3/impl.

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

   • If you don't want to recompile all of gui-distribution every time a bundle is modified:

     1. Go to assembly/target/features-repo and copy your newly compiled bundle to the appropriate location. features-repo follows the conventions of a local Maven repository.

     2. Delete

     3. Restart Cytoscape

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

5. Alternatively, you can install your bundle through Karaf console -- Cytosape interactive shell. On the console window, press "Enter" to get command prompt and look at this page for the commands and syntax.