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

• 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)

• 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

  2. Remove the karaf_data cache and restart Cytoscape:

     • rm -rf ~/CytoscapeConfiguration/3/karaf_data