This project contains metadata for working with all the Cytoscape core subprojects, each of which have their own Git repository. Most people won't need to clone this repository. Keep reading below to learn about how to work with Cytoscape's source code.

If you are interested in building Cytoscape apps, you don't need to build Cytoscape from source. You can follow the guide here:

http://wiki.cytoscape.org/Cytoscape_3/AppDeveloper

You need the following tools to build Cytoscape 3:

• JDK 6 or later
• Maven 3.0.x series
  • The latest version of maven is 3.1.0, but we have not tested the build system with 3.1 as of 9/11/2013
• Git
• git-flow
• cy - Utility script for Cytoscape developers

• parent
• api
• impl
• support
• gui-distribution
• headless-distribution
• app-developer

• samples

1. Install JDK, maven, git, and git-flow.
2. Download latest version of cy script and unzip it to your local disk.
3. cy command is a shell script. You need to change permission to execute it.
4. Execute the following command:

cy init

cy -r init

This clones read-only repository from github.

Now you can find a new directory named cytoscape. It should contains the following:

• README.md
• api
• app-developer
• gui-distribution
• headless-distribution
• impl
• parent
• pom.xml
• support

Switching branches is easy with cy script. Simply go to the top level directory and type:

cy switch BRANCH_NAME

where BRANCH_NAME is the name of the branch you want to switch. All Cytoscape sub-projects are following git-flow style branching scheme. Master is used only for releases, and develop is the latest development branch.

From the top directory, type:

mvn -fae clean install

The option -fae is short for "fail at end", which allows the build to continue even if unit tests fail. When Maven is done, you can find the application in gui-distribution/assembly/target/cytoscape.