Cytoscape_3/AppDeveloper/SettingUpAnIDE/CommandLine

Introduction

You need the following tools on your machine.

• JDK 6

• Apache Maven: the build system used by Cytoscape

• A Git client. We recommend Source Tree

Mac

Maven

OS X 10.5 and later come with Maven pre-installed. However, Cytoscape 3.0 requires Maven 3.0 to build. To check which version your have, run this command:

mvn -version

If you don't have Maven installed, or your version is older than 3.0, follow these instructions:

1. Download the binary distribution of Maven 3.0.
2. Extract the archive to a convenient place.

3. Include the Maven bin directory in your $PATH.

   1. Open ~/.bash_profile. If you don't have a .bash_profile, create one by entering:

      • touch ~/.bash_profile; chmod +x ~/.bash_profile

   2. Add a line like this:

      • export PATH="$PATH:/path/to/Maven/bin/"

   3. Save .bash_profile.

4. Check to see if you installed Maven correctly by creating a new terminal window and entering the command:

   • which mvn

   • If the command prints nothing, then Maven was not installed correctly.

Linux

Maven

If your package manager doesn't have Maven, or if the Maven version it has is very old, follow the steps for installing Maven on the Mac.

Windows

Maven

Follow these steps.

Clone development environment from GitHub

First, you need to clone the Cytoscape 3 App Developer project:

git clone git://github.com/cytoscape/cytoscape-app-developer.git app-developer

Compile

cd app-developer
mvn clean install

Run Application

Mac OS/Linux/Unix

cd target
./cytoscape.sh

Windows

cd target
cytoscape.bat

Installing Apps

You can use the App Manager to install simple apps. For bundle apps, copy your JAR file to ~/CytoscapeConfiguration/3/apps/installed. If Cytoscape is already running, it will automatically attempt to load and start any bundles in that directory. If you overwrite a bundle there, Cytoscape will automatically restart that bundle and all of its dependents.

Debugging

To enable remote debugging, pass the debug argument to the start up script:

Mac OS/Linux/UNIX

./cytoscape.sh debug

Windows

cytoscape.bat debug

At this point, Cytoscape will pause until a debugger is connected to port 12345. For example, this is how you would start a debugging session using jdb:

jdb -attach 12345

Issues

List any issues, conflict, or dependencies raised by this proposal

Comments

• See also: Interactive Shell

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