Cytoscape_3/AppDeveloper/SettingUpAnIDE/CommandLine

Introduction

You need the following tools on your machine.

• JDK 6

• Apache Maven: the build system used by Cytoscape

• Subversion client: version control management tool used by Cytoscape

Checkout code from SVN

First, you need to check out Cytoscape 3 App Developer module:

svn co http://chianti.ucsd.edu/svn/core3/app-developer/trunk/ 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 target/framework/deploy. 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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