Cytoscape Wiki|
← Revision 6 as of 2012-03-23 16:15:20
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← Revision 7 as of 2012-03-23 16:47:46 →
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| First, you need to check out Cytoscape 3 GUI distribution bundle: | First, you need to check out Cytoscape 3 App Developer module: |
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| svn co http://chianti.ucsd.edu/svn/core3/gui-distribution/trunk/ gui-distribution | svn co http://chianti.ucsd.edu/svn/core3/app-developer/trunk/ app-developer |
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| cd gui-distribution | cd app-developer |
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The Cytoscape developer distribution contained in {{{assembly/target/cytoscape}}} is configured to load OSGi bundles from your local Maven repository. If it can't find a bundle there, it will fall back to Cytoscape's repository on {{{code.cytoscape.org}}}. That means you don't have to do a full build of the application to test your changes. All you need to do is {{{mvn install}}} the bundles you change and then run the start up scripts as follows: |
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| cd assembly/target/cytoscape | cd target |
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| cd assembly\target\cytoscape | cd target |
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| Cytoscape caches installed bundles so it can start up faster. If you use {{{mvn install}}} to overwrite an existing bundle without changing the OSGi version number, Cytoscape might not load up the new version of the bundle. In this case, you'll need to delete the bundle cache directory before starting Cytoscape: | == Installing Apps == |
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=== Mac OS/Linux/UNIX === {{{ cd assembly/target/cytoscape rm -rf framework/data }}} === Windows === {{{ cd assembly\target\cytoscape rd /s framework\data }}} |
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. |
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Setting up an IDE : Command Line |
Editor(s): PietMolenaar |
Date: March 23, 2012 |
Status: First version |
Contents
Introduction
You need the following tools on your machine.
- JDK 6
- Apache Maven
- Subversion client
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.
Issues
List any issues, conflict, or dependencies raised by this proposal
Comments
See also: Interactive Shell
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