Cytoscape Wiki|
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| || '''Setting up an IDE''' : Command Line|| '''Editor(s)''': PietMolenaar || '''Date''': February 16th 2011 ||'''Status''': Page created, content stubs added || | || '''Setting up an IDE''' : Command Line|| '''Editor(s)''': PietMolenaar || '''Date''': March 23, 2012 ||'''Status''': First version || |
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| <<TableOfContents(3)>> | <<TableOfContents(2)>> |
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=== UNIX (e.g. Mac OS)/Linux === ==== Checkout code from SVN ==== |
== Checkout code from SVN == |
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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/gui-distribution/trunk/ gui-distribution |
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| ==== Compile ==== | == Compile == |
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% cd gui-distribution % mvn clean install |
cd gui-distribution mvn clean install |
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| ==== Run Application ==== |
== Run Application == 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: === Mac OS/Linux/UNIX === |
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% cd distribution/target/cytoscape-${version}-null.dir/cytoscape-${version} % cytoscape.sh |
cd assembly/target/cytoscape ./cytoscape.sh |
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=== Windows === {{{ cd assembly\target\cytoscape cytoscape.bat }}} 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: === Mac OS/Linux/UNIX === {{{ cd assembly/target/cytoscape rm -rf framework/data }}} |
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| TBD |
{{{ cd assembly\target\cytoscape rd /s framework\data }}} == 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. |
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| * See also: [[Cytoscape_3/Interactive_Shell|Interactive Shell]] |
Setting up an IDE : Command Line |
Editor(s): PietMolenaar |
Date: March 23, 2012 |
Status: First version |
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 GUI distribution bundle:
svn co http://chianti.ucsd.edu/svn/core3/gui-distribution/trunk/ gui-distribution
Compile
cd gui-distribution mvn clean install
Run Application
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:
Mac OS/Linux/UNIX
cd assembly/target/cytoscape ./cytoscape.sh
Windows
cd assembly\target\cytoscape cytoscape.bat
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:
Mac OS/Linux/UNIX
cd assembly/target/cytoscape rm -rf framework/data
Windows
cd assembly\target\cytoscape rd /s framework\data
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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