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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* JDK 6 * Apache Maven * Subversion client |
* [[http://www.oracle.com/technetwork/java/javase/downloads/index.html|JDK 6]] * [[http://maven.apache.org/download.html|Apache Maven]]: the build system used by Cytoscape * Subversion client: version control management tool used by Cytoscape |
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| === Mac === | |
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| === UNIX (e.g. Mac OS)/Linux === | '''Maven''' |
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==== Checkout code from SVN ==== First, you need to check out Cytoscape 3 GUI distribution bundle: |
1. Download the binary distribution of Maven. 1. Extract the archive to a convenient place. 1. Include the Maven `bin` directory in your `$PATH`. 1. Open `~/.bash_profile`. If you don't have a `.bash_profile`, create one by entering: {{{ touch ~/.bash_profile; chmod +x ~/.bash_profile }}} 1. Add a line like this: {{{ export PATH="$PATH:/path/to/Maven/bin/" }}} 1. Save `.bash_profile`. 1. 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. == Checkout code from SVN == 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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| ==== Compile ==== | == Compile == |
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% cd gui-distribution % mvn clean install |
cd app-developer mvn clean install |
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| ==== Run Application ==== |
== Run Application == === Mac OS/Linux/UNIX === |
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% cd distribution/target/cytoscape-${version}-null.dir/cytoscape-${version} % cytoscape.sh |
cd target ./cytoscape.sh |
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=== 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 }}} |
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| TBD |
{{{ 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 }}} |
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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 |
Contents
Introduction
You need the following tools on your machine.
Apache Maven: the build system used by Cytoscape
- Subversion client: version control management tool used by Cytoscape
Mac
Maven
- Download the binary distribution of Maven.
- Extract the archive to a convenient place.
Include the Maven bin directory in your $PATH.
Open ~/.bash_profile. If you don't have a .bash_profile, create one by entering:
touch ~/.bash_profile; chmod +x ~/.bash_profile
- Add a line like this:
export PATH="$PATH:/path/to/Maven/bin/"
Save .bash_profile.
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.
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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