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| 1. Download the binary distribution of 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. |
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| {{{ touch ~/.bash_profile; chmod +x ~/.bash_profile }}} | {{{touch ~/.bash_profile; chmod +x ~/.bash_profile}}} |
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| {{{ export PATH="$PATH:/path/to/Maven/bin/" }}} | {{{export PATH="$PATH:/path/to/Maven/bin/"}}} |
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| 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. |
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. '''Subversion''' There are GUI clients available for Mac, but many are not free. If you want to install the free command-line client: 1. Install [[http://mxcl.github.com/homebrew/|Homebrew]]. 1. Enter the command: {{{brew install subversion}}} === 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 [[http://www.mkyong.com/maven/how-to-install-maven-in-windows/|these]] steps. '''Subversion''' We recommend [[http://tortoisesvn.tigris.org/|Tortoise SVN]]. |
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| 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. | 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. |
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
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:
- Download the binary distribution of Maven 3.0.
- 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.
Subversion
There are GUI clients available for Mac, but many are not free. If you want to install the free command-line client:
Install Homebrew.
Enter the command: brew install subversion
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.
Subversion
We recommend Tortoise SVN.
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 ~/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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