## page was renamed from Cytoscape_3/PluginDeveloper/SettingUpAnIDE/CommandLine
## page was renamed from Cytoscape_3.0/PluginDeveloper/SettingUpAnIDE/CommandLine
## page was renamed from RFC Template

|| '''Setting up an IDE''' : Command Line|| '''Editor(s)''': PietMolenaar || '''Date''': March 23, 2012 ||'''Status''': First version ||

<<TableOfContents(2)>>

== Introduction ==
You need the following tools on your machine.

 * [[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
 * A [[http://git-scm.com/|Git]] client.  We recommend [[http://www.sourcetreeapp.com/|Source Tree]] 

=== 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:

 1. Download the binary distribution of Maven 3.0. 
 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.

=== 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.

== Clone development environment from GitHub ==
First, you need to clone the Cytoscape 3 App Developer project:

{{{
git clone git://github.com/cytoscape/cytoscape-app-developer.git 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 ==
##If you want to create a separate subpage for Comments, then provide this link:  ["/Comment"]

 * See also: [[Cytoscape_3/Interactive_Shell|Interactive Shell]]
 *''Add comment here…''

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