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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

Introduction

You need the following tools on your machine.

  • JDK 6

  • Apache Maven: the build system used by Cytoscape

  • Subversion client: version control management tool used by Cytoscape

Mac

Maven

  1. Download the binary distribution of Maven.
  2. Extract the archive to a convenient place.
  3. 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 

    2. Add a line like this:
      •  export PATH="$PATH:/path/to/Maven/bin/" 

    3. Save .bash_profile.

  4. 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

How to Comment

Edit the page and add your comments under the provided header. By adding your ideas to the Wiki directly, we can more easily organize everyone's ideas, and keep clear records. Be sure to include today's date and your name for each comment. Try to keep your comments as concrete and constructive as possible. For example, if you find a part of the RFC makes no sense, please say so, but don't stop there. Take the extra step and propose alternatives.

Cytoscape_3/AppDeveloper/SettingUpAnIDE/CommandLine (last edited 2013-04-09 21:03:16 by 192)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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