Diff for "Cytoscape_3/CoreDevelopment/GettingStarted"

Differences between revisions 27 and 29 (spanning 2 versions)

Cytoscape 3 Documentation : Getting Started

Editor(s): SamadLotia

Date: December 5th 2011

Status: First version

Contents

Purpose
Check out, build and run
Modifying a bundle

Purpose

This document covers how to fetch the Cytoscape 3 source code from our repository, how to build using Maven, and how to get Cytoscape 3 running. In addition, it covers how to make your first changes to the core code and then rebuild and run.

Check out, build and run

Clone the git repositories.
Go to gui-distribution/assembly/target/cytoscape, then run cytoscape.sh if you're on Mac or Linux or cytoscape.bat if you're on Windows.

Modifying a bundle

For isolated changes, at a minimum, you need to...
1. Rebuild the bundles you modify, e.g.,
  - mvn -pl impl/work-impl clean install
2. Then update the bundle via the Cytoscape console:
  - update [bundle id]
  - Note: you can get the bundle id with list|grep [part of bundle name] (more commands)
3. Depending on the bundle and its dependencies you may need to restart the Cytoscape Application.
For more extensive changes and prior to committing changes, you should...
1. Rebuild the bundles you modify and all dependencies, with tests, e.g.,
  - mvn -amd -pl api/work-api,impl/work-impl clean install
  - Note: use a comma between projects
2. Remove the karaf_data cache and restart Cytoscape:
  - rm -rf ~/CytoscapeConfiguration/3/karaf_data

Cytoscape_3/CoreDevelopment/GettingStarted (last edited 2013-03-21 19:33:45 by 192)

-  ← Revision 27 as of 2012-09-25 17:25:23 →
  Size: 3414
  Editor: AlexPico
  Comment:
+  ← Revision 29 as of 2013-03-21 19:28:25 →
  Size: 1640
  Editor: 192
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 6:
-This document covers how to check out the cytoscape 3 source code form cy3 repository, how to build using maven, and how to get Cytoscape 3 running. In addition, it covers how to make your first changes to the core code and then rebuild and run.
+This document covers how to fetch the Cytoscape 3 source code from our repository, how to build using Maven, and how to get Cytoscape 3 running. In addition, it covers how to make your first changes to the core code and then rebuild and run.
 Line 9:
-. If you are using Eclipse development environment, please look at [[http://wiki.cytoscape.org/Cytoscape_3/AppDeveloper/SettingUpAnIDE/Eclipse|this page]] first.

 1. Check out Cytoscape with Subversion:

  A. '''''Public Access''' (no account required; read-only)''

   {{{svn co http://chianti.ucsd.edu/svn/core3/cy3 cy3}}}

   * This will take a few seconds to start, then will sequentially fetch each subfolder. The entire checkout will take many minutes to complete.

  A. '''''Private Access''' (you must be a Cytoscape developer and have account at grenache.ucsd.edu; read-write access)''

   {{{svn co svn+ssh://grenache.ucsd.edu/cellar/common/svn/core3/cy3 cy3}}}

   * If it's been a while since you last checked anything out, make sure you can {{{ssh}}} into {{{grenache.ucsd.edu}}} before doing a check out to make sure your password has not expired.

   * When using the command line to do a check out:

    * If your local machine's user name differs from your user name on {{{grenache}}}, Subversion may incorrectly switch from using your {{{grenache}}} user name to your local machine's user name, preventing you from completing a check out. To fix this, open {{{~/.subversion/config}}} and under the {{{[tunnels]}}} section, add this line:

      {{{ssh = $SVN_SSH ssh -l }}} ''user-name''

    * The above line forces Subversion to call {{{ssh}}} with the {{{-l}}} parameter whenever it does ssh tunneling. Note that you will have to comment out this line if you have to work with another Subversion repository that uses ssh tunneling with a different user name.

    * If you don't want {{{ssh}}} to repeatedly ask for your password, see this: http://oreilly.com/pub/h/66



 1. Do {{{mvn install}}} in {{{cy3/gui-distribution}}}. Here is a [[attachment:giddyup.sh|handy script]] for subsequent svn updates and maven builds.



 1. Go to {{{cy3/gui-distribution/assembly/target/cytoscape}}}, then run {{{cytoscape.sh}}} if you're on Mac or Linux or {{{cytoscape.bat}}} if you're on Windows.
+. [[https://github.com/cytoscape/cytoscape#readme|Clone the git repositories]].

 1. Go to {{{gui-distribution/assembly/target/cytoscape}}}, then run {{{cytoscape.sh}}} if you're on Mac or Linux or {{{cytoscape.bat}}} if you're on Windows.