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| 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. |
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1. 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 at this URL: {{{svn+ssh://grenache.ucsd.edu/cellar/common/svn/core3/cy3}}} * You must be a Cytosape developer and have account at grenache.ucsd.edu touse this URL. Otherwise, please use this URL http://chianti.ucsd.edu/svn/core3/cy3/. With this URL, you will only have read-only permission. * 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}}}. 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. |
1. [[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. |
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| 1. Find the bundle you want to modify in either the {{{cy3/api}}} or {{{cy3/impl}}}. |
* For isolated changes, at a minimum, you need to... 1. Rebuild the bundles you modify, e.g., {{{mvn -pl impl/work-impl clean install}}} 1. 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]}}} ''([[http://wiki.cytoscape.org/Cytoscape_3/Interactive_Shell|more commands]])'' 1. Depending on the bundle and its dependencies you may need to restart the Cytoscape Application. |
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| 1. After making a change to the source code, run {{{mvn install}}}. | |
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1. Go back to {{{cy3/gui-distribution}}} and do {{{mvn clean install}}}. * If you don't want to recompile all of {{{gui-distribution}}} every time a bundle is modified, go to {{{assembly/target/features-repo}}} and copy your newly compiled bundle to the appropriate location. {{{features-repo}}} follows the conventions of a local Maven repository. 1. Now running Cytoscape in {{{cy3/gui-distribution/assembly/target/cytoscape}}} should pick up your newly compiled bundle. |
* 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'' 1. Remove the karaf_data cache and restart Cytoscape: {{{rm -rf ~/CytoscapeConfiguration/3/karaf_data}}} |
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| 1. Alternatively, you can install your bundle through Karaf console -- Cytosape interactive shell. On the console window, press "Enter" to get command prompt and look at [[http://wiki.cytoscape.org/Cytoscape_3/Interactive_Shell|this page]] for the commands and syntax. |
Cytoscape 3 Documentation : Getting Started |
Editor(s): SamadLotia |
Date: December 5th 2011 |
Status: First version |
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
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...
- Rebuild the bundles you modify, e.g.,
mvn -pl impl/work-impl clean install
- 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)
- Depending on the bundle and its dependencies you may need to restart the Cytoscape Application.
- Rebuild the bundles you modify, e.g.,
- For more extensive changes and prior to committing changes, you should...
- 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
- Remove the karaf_data cache and restart Cytoscape:
rm -rf ~/CytoscapeConfiguration/3/karaf_data
- Rebuild the bundles you modify and all dependencies, with tests, e.g.,