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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. If you are using Eclipse, please look at [[http://wiki.cytoscape.org/Cytoscape_3/AppDeveloper/SettingUpAnIDE/Eclipse|this page]] first. 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 you bundle through Karaf console -- Cytosape interactive shell. 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
If you are using Eclipse, please look at this page first.
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.,