How to set up an update site for Bioclipse
If you have created a feature and would like to host it on your own server, here is what you do.
1) In Eclipse, create a new Update Site Project (Menu: New > Project.. > Other.. and in dialog choose under Plugin-Development: Update Site Project
2) The Site.xml is the only required file in the update site project, all other are derived from it. Open the Update Site Editor by double-clicking on site.xml.
3) On the tab "Site Map" create a category. Below this, add your feature.
4) Click 'build all'.
5) Upon completion, you might need to refresh the project to reveal the generated folders/files. Note: these should NOT be committed to repository as they are generated just-in-time.
6) Set up a folder on your web server for HTTP access and upload all files in the update site here
7) In Bioclipse, open preferences, update sites section, and add the site with the web URL to the folder in 6)
8) Verify it shows up by running Bioclipse Software updates from the Help menu and that it installs correctly.
Errors building the site
Building an update site uses another building procedure than when running inside Eclipse. More specifically, you cannot have any java classes "excluded from classpath", and you must also ensure that all resources that should be bundled are listed in build.properties in all plugins. It is very easy to miss addded images, the icons folder etc, which will make these not be added to the update site. If there are errors produced, a zip file with logs will be generated in the update site folder. Unzip it, try to resolve the problem(s) and remove the zip file and the logs.
See the excellent Eclipse article: http://www.eclipse.org/articles/article.php?file=Article-Update/index.html