Checking out Bioclipse with eGit

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Some pointers for checking out Bioclipse with egit. See page Checking out Bioclipse 2.4 for detailed instructions about general procedure.

This is documentation for checking out and running the 2.4.x branch of Bioclipse, as of date 2007-07-07.

there is a more recent guide for Bioclipse 2.6 Checking out Bioclipse 2.6 and Checking out Bioclipse 2.6 with eGit.

Contents

Before we start

  • Install egit in Eclipse.
  • Create a new, empty workspace in Eclipse

Clone and import plugins using eGit

  • Menu: Import... then in dialog select Git > Git Repository
    • Enter URI: git://github.com/bioclipse/bioclipse.core.git then click Next, select ONLY the 2.4.x branch, Next, Next, make sure all plugins are selected and the option "Enable git team operations on imported projects" is checked, then Finish.
  • Repeat the above process for all the repository URIs:
    • git://github.com/bioclipse/bioclipse.core.git
    • git://github.com/bioclipse/bioclipse.balloon.git
    • git://github.com/bioclipse/bioclipse.statistics.git
    • git://github.com/bioclipse/bioclipse.cheminformatics.git
  • Clone the URI: git://github.com/bioclipse/org.openscience.cdk.git but here only select branch bioclipse2.4

If your checkout is interrupted but the cloning is complete, you can follow these steps to ensure that all plugins were imported:

  • Menu File > Import... select Existing Projects into Workspace
  • Select root directory to your Eclipse workspace (egit clones the git repositories here by default). You will get a list of all plugins in all five repositories, see screenshot below. Most are unchecked and garyed, because they are already imported. However, if an import failed then you can now import the plugins from the repository. Simply click "Finish" to do so. If "Finish" is disabled, this means you have already imported all plugins and you are good to go.

Set target platform

Plugins now have a branch label after the name, e.g. net.bioclipse.core [2.4.x].

  • Many plugins have errors, this is because we have not set target platform. Do this:
Open target-platform.target in net.bioclipse.target.platform and click "Set as Target Platform" in the top right corner of the editor frame. It has been reported to fail, after which a background process will continue downloading the required depedencies. Wait for that process to finish, and reset the target platform once more.
  • Close the project "org.openscience.cdk.log4j". Bioclipse uses logback, so this is obsolete and not used.
  • Now, all errors should have disappeared. If not, see Troubleshooting below.

Starting Bioclipse

  • Open bioclipse.product, click in upper right corner of the product editor on the button "Run as Eclipse application".
  • Watch the splash, and see Bioclipse start.

Troubleshooting

Target platform is very likely the source of many problems. Sometimes, setting it multiple times helps. An alternative way to set the target platform is to go to the menu option Preferences.. and then under section Plugin-development > Target Platform clicking on Reload (see screenshot below).

Else, you can try one or many of the following:

  • Clean all projects (Menu: Project > Clean...)
  • Refresh the workspace (select all projects, press F5 or select "Refresh" from context menu)
  • Set target platform again (using the two above mentioned methods)
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