Checking out Bioclipse 2.0

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Obtaining the necessary Bioclipse 2 plugins

See also Checking out Bioclipse 2.2.

Setting up Eclipse for Bioclipse 2 development

  1. Install Eclipse version ≥ 3.4 (Ganymede) NOTE : The Eclipse SDK is essential - install it if you don't have it already. (Note: Eclipse 3.5 is not working for Bioclipse 2.0).
  2. Install Git
    • the egit 0.5.0 plugin for Eclipse (or better)
    • the git command line utilities
  3. Install the Apache Commons Codec Feature
    • Choose the Help -> Software Updates menu
    • Choose the tab Available Software
    • Filter on 'apache' (see below)
    • Select Apache Commons Codec Feature and install

Getting the Bioclipse 2 plugins and features as projects in the Eclipse workspace

  1. Clone the git repository at
  2. Make sure you are working in the 2.0.x branch:
    • git checkout -b 2.0.x origin/2.0.x
  3. Open all features and plugins in this git checkout in a clean Eclipse workspace
    • File -> Import ..., and select from the dialog 'General' -> 'Existing Projects into WorkSpace'
    • select the just checked out bioclipse.core/ as root folder.
    • make sure all plugins and features are selected for import. Make sure 'Copy project into workspace' is not selected:
      The result should be many projects opened in your 'Project Explorer':
  4. Open in and click "Set as Target Platform" in the top right corner of the editor frame. You will probably get a dialog telling you about missing plugins, because the target definition file mentions plugin fragments that are specific to the various operating system Bioclipse can be built on. As long as you are not lacking any critically needed plugins for your particular OS, you should be able to continue anyway. Give it a try.
  5. Rebuild your workspace, or, if you have automatic build turned on, wait for it to finish to be sure that you have no build errors in the projects you need.

Getting ready to run Bioclipse 2

  1. In the plugin net.bioclipse.platform_feature, double-click the bioclipse.product file (or do in Eclipse Ctrl-Shift-R and type bioclipse.product), and on the overview tab choose "Launch an Eclipse application". If the application runs and all your plugins are in place, you're done and good to go. Otherwise, follow the rest of the steps. Make sure that the ID and Application are properly set (as the sometimes seem to reset to Eclipse variants):


  1. From the menu, pick Run -> Open run dialog and select your new run configuration (which is probably called "bioclipse.product").
  2. Under the Plug-ins tab, press Deselect All.
  3. Uncheck Include optional dependencies when computing required plugins.
  4. Check the required Bioclipse plugins, same as in the list above.
  5. Press "Add Required Plug-ins". This will resolve any remaining plugin dependencies.
  6. It is advisable to check the box "Validate plug-ins automatically prior to launching", as it will save you effort if plugin dependencies change with time. (You don't need to worry about the -consoleLog paramater as you had to in Bioclipse 1, since that one is added automatically by the product.)
  7. If you have run Bioclipse 1.1.x, you should clear the runtime workspace. Go to menu Run... -> Open Run Dialog... and under the tab Main, tick Clear workspace. Do that only once, otherwise it will wipe your newly created projects on every startup.

That should be it.
--Jonalv 18:08, 15 January 2008 (CET)
--updated: Rklancer 05:53, 10 March 2008 (CET) --- updated for externals and cdk-externals egonw 15:01, 14 January 2009 (CET)

Other Git repositories for other Bioclipse Features

The above bioclipse.core repository contains the bare Bioclipse minimum. There are many other Git repositories around, for various extensions of the Bioclipse core (in alphabetical order):

Non-Git repositories:

Eclipse Extensions you may Need

Some plugins require Eclipse plugins that are not part of the core Eclipse distribution, such as EMF and Zest. If you cannot find the missing plugin listed as dependency for a Bioclipse plugin, you can search it on the update sites already listed in Eclipse, or after adding the following update sites:

Make sure to rerun 'Set as target Platform' after the installation is finished, in order for Eclipse to find them.