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1. Check out IGB from https://genoviz.svn.sourceforge.net/svnroot/genoviz/trunk into a new directory - we will refer to the project directory below as IGB_HOME. in eclipse, Project Explorer, right click on open space, and select "Import..." Ann's comment: When I did this, I did not see a folder labeled "Plug-in Development." Is this something unique to how your Eclipse is set up? I did a Web search for "Helios" - is that what I need to develop a plug-in? I tried using the "Install New Software" option under the "Help" menu in Eclipse, but there were so many options I had no idea what to choose.  Please give more details. ## Select
   • open a command prompt in IGB_HOME, run "svn co https://genoviz.svn.sourceforge.net/svnroot/genoviz/trunk"
   • in eclipse, project explorer, "File>Import"
   • in the Import popup, under "General", select "Existing Projects into Workspace"
   • "Next >" button
   • make sure "Select root directory:" is selected, and fill in the IGB_HOME directory
   • click the "Finish" button Ann's comment: I followed the directions exactly, even checking an all-new copy of genoviz-trunk into a newly created directory (I called it IGB_HOME) but Eclipse refused to let me proceed, showing an error message on the "Import" window that syas Because I already had another Eclipse project set up for IGB, I got an error message: "Some projects cannot be imported because they already exist in the workspace." I got it to work only after I deleted another copy This is likely to happen for others if they happen to have branches and trunk checked out. One way to deal with this would be to change the name of the IGB project . Is it not possible to have to separate IGB projects on the same computer without Eclipse causing a problem? I need to be able to develop on branch and the trunk checked out into different locations. How do I do this?
2. Open a command prompt in IGB_HOME, and do an "ant clean" and "ant jar"
3. Make sure Eclipse is displaying the Project Explorer Tab. (If not, click View>Show View>Project Explorer.)
4. In eclipse, Project Explorer, right click the IGB project and select "refresh."
5. • on branches to something like "IGB 6.5" or the like. This would allow developers to have both branch and trunk checked out at the same time. Changing the name of the project can be done in Eclipse by right-clicking the "Integrated Genome Browser" folder icon under the Ecipse Project Explorer and choosing "Refactor>Rename..." What this will do is modify an XML file currently under version control called ".project" - thus it's important to ensure that if a developer changes this, the change doesn't get checked into subversion unless the change should affect everybody.
6. Open a command prompt in IGB_HOME, and do an "ant clean" and "ant jar"
7. Make sure Eclipse is displaying the Project Explorer Tab. (If not, click View>Show View>Project Explorer.)
8. In Eclipse, Project Explorer, right click the IGB project and select "refresh."
9. In Eclipse, Project Explorer, right click on open space, and select "Import..." > "Plug-ins and Fragments" under "Plug-in Development", click the "Next >" button
   1. under "Import From", select "Directory:",
   2. under "Plug-ins and Fragments to Import" select "Select from all plug-ins and Fragments",
   3. under "Import As" select "Binary Projects"
   4. for "Directory:", click the "Browse..." button and select the IGB_HOME/extbundles, click the "OK" button
   5. click the "Next >" button
   6. under "Plug-ins and Fragments Found:", select affx_fusion, colt, freehep, image4j, jlfgr, picard, and sam
   7. click the "Add -->" button to add these all to "Plug-ins and Fragments to Import:", click the "Finish" button
   8. Ann's note: The user must have already installed the Eclipse Plug-in Development Environment, under "General" in the Help>Install New Software window.
10. Do the following for the directories under IGB_HOME, genometryImpl, common, genoviz_sdk, igb, plugins/igb_service, plugins/window_service
    • in eclipse, project explorer, right click on open space, and select "Import..."
    • Select "Existing Projects into Workspace" under "General", click the "Next >" button
    • click "Select root directory:" and click the "Browse..." button on the right
    • select the project folder under IGB_HOME, and click "OK"
    • click "Finish"

• note - you will find it easier to debug in eclipse if you use the Debug project. You can add the Activator for your bundle (whatever one you are developing) in com.affymetrix.igb.debug.Debug, in the static statement at the top. Choose Run>Debug>Debug As Then on Debug, you can "Debug As" "Java Application", and
  this will run IGB using a dummy OSGi implementation, so that you can easily step through code, set breakpoints, etc. Please explain in more detail.** import the "debug" project
  • The benefit of this is that Eclipse will be able to compile as you go.
  • right-click Debug Configure Build Path ,c change it to always put every resource path

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