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1. Now, compile and jar these files into MyTransformer.jar (the jar command has a -m option for the manifest file).
2. At this point, you want to put your jar into a web server using OBR (see above).
   • To add the plugin to a web server without OBR, in the plugins directory, from the command line run
   • java -cp IGB_HOME/igb_server/lib/bindex.jar -jar bindex.jar -n IGB -q -r repository.xml .
   • where IGB_HOME is your checked-out copy of the genoviz-trunk repository from Sourceforge.net. 
3. this will create a repository.xml file listing all the bundles and their requirements.
4. make sure the repository.xml file and the bundles directory are accessible to the web server.
5. in IGB, open the File>Preferences page, Plugin Repositories tab
6. click the add Add ... button at the bottom
7. enter the web server URL for the directory that has the repositories.xml file that you created - you can use whatever you want for the name.
8. Click the "Add Server" button
9. close the Preferences page.
10. Open the Plugins tab
11. you should see your bundle in the table, click on the install checkbox.
12. Once you have installed your bundle, select a graph track on the main view, and open the Graph Adjuster tab. Now if you click on the Transformation drop down, you will see MyTransformer in the list. Select it and click the Go button, and you will see a new track using your bundle.

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1. In the Project Explorer - blank area, right-click
   • New > Project ... > Plug-in Project > "Next >" button
   • Project name: "HelloWorld"
   • "Next >" button
   • Version: "1.0.0"
   • check "Generate an activator ..."
   • Activator helloworld.Activator
   • Rich Client Application click "No"
   • "Next >" button
   • Uncheck "Create a plug-in using one of the templates"
   • "Finish" button
2. Under the new HelloWorld project, find the META-INF directory, and open the MANIFEST.MF file by double-clicking on it.
3. Click on the "Dependencies" tab,
   • in the "Required Plug-ins" box, highlight org.eclipse.core.runtime, and click the "Remove" button on the right.
   • next to the "Imported Packages" box, click the "Add..." button, in the "Package Selection" popup in the text box, enter com.affymetrix.genoviz.util and click the "OK" button.
   • Do the same for org.osgi.framework (there may be a version number in parentheses after the name).
4. Right click on the blank area at the top, next to "Dependencies" and
   • a context menu comes up, click "Save".
5. Open the Activator.java file under src/helloworld
   • add the import statement
   • import com.affymetrix.genoviz.util.ErrorHandler;
   • at the top, and add the line
   • ErrorHandler.errorPanel("Hello World");
   • at the end of the start() method, and
   • ErrorHandler.errorPanel("Goodbye World");
   • at the end of the stop method
6. Save the file
7. In the Project Explorer
   • Right click the HelloWorld project
   • > "Export ..."
   • "Deployable plug-ins and fragments"
   • "Next >" button
   • Under "Available Plug-ins and Fragments:", check only Hello World
   • "Directory:" use any directory you like
   • click the "Finish" button.
8. The HelloWorld_1.0.0.jar file will be in the plugins directory under the directory the you specified. This is your bundle
9. In the plugins directory, from the command line run
   • java -cp IGB_HOME/igb_server/lib/bindex.jar -jar bindex.jar -n IGB -q -r repository.xml .
   • where IGB_HOME is your IGB directory.
10. Now, if you can access your plugins directory from a local web server, you can open up the Plug ins tab in IGB
    • (http://wiki.transvar.org/confluence/display/igbman/IGB+Tabbed+Panels#IGBTabbedPanels-PluginsPanel)
    • click on the "Repositories..." button on the lower right
    • Click the "Add..." button
    • put the URL for your local plugin directory, fill in the name with whatever you want.
    • Click the "Add Server" button
    • close the Preferences popup
11. You should now see your Hello World plugin.
    • If you install the plugin you will see an Error popup "Hello World"
    • When you uninstall the plugin, you will see an Error popup "Goodbye World"
12. Congratulations!

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