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Revision as of 16:13, 27 January 2014 by Jprocter (Talk | contribs)

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Setting up the Jalview Yoxos Eclipse development environment

  1. Install the yoxos launcher
  2. Download and double click the jalviewDeveloper-www profile
  3. wait a few minutes then click the 'I accept button' and OK
  4. wait a few minutes more for the eclipse download to happen
  5. If you want to do commits, then you’ll need to get a username and password over at
  6. Press ok for default eclipse workspace paths.
  7. use your the username and password to log in to Jalview's git repository at if you have one, otherwise you can hit cancel when it prompts you for username/password (If you hit ok then you'll need to set master password details).
  8. Wait a bit more - Jalview's git repository will be cloned automatically
  9. Open git repository browser and Switch branches to Release_2_8_Branch to get the latest patched release branch in your desired repository.
  10. Choose Import ..-> From Git -> Import Existing project -> From Local Repository -> pick the public or personal repository
  11. Fix paths (some of the below may not be necessary)
    1. Open builders - there's one invalid builder that you'll need to get rid of
    2. Open build path - VARNAv3.9-dev.jar reports being not found:
    • first remove from project path.
    • then add it again by right clicking after browsing to the 'lib' directory
    1. Fix the plugin.jar user library
    • select plugin.jar in the build path and hit 'Edit ...'
    • select 'user libraries ...' button.
    • create a new user library called plugin.jar that links to the jalview 'plugin.jar' classpath entry
    • select 'Add external jar' and locate plugin.jar on your system "Program files (x86)/Java then search for plugin.jar
    • hit ok then finish then ok to finish editing the classpath.
  12. source should be ready to hack ! You can test that you can launch Jalview by :
    1. right click on project and pick Run As -> External Application
    2. once main types are found look for jalview.bin.Jalview
    3. let the program launch.
    4. to double check - make sure you can import the example alignment at
  13. Building the applet is tricker (need to use the makeapplet target to build the jalviewApplet.jar), but it should launch via the appletviewer using as 'launch java applet' runtime profile. Use parameters from one of the examples in the examples/applets.html page.