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The .fileprefs copied into the package should have most of the below configured.  You Plugins will likely need to login to the server to access and index data (step 7 and 8)be updated (Step 3). 

  1. Unzip the protege package in your chosen directory
  2. Run the bat or sh file
  3. Do NOT immediately accept download of plugins.  
    1. Go to Launcher/Preferences then the plugins tab.  Make sure you are pointed to the correct plugins location.
    2. Go to File/Check for plugins and select all plugins
    3. Restart protege
  4. Set up Lucene - Go to File/Preferences and choose Lucene in the General tab
  5. Set up Pellet - Go to File/Preferences, the Reasoner tab and the Pellet sub-tab.  
    1. Select Remote as the reasoner type
    2. Enter the server address for pellet
  6. Optional - restart Protege
  7. Choose "File Open from Protege Server".  Enter the credentials and wait.
  8. Once open, go to Lucene tab and wait for it to index.
  9. Once indexing done go to Reasoner on the menu and select "Pellet" as the reasoner.
  10. Under Reasoner on the menu select "Start Reasoner"