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1. Navigate to /local/project/protegeClientPackage
2. Remove and previous zip files and client directories but leave java and the run scripts
3. Create directory nci-protege5_V2.1.00v
4. Copy in the desktop client "cp r /local/content/protege/protegedesktop/* ./nci-protege5_V2.1.00v"
5. Copy the jre and run scripts into the new directory

   1. cp -r ./jre1.8.0_102 ./nci-protege5_V2.1.00v/

   2. cp run.* ./nci-protege5_V2.1.00v/

6. Create a zip "zip -r nci-protege5_V2.1.00v.zip nci-protege5_V2.1.00v"

7. Copy the zip to your local machine, unzip and test

8. Put zip on sFTP under evs/Protege/Protege-2.0

Deployment

1. Unzip the protege package in your chosed directory
2. Run the bat or sh file
3. Do NOT immediate 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 as in tne 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. Profit