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• bookmark : this folder contains SPARQL query text files for use in the SPARQL query tab.  New queries are usually sent over email and should be copied to this folder and checked into github at https://github.com/NCIEVS/sparql-query-plugin/tree/master/bookmark.  NOTE: Anything we check into github should NOT have any service or server names, or login credentials.  
• Protege Logs Email - Macro.xlsm : This is an Excel macro that allows users to send logs and error reports to the Protege admins.  Updates to this file are normally sent by email and should be copied to this folder
• removeOldPlugins.bat : Removes outdated plugins from Windows
• run.bat : Runs the protege client on Windows.  Overwrites the run.bat provided in the protegedesktop build. This differs from the provided run.bat in that it:
  • Calls the removeOldPlugins.bat
  • Increases the memory Xmx to 12000M
  • Calls the zulu jre
• run.bat.admin
• run.command : For running the Protege client on Mac
• runLowerMemory.bat : For running Protege client on Windows with a lower memory setting, for machines with resource constraints
• run.sh : For running the Protege client on Linux or from shell in Mac
• zulu8.38.0.13-ca-jre8.0.212-win_x64 : JRE for use in Windows

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Due to limitations in X-windows, it is likely that you will need to copy the zip package down to your local machine in order to do the client configuration steps.  Configuration details can be found at NCI Protege 5 desktop set up.

Once the client is configured you will want to zip it back up.  If working on a Mac you will want to make sure to exclude the .DS_Store hidden files : zip -r nci-protege-V3.9.0-dev2.zip nci-protege-V### -x "*.DS_Store"

Copy the package and copy it to the secure FTP at caftps2.nci.nih.gov.  You will need to use SFTP and log in using your NIH username and password. 

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