Replacing JRE in Scaffold when running Mac OS X

The NCBI recently updated its database to require Java version 1.8 to connect and pull down NCBI annotations. If you are seeing an error message when attempting to connect to the NCBI in Scaffold it is likely that updating the JRE in Scaffold will correct this issue. Open Scaffold and go to Help > About Scaffold and check the Java version; if it is not 1.8, follow the steps below to replace the JRE bundle.

1. Download Java 1.8 from their website (be sure to download the version for Mac OS X) Follow this link: http://www.java.com/en/download/manual.jsp
2. Run the installer on your system (See Java documentation for details on installation)
3. To verify the proper version of Java is installed open System Preferences > Java > About. Make sure the current version installed is 1.8
4. To perform the swap hidden folders must be made visible. This can be done from the terminal
5. Open your Terminal: Finder > Utilities > Terminal, paste defaults write com.apple.finder AppleShowAllFiles YES into the terminal and press return, Hold the Option/Alt key and right click the Finder icon, click relaunch. This will relaunch the the Finder menu and hidden folders should now be available
6. Now we must find the new JRE version 1.8. From the Go menu: Computer/Library/Internet Plug-Ins/JavaAppletPlug-Ins. Right click Show Package Contents. Then go to Contents/Home, copy the entire Home folder
7. Follow this file path to open the Scaffold folder where the JRE is located: /Applications/Scaffold 4/.install4j/jre.bundle. Right click Show Package Contents . Then go to Contents/Home/jre
8. Rename the jre file jre_orig
9. Paste the Home folder you copied earlier under the folder now named jre_orig.
10. Rename the Home folder jre
11. Restart Scaffold and check the Java version under the Scaffold help menu. The version should be 1.8 and NCBI annotations should add correctly

Note, if you would like to hide hidden folders after successfully changing the JRE simply return to the terminal, paste defaults write com.apple.finder AppleShowAllFiles NO and press return. Relaunch Finder and you should not see hidden folders.