I had some trouble when I developed on IntelliJ IDEA.
Although I exported JAVA_HOME in .bashrc, it wasn't reflected to GUI app(IDEA).

R3 CordaはKotlinを使っています。ということでIntelliJ IDEAを使うことにしたのですが、
JAVA_HOMEの設定が反映されずにいて困っていました。

Please see the following steps.

ということで、以下のステップを御覧ください。

Step1. set JAVA_HOME in your .bash_profile

.bash_profile

# Your other settings

export JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_111.jdk/Contents/Home

run: source ~/.bash_profile

Step2. make .osx-env-sync.sh

~/.osx-env-sync.sh

grep export $HOME/.bash_profile | while IFS=' =' read ignoreexport envvar ignorevalue; do
  launchctl setenv ${envvar} ${!envvar}
done

Step3. make osx-env-sync.plist

~/Library/LaunchAgents/osx-env-sync.plist

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
  <key>Label</key>
  <string>osx-env-sync</string>
  <key>ProgramArguments</key>
  <array>
    <string>bash</string>
    <string>-l</string>
    <string>-c</string>
    <string>
      $HOME/.osx-env-sync.sh
    </string>
  </array>
  <key>RunAtLoad</key>
  <true/>
</dict>
</plist>

Step4. change mode the file to executable

chmod +x ~/.osx-env-sync.sh

Step5. make these preference valid

launchctl unload ~/Library/LaunchAgents/osx-env-sync.plist
launchctl load ~/Library/LaunchAgents/osx-env-sync.plist

Done! Please check if your GUI apps can read JAVA_HOME!!
I hope this article could be useful.

以上です。
GUIアプリに環境変数が反映されたことを確認出来たでしょうか？
少しでもお役に立てたら幸いです。