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If it is about setting JAVA_HOME system-wide, /etc/profile.d/ would be a good choice.
/etc/profile.d/
echo export JAVA_HOME="put path to java home here">/etc/profile.d/javaenv.sh chmod 0755 /etc/profile.d/javaenv.sh
on your next logon you'll have it
echo JAVA_HOME="put path to java home here">/etc/profile.d/javaenv.sh chmod 0755 /etc/profile.d/javaenv.sh
