bin/permgen.sh contains the following lines - probably set by the linux installer:

# DO NOT remove the following line
JAVA_HOME="/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.55.x86_64/jre"; export JAVA_HOME

That specific version of the JDK got removed here via a yum update (moved to 1.7.0.65).

Possible solution

Instead of setting the JAVA_HOME in permgen.sh, save it in /etc/environment or ~/.profile when it's not specified. This lets customer continue using their system JRE (gives more control and won't needlessly bloat their system), but without the risk of overwriting changes in the JAVA_HOME variable during Stash startup. This is more inline with the instructions we use when manually installing Stash, as well.