If you want to use Java you need to set the JAVA_HOME environment variable in your .bashrc. The installer won't do it for you. But knowing what to set it to seems to vary widely between distributions.
On Ubuntu 9.04 jaunty I set mine to this:
export JAVA_HOME=/usr/lib/jvm/java-6-openjdk
Note that I did note explicity install java, instead it was a dependency of apt-get install ec2-api-tools, so other installation paths may use a different JDK.
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