I can run Dr Java using java -jar drjava-stable... However, dr java does not find the compiler the Fedora Core 10 uses. I tried installing java_ee_sdk-5_07-jdk-6u16-linux.bin but Fedora Core 10 does not shut down properly (a smp error that causes a hang). I think there is a conflict between the two Java's and I would like to just use the Fedora Core java.
I use Ubuntu 9.04 rather than Fedora. In Ubuntu 9.04, the default JVM is OpenJDK which has its own compiler. The stable release of DrJava does not support this compiler but the new build http://www.cs.rice.edu/~javaplt/drjavarice/drjava.jar does. I DO NOT recommend using the OpenJDK compiler and JVM except as a stopgap. OpenJDK is buggy. Since Sun JDK 6 is free and readily available in all Linux distros, Sun JDK 6 should be used instead.
Do not use the Enterprise Edition of Java. It is incredibly heavy and seriously lags the Standard Edition with regard to Java language extensions and Java core libraries (versions of JDK). You should download sun-java6-jdk package (Ubuntu nomenclature) and change the symbolic link /usr/bin/java to point to the executable version of "java" in the downloaded JDK (something like /usr/lib/jvm/java-6-sun/bin/java). See support request 2853955.