Found it. System property ‘java.home’ is not JAVA_HOME environment variable. JAVA_HOME points to the JDK, while java.home points to the JRE. See that page for more info.
Soo… My problem was that my startpoint was the jre folder (C:\jdk1.6.0_26\jre) and not the jdk folder (C:\jdk1.6.0_26) as I thought(tools.jar is on the C:\jdk1.6.0_26\lib folder ). The compile line in dependencies.gradle should be:
compile files("${System.properties['java.home']}/../lib/tools.jar")