diff --git a/Dockerfile b/Dockerfile
index 7b7541e5a76..1979ec2c9ac 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -40,6 +40,7 @@ RUN echo "source activate gatk" > /root/run_unit_tests.sh && \
 WORKDIR /root
 RUN cp -r /root/run_unit_tests.sh /gatk
 RUN cp -r gatk.jar /gatk
+ENV CLASSPATH /gatk/gatk.jar:$CLASSPATH
 RUN cp -r install_R_packages.R /gatk
 
 # Start GATK Python environment