I think you want to specify the truststore:
java -Djavax.net.ssl.trustStore=/home/gene/mycacerts ...
Or if you are using certs through JSSE (you probably are), you can copy your truststore to jssecacerts
in the $JAVA_HOME/jre/lib/security/
directory (although you’d still have to do that each time a JDK got installed/reinstalled). Sun’s JSSE looks for $JAVA_HOME/jre/lib/security/jssecacerts
before $JAVA_HOME/jre/lib/security/cacerts
.
See http://java.sun.com/javase/6/docs/technotes/guides/security/jsse/JSSERefGuide.html#X509TrustManager