Like bruno said, you're better configuring it yourself. Here's how I do it. Start by creating a properties file (/etc/myapp/config.properties).
javax.net.ssl.keyStore = /etc/myapp/keyStore
javax.net.ssl.keyStorePassword = 123456
Then load the properties to your environment from your code. This makes your application configurable.
FileInputStream propFile = new FileInputStream("/etc/myapp/config.properties");
Properties p = new Properties(System.getProperties());
p.load(propFile);
System.setProperties(p);