If you want to override Hadoop job configuration options, you can do so via command line -D key=value.
When I wanted to pass multiple configuration options including some special characters:
hadoop jar MyJob.jar MyJob -D key=something,else -D key2=jdbc:mysql://host?user=u&password=p
I got some errors like:
-bash: -D: command not found
The solution is to put values in quotes like this:
hadoop jar MyJob.jar MyJob -D key="something,else" -D key2="jdbc:mysql://host?user=u&password=p"