Most cTAKES modules use log4j and thus the logging for most of the pipeline is easily configurable when included in another application. However, the assertion module uses the java logger, and in order to configure the properties (for instance, add a file handler and suppress the output to the console) I believe it must be done where it is instantiated (somewhere inside the pipeline?). Logging configuration should be possible without checking out the project. Also, the System.out.println statements could be removed and a console handler used instead. This would make cTAKES easier to use inside other applications.