The EMBOSS command line (Chapter 6, The EMBOSS Command Line) is the probably the best supported way to launch applications. The command line behaviour is consistent across all applications and provides a simple interface to (and complete control over) them. When developing or testing EMBOSS applications, or in the case of difficulty, it's advisable to run them from the command line, regardless of what interface you would typically use.

An AJAX Command Definition (ACD) file defines the command line interface of an application and, by extension, the basic functionality of all other types of interface. The ACD file gives a complete (but terse) description of an application including all its inputs and outputs, it therefore defines the possible flow of information between applications. The ACD file also defines the application command line behaviour, such as permissible ranges of values for parameters, default values and re-prompting behaviour in the case an input error. Typically, there is one ACD file per application, although multiple interfaces (ACD files) can in principle be defined for a single application. Regardless of the interface used and the application run, an ACD file has to be read (in one form or another) before the application proper can start.

All parameters may be specified on the command line, thereby giving the program all the information it needs at once. If required parameters are not specified, however, then EMBOSS invokes a question-answer session, prompting for values for required parameters that were omitted on the command line. User input is converted to the internal equivalent of a properly constructed command line before the application is run.