Arachne's executable modules accept command-line arguments, in much the same style as Unix shells. Command-line arguments specify important details about a module's execution, such as the directories in which it finds input and output files, flags for what algorithms to run, and numeric parameters for its algorithms.
The general syntax for any executable module is
<module location and name> ARG1=val1 ARG2=val2 ...
where the ARGs and vals are command-line arguments and their values. Note that there can be no spaces before or after the equals signs, unless you are specifying a null value (which is legitimate.)
Each module has a set of command-line arguments that it handles. Some arguments must be specified, or the module will not run; other arguments are optional, and if you do not specify them, they will take on default values. In certain cases (such as ARACHNE_PRE) you can specify a default value for a command-line argument as an environment variable. To get a complete list of a module's arguments and their default values, run the module with no arguments.
Command-line arguments may be any of the following types:
By convention, directory names and other module-invariant argument names are in ALL CAPS. Other arguments may be in ALL CAPS or lowercase; there is little consistency.