If the program can't find the helpfile, then you will be prompted for its location. The directory can be relative or complete, and should have the standard directory delimiter appended to it. All input and ouput files would have to be in this directory. In UNIX, you can set a path variable pointing to the programs and simply set your current working directory to the working directory. For Mac, you double click the icons and should use a working directory variable.
Relative paths are also possible.
The two colons mean go up one level and then go into the data folder. The filename stem is an important concept in the usage of this package. Beginning with version 1.12, the programs utilize the filename stem qtlcart . All files are then named using this stem and filename extensions relevant to the filetype. For example, if the -X option is followed by corn , then when new files are created, they will have the stem corn followed by a logical extension.