You can specify a working directory (or folder) with the -W option. This directory (folder) must exist prior to running any of the programs. The directory can be relative or complete, and should have the standard directory delimiter appended to it. For example
-W /home/user/qtlcart/work/
would use /home/user/qtlcart/work as the working directory. All input and ouput files would have to be in this directory. For a Windows system, the line might be
-W c:\qtlcart\work\
whereas a Macintosh would require
-W HardDrive:qtlcart:work:
The equivalent line in the resource file would have -workdir instead of just -W.
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. For example, if the programs reside in a bin folder in the qtlcart folder on a Macintosh, then you can have a data folder in the qtlcart folder and use
-W ::data:
as the working directory. The two colons mean go up one level and then go into the data folder.
On a Windows system, you can either open a command window and type in commands as you would under UNIX, or double click program icons as you would on a Macintosh. If you use the Macintosh mode, then you will need to set a working directory as the resource file is saved in the same directory where the binaries reside. If you use the command line mode, then you should have the binary directory in the PATH variable so that you can run the programs in the working directory and not have to set that variable.
Newer versions of the Macintosh have UNIX underneath the windowing system. QTL Cartographer can be compiled and used in the UNIX enviroment on the Macintosh as under any UNIX system. You will need to get the developer package and install it on your Macintosh to do this.