Conventions

The exact way to run the programs is slightly different under UNIX, Macintosh and Windows. When specific commands are presented, they will be shown as typed on a UNIX workstation. For example, if the current working directory has the mletest.map and mletest.cro files in it, then you could run Qstats in a terminal shell as follows:

% Qstats -A -V -X mletest

There are a few things to note:

1. The percent sign (%) is assumed to be the UNIX prompt. This prompt may differ on different UNIX systems. For example, the Statistical Genetics Group has a Solaris workstation called brooks and the prompt looks like brooks: /qwork % rather than a single percent sign.

2. The name of Qstats is Qstats, and in the UNIX environment, it is case sensitive. The command QSTATS is different and may not be recognized. Throughout this document, the proper UNIX names have been used for the various programs in the QTL Cartographer suite.

3. Command line options begin with a minus sign and end with a single letter (with a couple of exceptions...see Rmap). They should be surrounded by a space, and if they take an argument, that argument should be surrounded by spaces. Command line options cannot be combined. For example, you cannot combine -A -V as -AV. A command line option that requires an argument must have one provided: -X requires a filename stem.

Now we can contrast this with Windows and Macintosh. Macintosh programs are started by double clicking on their icons. The Windows programs can be run in a command window in a fashion similar to a UNIX shell, or by double clicking a program icon similar to the Macintosh system. Consider first the command line invocation. If you open a command window, you can type in QTL Cartographer commands just as you would in UNIX. The command window is not case sensitive, so qstats will work as well as Qstats. The command line options are case sensitive. Also, the actual programs have .exe extensions: These do not have to be typed. If the PATH variable has the QTLCartWin$\backslash$bin directory in it, then you can use the programs in any working directory and the resource file will reside there rather than where the binaries are. Suppose mletest.map and mletest.cro are in a directory c:$\backslash$QTLCartWin$\backslash$test. Then you might run Qstats as follows

c:> cd qtlcart\test
c:\QTLCartWin\test > qstats -A -V -X mletest

The command line options are still case sensitive.

Figure 5.1: Macintosh Console Schematic

You can also double click on program icons in the file manager (Windows) or Finder (Macintosh). If in Windows, you will not be able to enter any command line options. The Macintosh versions will present a dialog box similar to Figure 5.1. You can enter command line parameters into the Argument: box and then click on the OK button to run the program. Do not click on the input/output redirection buttons. When double clicking on icons in either Windows or Macintosh, you will need to specify a working directory because the qtlcart.rc file will reside in the same place as the binaries.