All the programs in the QTL Cartographer suite behave in the same general way. They were originally UNIX programs and can be run as such (using command line options). More recently, we have added an interactive menu that allows the user to set parameters. Once inside any of the programs, all the parameters of the program are displayed with their current values. The user chooses whichever parameter he or she wishes to change by selecting a number. The menu is in a loop. Choosing 0 will end the loop and proceed with the current parameter values.
The menu is also where one can get online help. Online help will be a numbered option in the list of parameters. Choose it and specify the location of the help file if the program couldn't find it.
When the programs begin to run, they will print out their parameter values to a log file (qtlcart.log by default).
Here is an example of the Rcross menu:
==================================================================
No. Options Values:
------------------------------------------------------------------
0. Continue with these parameters
1. Input File
2. Output File qtlcart.cro
3. Error File qtlcart.log
4. Genetic Linkage Map File qtlcart.map
5. QTL Data File qtlcart.qtl
6. Random Number Seed 1014739725
7. Output format (0,1,2) 0
8. Cross (1,2,3) => (B1,B2,F2) B1
9. Heritability 0.500000
10. Replications (Not yet active) 0
11. Interactive Crosses? (0,1) => (no,yes) 0
12. Environmental Variance (used if > 0) -1.000000
13. Sample Size 200
-------------------------------------------------------------------
14. Specify Resource File qtlcart.rc
15. Change Filename stem qtlcart
16. Change Working Directory:
17. Quit
18. Quit, but update the Resource File
===================================================================
Please enter a number...
This menu is in a loop. To change a parameter, select its number and press return. You will be prompted for a new value or filename. You can clear out a filename or working directory by inputting a single period (.). When satisfied that the parameters are set correctly, you can select 0 to run the program. If you want to quit without changing the resource file, simply select 17. Selecting 18 will update the resource file with any parameter changes you have made.
Each program will have a different number of parameters, thus the last five options may not have the same numbering as in the Rcross example above. In addition, Rmap, Rqtl and Rcross have options that only make sense if you are simulating data. These options disappear if you set an input file to translate and thus the last five options are renumbered.