GenGen installation

Most of the programs in GenGen package are written in Perl, but some programs require a component written in C and are therefore less cross-platfrom compatible. Although pre-compiled executables for 32/64-bit Linux (with Perl 5.8 installation) are included in the software package, they may not match the specific system architecture that users may have; therefore, re-compilation of the source code is always recommended. In addition, if you have Perl 5.10 installed in the system, re-compilation is necessary as well, otherwise there will be run-time problems that are not easily detectable or noticeable.

If using Unix/Linux system, please re-compile executable by these steps:

1. unzip the source tar.gz file (for example, using "tar xvfz gengen.tar.gz"
2. cd into the kext/ directory
3. optionally edit the “Makefile” to change options
4. type “make”
5. If there is no error message, the installation is done! Now try to add the installation directory to your system PATH environment variable.

Known issues

1. Several people reported that the calculate_association.pl program reports the same chi2 values and P-values for SNPs. Try recompile the source code. If the problem persists, I do not know how to solve it. I suspect that it is a GCC issue, but I do not have a compuer to reproduce this issue to further investigate this. It is best to switch to a different computer and try it again.