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Hi,As the availability of this software is restricted, it may be difficult for this list to help, even if your question is relevant to cygwin. The page you refer to indicates the software should be installed with Sun JDK, but makes no reference to compatibility with cygwin, implying this would be off topic.
I'm having problems installing the program Haplotyper (http://www.people.fas.harvard.edu/~junliu/Haplo/docMain.htm) using Cygwin. I've managed to install Cygwin using Setup.exe. When I try to install Haplotyper, the software is detected by Cygwin but as soon as I start the installation the program crashes. I'm running setup.exe as an administrator, I have writable access to the directory that I'm trying to install it to and the setup.exe is in a directory different to the one of Haplotyper. I've disabled the antivirus software (McAfee Antivirus 8) and I've also tried the installation in safe mode. Nothing worked.
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