hmmSNP README FILE
==================

see Szatkiewicz JP, Beane GL, Ding Y, Hutchins L,
  Pardo-Manuel de Villena F, Churchill GA. "An imputed genotype
  resource for the laboratory mouse"



This code is RESEARCH GRADE, however if you experience any errors or crashes, 
please report them to glen.beane@jax.org

The code has been compiled and tested on various Linux flavors and Mac OS X. 
It may work with Cygwin on Windows, but it is untested. A POSIX environment 
is assumed.

This code is released under the GPL version 3 or (at your option) any later 
version.  See the file named COPYING for the GPLv3 terms.  




INSTALATION
-----------


This code uses a standard GNU autotools based build system.  If you obtained
the source from out Github, then you will need to run the script "autogen.sh" 
to run the autotools. If you downloaded a .tar.gz file this step should be 
unnecessary.  

  ./autogen.sh
  
See INSTALL for generic installation instructions. Here are the basics of 
compiling and installing hmmSNP

 - these commands will result in hmmSNP installed into /usr/local/bin

     ./configure
     make
     sudo make install
  
-  If you do not have sudo and wish to install in some other location, you can 
   pass the --prefix option to the configure script.  For example, these
   commands will install the hmmSNP executable into /home/username/bin/

     ./configure --prefix=/home/username
     make
     make install