compile mb 3.2.2 with beagle on ubuntu

build-mb-3.2.2-with-beagle.sh

#!/bin/sh
PREFIX_PARENT="${HOME}/envs"
set -x


mkdir -p "${PREFIX_PARENT}/beagle" || exit
svn checkout https://beagle-lib.googlecode.com/svn/trunk/ beagle-lib  || exit
cd beagle-lib
sh autogen.sh 
mkdir build  || exit
cd build  || exit
../configure --prefix="${PREFIX_PARENT}/beagle" || exit
make || exit
make check || exit
make install || exit
cd ../..


wget http://downloads.sourceforge.net/project/mrbayes/mrbayes/3.2.2/mrbayes-3.2.2.tar.gz || exit
tar xfvz mrbayes-3.2.2.tar.gz || exit
cd mrbayes_3.2.2/src || exit
autoconf || exit
./configure --with-beagle="${PREFIX_PARENT}/beagle" || exit
make || exit


cat <<EndOfExplanation
you are going to have to run:

    export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${PREFIX_PARENT}/beagle/lib"

before each shell that uses this version of mrbayes.
You might want to add that and 

    export PATH="\${PATH}:$PWD"

to your .bash_profile
EndOfExplanation