compiling mrbayes with beagle in ubuntu. You may want to change the second line to whatever dir you would like to use as the parent of the prefix of the beagle installation.

mb-and-beagle-from-svn.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 ../..
svn checkout svn://svn.code.sf.net/p/mrbayes/code/trunk mrbayes-code || exit
cd mrbayes-code/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