The SCons wiki has moved to https://github.com/SCons/scons/wiki/LyxBuilder
Teaching PDF to understand .lyx files
Note that this builder has been added to the SCons "contrib" repo at https://bitbucket.org/scons/scons-contrib , as of 2016-12-07! Get your latest copy from there...
#!python env = Environment(tools=['default','pdftex','pdflatex','lyx']) env.PDF(source='test.lyx')