Install Dev Tools
    ~45 minutes
Install Subversion.
    http://metissian.com/projects/macosx/subversion/
    ~5 minutes

The third-party install supports Intel Macs, so these two Boost steps can be skipped.
Download Boost-jam
    http://sourceforge.net/project/showfiles.php?group_id=7586&package_id=72941
    The PPC version seems to work on Intel Macs.
    Copy/link to /usr/local/bin
    ~5 minutes
Download and install Boost 1.33.1
    http://prdownloads.sourceforge.net/boost/boost_1_33_1.tar.gz?download
    'sudo bjam "-sTOOLS=gcc" --prefix=/usr/local/boost_1_33_1-gcc4_0 install'
    ~45 minutes
    
Download and install FFTW
    http://www.fftw.org
    ./configure;make;sudo make install
    <1 hour
Blas and LibXML are already installed

Check out third-party
    svn co svn+ssh://mplab.ucsd.edu/usr/local/svnroot/third-party
    Untar any desired packages (at least the Boost package) and install them.
    ~10 minutes
Check out MPUtil
    svn co svn+ssh://mplab.ucsd.edu/usr/local/svnroot/MPUtil
Check out FeatureLearning
    svn co svn+ssh://mplab.ucsd.edu/usr/local/svnroot/FeatureLearning/trunk FeatureLearning
Check out CERT
    svn co svn+ssh://mplab.ucsd.edu/usr/local/svnroot/CERT/trunk CERT
    If Matlab is not installed on the machine you will also need to get all of the Kernel sources and the SVM weights files.

Install CocoaSequenceGrabber
    Make sure the 'Installation Directory' build setting is set to '@executable_path/../Frameworks'.

In the two Xcode projects a number of header and library search paths may need to be modified to point to the correct locations.
Also make sure the architecture setting is set properly.
If the svnversion executable is not available, delete or disable the shell script phase in the CERTFramework project. It can be installed via Fink.