Register an account and download the latest.
http://developer.apple.com/devcenter/mac/index.action and download Xcode. (You will need an account to install the Java Development Kit as well -- see below)

If you have installed Xcode before, check you have /Developer/SDKs/MacOSX10.6.sdk/usr/X11; otherwise, rerun the installer and ensure X11 development files are installed.

Install X11 on Mac OS X (This is already installed from the above step)

If you can find "Applications" > "Utilities" > "X11.app", then skip to MacPorts install; if not:

1. Insert the system DVD into the optical drive (labeled "Mac OS X Install DVD").
2. Navigate and open "Optional Installs" > "Optional Installs.mpkg".
3. Customize the install and check "Applications" > "X11".

Install Java Development Kit (As one dependency of openmotif from MacPorts)

NOTE: even if you can invoke 'javac' in Terminal, you might still need this JDK.
Download JDK for Mac OS X from https://connect.apple.com/cgi-bin/WebObjects/MemberSite.woa/wa/getSoftware?bundleID=20719.

Install MacPorts

First check to see if they are already installed in
/opt/local/var/macports
and that you have a ~/.profile with the PATH that includes the macport binaries /opt/local/bin
If not - download and install the MacPorts binary package:
Refer to http://www.macports.org/install.php.

Install openmotif and OpenGL binding with MacPorts

Open Terminal ("Applications" > "Utilities" > "Terminal.app"). run
sudo port install openmotif
this takes a while...
sudo port install mesa
this also takes a while...


List of installed ports on a functioning compile system:
Macintosh:bin cwvhogue$ sudo /opt/local/bin/port installed
The following ports are currently installed:
  bzip2 @1.0.6_0 (active)
  db46 @4.6.21_6 (active)
  expat @2.0.1_1 (active)
  fontconfig @2.8.0_0 (active)
  freetype @2.4.4_0 (active)
  gdbm @1.8.3_3 (active)
  gettext @0.18.1.1_2 (active)
  glut @3.7_3 (active)
  gperf @3.0.4_0 (active)
  jpeg @8b_0 (active)
  libiconv @1.13.1_0 (active)
  libpng @1.4.5_0 (active)
  libxml2 @2.7.8_0 (active)
  makedepend @1.0.3_0 (active)
  mesa @7.8.2_2 (active)
  ncurses @5.7_1 (active)
  ncursesw @5.7_1 (active)
  openmotif @2.3.2_3 (active)
  openssl @1.0.0c_0 (active)
  pkgconfig @0.25_1 (active)
  python27 @2.7.1_1 (active)
  readline @6.1.002_0 (active)
  sqlite3 @3.7.4_0 (active)
  xbitmaps @1.1.1_0 (active)
  Xft2 @2.2.0_0 (active)
  xorg-bigreqsproto @1.1.1_0 (active)
  xorg-dri2proto @2.3_0 (active)
  xorg-fixesproto @4.1.2_0 (active)
  xorg-glproto @1.4.12_0 (active)
  xorg-inputproto @2.0.1_0 (active)
  xorg-kbproto @1.0.5_0 (active)
  xorg-libice @1.0.7_0 (active)
  xorg-libpthread-stubs @0.3_0 (active)
  xorg-libsm @1.2.0_0 (active)
  xorg-libX11 @1.4.1_0 (active)
  xorg-libXau @1.0.6_0 (active)
  xorg-libxcb @1.7_0+python27 (active)
  xorg-libXdmcp @1.1.0_0 (active)
  xorg-libXext @1.2.0_0 (active)
  xorg-libXfixes @4.0.5_0 (active)
  xorg-libXi @1.4.0_0 (active)
  xorg-libXmu @1.1.0_0 (active)
  xorg-libXp @1.0.1_0 (active)
  xorg-libXt @1.0.9_0 (active)
  xorg-printproto @1.0.5_0 (active)
  xorg-renderproto @0.11.1_0 (active)
  xorg-util-macros @1.11.0_0 (active)
  xorg-xcb-proto @1.6_0+python27 (active)
  xorg-xcmiscproto @1.2.1_0 (active)
  xorg-xextproto @7.1.2_0 (active)
  xorg-xf86bigfontproto @1.2.0_0 (active)
  xorg-xproto @7.0.20_0 (active)
  xorg-xtrans @1.2.6_0 (active)
  xrender @0.9.6_0 (active)
  zlib @1.2.5_0 (active)
Macintosh:bin cwvhogue$

Compile NCBI C Tool Kit

1. Download the toolkit source tar ball from ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/ncbi.tar.gz.
2. Unpack the tar ball into a directory of your choice tar -xvf ncbi.tar
3. Dowload one of the files attached below as the base /platform file
   depending on whether you want PPC supporting universal binaries or just intel binaries:
   
   darwin.ncbi.mk  for 10.6 Intel binaries or:
   

          darwin-univ.ncbi.mk rename to darwin.ncbi.mk     for Intel/PPC 10.4 compatible universal binaries     
     
          issue the build command:

     ./ncbi/make/makedis.csh 2>&1 | tee build_ncbi.log

When finished, ncbi/lib should have 27 libraries:

libblast.a
libblastapi.a
libblastcompadj.a
libddvlib.a
libncbi.a
libncbiCacc.a
libncbiNacc.a
libncbiacc.a
libncbicdr.a
libncbicn3d.a
libncbicn3dOGL.a
libncbidesk.a
libncbiid1.a
libncbimla.a
libncbimmdb.a
libncbiobj.a
libncbitool.a
libncbitxc2.a
libnetblast.a
libnetcli.a
libnetentr.a
libregexp.a
libvibgif.a
libvibnet.a
libvibrant.a
libvibrantOGL.a
ncbithr.o