Below are the build directions for EMBOSS (European Molecular Biology
 Software Suite) on Mac OS X.
 
 http://www.uk.embnet.org/Software/EMBOSS/
 
 EMBOSS needs libgd and X11R6 and libgd needs libpng and libjpeg.
 Below are build directions for the whole shootin' match.
 Things have been built such that headers, libraries, binaries, and man
 pages are installed in /usr/local/[include|lib|bin|man].
 This doesn't seem to be the Mac OS X way, but people smarter than me
 claim this is the UNIX way, so that's the way I set things up.
 
 Lines beginning with "#" are comments. Lines beginning with nothing are
 commands executed from the terminal.
 I used a build of Mac OS X and developer tools that are of an
 unmentionable version number so I hope this works on 10.0.4 (which I no
 longer have available to me).
 Good luck!!
 
 # Login as user with Administrator privileges
 # Launch Terminal application
 # sudo to root
 
 sudo -s
 
 # Make local directories
 
 mkdir /usr/local
 mkdir /usr/local/bin
 mkdir /usr/local/include
 mkdir /usr/local/lib
 mkdir /usr/local/man
 mkdir /usr/local/man/man1
 
 # Make a working directory and change directory to it
 
 mkdir ~/scratch
 cd ~/scratch
 
 # Get and install XFree86
 
 wget -r ftp://ftp.xfree86.org/pub/XFree86/4.1.0/binaries/Darwin-ppc/
 cd ftp.xfree86.org/pub/XFree86/4.1.0/binaries/Darwin-ppc/
 sh Xinstall.sh
 
 # Answer "y" to all of the questions, but the last one
 # Do you wish to have this link installed (y/n)? [n]
 
 # Add X11 to PATH and MANPATH  for all users
 
 echo 'setenv PATH "${PATH}:/usr/X11R6/bin"' > /usr/share/init/tcsh/path
 echo 'setenv MANPATH "${MANPATH}:/usr/X11R6/man:/usr/local/man"' 
 /usr/share/init/tcsh/path
 
 # Get and install XDarwin
 
 cd ~/scratch
 wget http://prdownloads.sourceforge.net/xonx/XDarwin1.0a1.tgz
 cp XDarwin1.0a1.tgz /
 cd /
 tar zxvf XDarwin1.0a1.tgz
 rm XDarwin1.0a1.tgz
 
 # Get and install libpng
 
 cd ~/scratch
 wget http://www.libpng.org/pub/png/src/libpng-1.0.12.tar.gz
 tar zxvf libpng-1.0.12.tar.gz
 cd libpng-1.0.12
 cp scripts/makefile.macosx Makefile
 
 # Patch Makefile
 
 echo "11,12c11,12"  Makefile.diff
 echo "< ZLIBLIB=../zlib"  Makefile.diff
 echo "< ZLIBINC=../zlib"  Makefile.diff
 echo "---"  Makefile.diff
 echo "> ZLIBLIB=/usr/lib"  Makefile.diff
 echo "> ZLIBINC=/usr/include"  Makefile.diff
 patch Makefile Makefile.diff
 make
 make test
 make install
 
 # Get and install libjpeg
 
 cd ~/scratch
 wget http://www.darwinfo.org/pub/darwin/X11/jpegsrc.v6b-src.tar.gz
 tar zxvf jpegsrc.v6b-src.tar.gz
 cd jpeg-6b
 ./configure
 make
 make test
 make install
 make install-lib
 
 # Get and install libgd
 
 cd ~/scratch
 wget http://www.boutell.com/gd/http/gd-2.0.1.tar.gz
 tar zxvf gd-2.0.1.tar.gz
 cd gd-2.0.1
 
 # Patch Makefile and gdcache.h
 
 echo "43c43"  gdcache.h.diff
 echo "< #include <malloc.h>"  gdcache.h.diff
 echo "---"  gdcache.h.diff
 echo "> /*#include <malloc.h>*/"  gdcache.h.diff
 patch gdcache.h gdcache.h.diff
 echo "7c7"  Makefile.diff
 echo "< COMPILER=gcc"  Makefile.diff
 echo "---"  Makefile.diff
 echo "> COMPILER=cc"  Makefile.diff
 echo "17c17"  Makefile.diff
 echo "< CFLAGS=-g -DHAVE_LIBPNG -DHAVE_LIBJPEG -DHAVE_LIBFREETYPE" 
 Makefile.diff
 echo "---"  Makefile.diff
 echo "> CFLAGS=-g -DHAVE_LIBPNG -DHAVE_LIBJPEG -DHAVE_LIBFREETYPE
 -DHAVE_XPM"  Makefile.diff
 echo "26c26"  Makefile.diff
 echo "< LIBS=-lgd -lpng -lz -ljpeg -lfreetype -lm"  Makefile.diff
 echo "---"  Makefile.diff
 echo "> LIBS=-lgd -lpng -lz -ljpeg -lfreetype -lxpm -lm"  Makefile.diff
 echo "33c33"  Makefile.diff
 echo "< INCLUDEDIRS=-I. -I/usr/include/freetype2 -I/usr/include/X11
 -I/usr/X11R6/include/X11 -I/usr/local/include "  Makefile.diff
 echo "---"  Makefile.diff
 echo "> INCLUDEDIRS=-I. -I/usr/X11R6/include/freetype2
 -I/usr/X11R6/include -I/usr/X11R6/include/X11 -I/usr/local/include
 -I/usr/include"  Makefile.diff
 echo "39c39"  Makefile.diff
 echo "< LIBDIRS=-L/usr/local/lib -L/usr/lib/X11 -L/usr/X11R6/lib" 
 Makefile.diff
 echo "---"  Makefile.diff
 echo "> LIBDIRS=-L/usr/lib -L/usr/local/lib -L/usr/lib/X11
 -L/usr/X11R6/lib"  Makefile.diff
 echo "46c46"  Makefile.diff
 echo "< INSTALL_LIB=/usr/lib"  Makefile.diff
 echo "---"  Makefile.diff
 echo "> INSTALL_LIB=/usr/local/lib"  Makefile.diff
 echo "49c49"  Makefile.diff
 echo "< INSTALL_INCLUDE=/usr/include"  Makefile.diff
 echo "---"  Makefile.diff
 echo "> INSTALL_INCLUDE=/usr/local/include"  Makefile.diff
 patch Makefile Makefile.diff
 make install
 
 # Ignore error
 # make: *** [libgd.so.2.0.0] Error 1
 
 make libgd.a
 cp -r libgd.a /usr/local/lib
 ranlib /usr/local/lib/libgd.a
 
 # Get and install EMBOSS
 
 cd ~/scratch
 wget ftp://ftp.uk.embnet.org/pub/EMBOSS/EMBOSS-2.0.1.tar.gz
 tar zxvf EMBOSS-2.0.1.tar.gz
 cd EMBOSS-2.0.1
 cp /usr/libexec/config.* .
 ./configure
 make
 make install
 
 # Exit from sudo
 exit