Installing DOMALIGN.

a) from the anonymous cvs code.
    
       1) Go to the package directory
       cd embassy/domalign

       2) make the configuration file
       aclocal -I m4
       autoconf
       automake -a

       3) configure and compile
       Configuration should be done using the same options you used
       for the main package. So, if you used:

           ./configure --with-pngdriver=/opt/lib

       for the main package then use the same command for the
       embassy package. Then:

       make
       make install


b) From the FTP server

    The package is available from our FTP server
    ftp://emboss.open-bio.org/pub/EMBOSS/ 


    If you have done a full installation of EMBOSS using a 'prefix'
    e.g. you configured with ./configure --prefix=/usr/local/emboss
    and followed this with a 'make install' (highly recommended) then:

       1) gunzip and untar the file anywhere (e.g.)
       gunzip DOMALIGN-0.1.0.tar.gz
       tar xvf DOMALIGN-0.1.0.tar

       2) go into the domalign directory
       cd DOMALIGN-1.0.0

       3) Configuration should be done using the same options you used
       for the main package. So, if you used:

       ./configure --prefix=/usr/local/emboss --with-pngdriver=/opt/lib

       for the main package then use the same command for the
       embassy package. Then:

       make
       make install

       If you configured without using a prefix but did do
       a 'make install' (or specified a prefix of /usr/local,
       which amounts to the same thing) then you must configure
       using (e.g.):
            ./configure --prefix=/usr/local --with-pngdriver=/fu/bar
               --enable-localforce

       Note the --enable-localforce switch.

    If, on the other hand, you did not do a 'make install' of EMBOSS
    then:

       1) Go to the emboss directory 
       cd EMBOSS-4.0.0

       2) make new directory embassy if it does not exist already.
       mkdir embassy

       3) Go into that directory
       cd embassy

       4) gunzip and untar the file
       gunzip DOMALIGN-0.1.0.tar.gz
       tar xvf DOMALIGN-0.1.0.tar

       5) go into the domalign directory
       cd DOMALIGN-0.1.0

       6) configure and compile
       Configuration should be done using the same options you used for the
       main EMBOSS package. So, if you used:

       ./configure --with-pngdriver=/fu/bar

       for the main package then use the same command for the
       embassy package. Then:

       make
   
       7) Set your PATH to include the full path of the 'src'
          directory
