You need to have write permission on the directory in which you eventually wish to install EMBOSS. You may also wish to put it somewhere else other than the standard location of /usr/local/emboss.
The installation directory is controlled by the -prefix argument. In my case I have all my applications owned by a non-priviledged user and installed in a package specific directory under /site/prog
% ./configure --prefix=/site/prog/embosswill install EMBOSS under /site/prog/emboss. The binaries will be installed in /site/prog/emboss/bin with shared libraries installed in /site/prog/emboss/lib. System wide data are installed in /site/prog/emboss/data, and the configuration files (ACD files) for the applications will be installed in /site/prog/emboss/share in directories corresponding to the package name. Documentation is installed in /site/prog/emboss/doc.
The individual directories for installation can be modified with other configuration commands but this is usually not neccessary. Run ./configure -help to get more information on the directories that can be changed and other configuration options.
Run ./configure with the options you wish to use. This may take a short time as various messages scroll up the screen.
Depending on your system you may need to explicitly configure the graphics. Please see the section 'Configuring EMBOSS graphics' below.
All should be well with this and configure should exit with a message like this:
... much output skipped creating ./config.status creating plplot/Makefile creating plplot/lib/Makefile creating nucleus/Makefile creating ajax/Makefile creating emboss/Makefile creating emboss/acd/Makefile creating test/Makefile creating test/data/Makefile creating test/embl/Makefile creating test/pir/Makefile creating test/swiss/Makefile creating test/swnew/Makefile creating test/wormpep/Makefile creating emboss/data/Makefile creating emboss/data/CODONS/Makefile creating emboss/data/REBASE/Makefile creating emboss/data/PRINTS/Makefile creating emboss/data/PROSITE/Makefile creating MakefileConfiguration is now complete.