Using EMBOSS on Gentoo systems

Codon data files location

The codon data files that are distributed with EMBOSS are installed in the 
"/usr/share/EMBOSS/data/CODONS.orig" directory instead of the usual
"/usr/share/EMBOSS/data/CODONS". This is done to avoid confusion between these
codon files and those installed with the CUTG database. The names of these files
sometimes vary only by their case. Having both sets of files in the same directory
is also impossible on systems such as MacOSX, where the root filesystem is case
insensitive. If you do not have the CUTG database installed and want to use the
codon files distributed with EMBOSS, you can symlink the "CODONS.orig" directory
to "CODONS":

	cd /usr/share/EMBOSS/data
	ln -s CODONS.orig CODONS

Restriction enzymes equivalence file location

The restriction enzymes equivalence file distributed with EMBOSS is installed as
"/usr/share/EMBOSS/data/embossre.equ.orig" rather than the usual
"/usr/share/EMBOSS/data/embossre.equ". This is done to avoid a file collision
with the equivalence file provided by the Rebase database. If you do not have the
Rebase database installed and want to use the equivalence file distributed with
EMBOSS, you can symlink the "embossre.equ.orig" file to "embossre.equ":

	cd /usr/share/EMBOSS/data
	ln -s embossre.equ.orig embossre.equ
