gentoo-overlay/sci-biology/emboss/files

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