gentoo-overlay/sci-biology/emboss/files

Administrating EMBOSS on Gentoo systems

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Codon data files location

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The codon data files that are distributed with EMBOSS are installed in the

``EPREFIX/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual

``EPREFIX/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 ${EPREFIX}/usr/share/EMBOSS/data

	# ln -s CODONS.orig CODONS





Restriction enzymes equivalence file location

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The restriction enzymes equivalence file distributed with EMBOSS is installed

as ``EPREFIX/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual

``EPREFIX/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 ${EPREFIX}/usr/share/EMBOSS/data

	# ln -s embossre.equ.orig embossre.equ