| Administrating EMBOSS on Gentoo systems |
| ======================================= |
| |
| |
| Codon data files location |
| ------------------------- |
| |
| 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 |
| --------------------------------------------- |
| |
| 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 |