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35 lines
1.5 KiB
35 lines
1.5 KiB
Administrating EMBOSS on Gentoo systems
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=======================================
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Codon data files location
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-------------------------
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The codon data files that are distributed with EMBOSS are installed in the
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``EPREFIX/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual
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``EPREFIX/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusion between
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these codon files and those installed with the CUTG database. The names of
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these files sometimes vary only by their case. Having both sets of files in
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the same directory is also impossible on systems such as MacOSX, where the
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root filesystem is case insensitive. If you do not have the CUTG database
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installed and want to use the codon files distributed with EMBOSS, you can
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symlink the ``CODONS.orig`` directory to ``CODONS``::
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# cd ${EPREFIX}/usr/share/EMBOSS/data
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# ln -s CODONS.orig CODONS
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Restriction enzymes equivalence file location
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---------------------------------------------
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The restriction enzymes equivalence file distributed with EMBOSS is installed
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as ``EPREFIX/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual
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``EPREFIX/usr/share/EMBOSS/data/embossre.equ``. This is done to avoid a file
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collision with the equivalence file provided by the Rebase database. If you do
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not have the Rebase database installed and want to use the equivalence file
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distributed with EMBOSS, you can symlink the ``embossre.equ.orig`` file to
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``embossre.equ``::
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# cd ${EPREFIX}/usr/share/EMBOSS/data
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# ln -s embossre.equ.orig embossre.equ
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