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authorOlivier Fisette <ribosome@gentoo.org>2006-01-23 20:57:32 +0000
committerOlivier Fisette <ribosome@gentoo.org>2006-01-23 20:57:32 +0000
commit7348fab74b2f54b7a4502118ca7bc4433463055a (patch)
tree37a800e4daadc0ea740c8967cefcd1ebe5e8dd64 /sci-biology/emboss/files
parentAdded ~ppc64; bug #97319 (diff)
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Added missing README file
(Portage version: 2.0.54)
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+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