Added updated Gentoo README file in reStructuredText format.

Package-Manager: portage-2.1.2.9

3 files changed, 47 insertions, 5 deletions

diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index 9dc703149859..8b0272743475 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/emboss
 # Copyright 2000-2007 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.43 2007/07/18 00:55:33 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.44 2007/07/18 01:24:12 ribosome Exp $
+
+  18 Jul 2007; Olivier Fisette <ribosome@gentoo.org>
+  +files/emboss-README.Gentoo-1:
+  Added updated Gentoo README file in reStructuredText format.
 
 *emboss-5.0.0 (18 Jul 2007)
 
diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest
index 0fc7449df76c..616e1a67f9c5 100644
--- a/sci-biology/emboss/Manifest
+++ b/sci-biology/emboss/Manifest
@@ -6,6 +6,10 @@ AUX README.Gentoo 1326 RMD160 bfaa4d7d1218d3bd4ea58d54d000da7f58b6bca6 SHA1 8cf1
 MD5 615888722f8d6a0c918f936e0cc1cfcd files/README.Gentoo 1326
 RMD160 bfaa4d7d1218d3bd4ea58d54d000da7f58b6bca6 files/README.Gentoo 1326
 SHA256 33b517b977cc85824847bd6cf4113489a5554fb014f1a6b1d22d6f80c3487e9f files/README.Gentoo 1326
+AUX emboss-README.Gentoo-1 1474 RMD160 a116b4516cd0d8e0b28734bf1e51f1e0833737c4 SHA1 ec23610137ebddc3fc15976757d2cdebd741f9ec SHA256 e97558bbc8296f2e9395080061e494b282303ed69e1d6eb45554846617b47abd
+MD5 f625f2d9c5bdbdc6799947f73c93da7c files/emboss-README.Gentoo-1 1474
+RMD160 a116b4516cd0d8e0b28734bf1e51f1e0833737c4 files/emboss-README.Gentoo-1 1474
+SHA256 e97558bbc8296f2e9395080061e494b282303ed69e1d6eb45554846617b47abd files/emboss-README.Gentoo-1 1474
 DIST EMBOSS-4.0.0.tar.gz 17651607 RMD160 5b29ac2946a1315928581bf0e40a0f6b5023c599 SHA1 784c729f2d2e746339a90048277c9e4f052e036a SHA256 bbfd127adc064a5211542f3b5400cbb13c7f74d9171fd16b8531cee9fd11b231
 DIST EMBOSS-5.0.0.tar.gz 20666560 RMD160 1bf510c0919d991e4ba67182137448dee49bab4d SHA1 1ad4edc4808a8225fe8d574e8a7d0686be99cac6 SHA256 64e6f09b82a719ff26de7f21fdf7d2bd605d2c664384c1c7b48f9d245d5f40ae
 EBUILD emboss-4.0.0.ebuild 2999 RMD160 f36fcba1fd3153ca27c1392be79ae9914344b56e SHA1 ef13303cd5a130501626a6b4dbcf9d23d79967e9 SHA256 46e5752122f3720db42ff667b377c465a47c017937530cd17a13c515e342ff59
@@ -16,10 +20,10 @@ EBUILD emboss-5.0.0.ebuild 3143 RMD160 765d21355731a6a790afd9e280e048998915190f
 MD5 f9201389e5075f12b859da8b327992d4 emboss-5.0.0.ebuild 3143
 RMD160 765d21355731a6a790afd9e280e048998915190f emboss-5.0.0.ebuild 3143
 SHA256 48055bdca89cc1add72998e251c4bb6904e7f2ee44237c13fc1af1fb85387d6e emboss-5.0.0.ebuild 3143
-MISC ChangeLog 7798 RMD160 8e04e1ae2e1dcb71fd7af7cb7fe45e48b9d006d7 SHA1 ef07bbf1d6ac28970877d3a48f54cfc3db081433 SHA256 f9186f6208805387119118e6aecda6e248bbdeadb7013fe4d01babfb70c3d7e0
-MD5 e7b3cbd71cd3687bcdefaee0083d7647 ChangeLog 7798
-RMD160 8e04e1ae2e1dcb71fd7af7cb7fe45e48b9d006d7 ChangeLog 7798
-SHA256 f9186f6208805387119118e6aecda6e248bbdeadb7013fe4d01babfb70c3d7e0 ChangeLog 7798
+MISC ChangeLog 7948 RMD160 4a4007157d407a9ef21e407c721babecea2db026 SHA1 5a5f802de71c5a77b3100cd13220ff2148c04db7 SHA256 5fdc0ffdcf9086a7d6a85caec83e9bcb43d2eac48aa28a76148a2e7fe2f22874
+MD5 24efdf32e3eacffa6663975231a5d5b8 ChangeLog 7948
+RMD160 4a4007157d407a9ef21e407c721babecea2db026 ChangeLog 7948
+SHA256 5fdc0ffdcf9086a7d6a85caec83e9bcb43d2eac48aa28a76148a2e7fe2f22874 ChangeLog 7948
 MISC metadata.xml 1021 RMD160 ee767f436af5f815ecb9526df9063438dab8eb14 SHA1 eff46db435f88e0b457ce2a38e5ff786ae6324e1 SHA256 0c5af548d0483d41a3344695cb04acaf0974fb56b70bc1e2ec0a9749ecbc45a0
 MD5 ecba11e4d50ee5cc740817f5becffa83 metadata.xml 1021
 RMD160 ee767f436af5f815ecb9526df9063438dab8eb14 metadata.xml 1021
diff --git a/sci-biology/emboss/files/emboss-README.Gentoo-1 b/sci-biology/emboss/files/emboss-README.Gentoo-1
new file mode 100644
index 000000000000..81e71988ae80
--- /dev/null
+++ b/sci-biology/emboss/files/emboss-README.Gentoo-1
@@ -0,0 +1,34 @@
+Administrating 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