proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

3 files changed, 64 insertions, 0 deletions

diff --git a/sci-biology/aaindex/Manifest b/sci-biology/aaindex/Manifest
new file mode 100644
index 000000000000..7b3eeafe5263
--- /dev/null
+++ b/sci-biology/aaindex/Manifest
@@ -0,0 +1 @@
+DIST aaindex-9.1.tar.bz2 133780 RMD160 6f5bd699de3c84bd366f9747f57712ba8aecf513 SHA1 7215e3dae85cd61919854ba5dd5abff29be91852 SHA256 ae2e5aec2fc47835f26c8d8b5776966464bc08a5fca422c130d8312880382caa
diff --git a/sci-biology/aaindex/aaindex-9.1.ebuild b/sci-biology/aaindex/aaindex-9.1.ebuild
new file mode 100644
index 000000000000..6c45282be145
--- /dev/null
+++ b/sci-biology/aaindex/aaindex-9.1.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+DESCRIPTION="Amino acid indices and similarity matrices"
+LICENSE="public-domain"
+HOMEPAGE="http://www.genome.ad.jp/aaindex"
+SRC_URI="mirror://gentoo/${P}.tar.bz2"
+
+SLOT="0"
+# Minimal build keeps only the indexed files (if applicable) and the
+# documentation. The non-indexed database is not installed.
+IUSE="emboss minimal"
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+
+DEPEND="emboss? ( sci-biology/emboss )"
+
+RDEPEND="${DEPEND}"
+
+src_compile() {
+	if use emboss; then
+		mkdir AAINDEX
+		echo
+		einfo "Indexing AAindex for usage with EMBOSS."
+		EMBOSS_DATA="." aaindexextract -auto -infile ${PN}1 || die \
+			"Indexing AAindex failed."
+		echo
+	fi
+}
+
+src_install() {
+	if ! use minimal; then
+		insinto /usr/share/${PN}
+		doins ${PN}{1,2,3} || die "Failed to install raw database."
+	fi
+	dodoc ${PN}.doc || die "Failed to install documentation."
+	if use emboss; then
+		insinto /usr/share/EMBOSS/data/AAINDEX
+		doins AAINDEX/* || die "Failed to install EMBOSS data files."
+	fi
+}
diff --git a/sci-biology/aaindex/metadata.xml b/sci-biology/aaindex/metadata.xml
new file mode 100644
index 000000000000..ccb567e64e02
--- /dev/null
+++ b/sci-biology/aaindex/metadata.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-biology</herd>
+	<longdescription>
+		Amino acid indices and similarity matrices maintained at Kyoto
+		University. An amino acid index is a set of 20 numerical values
+		representing any of the different physicochemical and biological
+		properties of amino acids.  The AAindex1 section of the Amino Acid
+		Index Database is a collection of published indices together with the
+		result of cluster analysis using the correlation coefficient as the
+		distance between two indices.  This section currently contains 494
+		indices. Another important feature of amino acids that can be
+		represented numerically is the similarity between amino acids.  Thus, a
+		similarity matrix, also called a mutation matrix, is a set of 210
+		numerical values, 20 diagonal and 20x19/2 off-diagonal elements, used
+		for sequence alignments and similarity searches.  The AAindex2 section
+		of the Amino Acid Index Database is a collection of published amino
+		acid mutation matrices together with the result of cluster analysis.
+		This section currently contains 83 matrices.
+	</longdescription>
+</pkgmetadata>