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

4 files changed, 66 insertions, 0 deletions

diff --git a/sci-biology/kalign/Manifest b/sci-biology/kalign/Manifest
new file mode 100644
index 000000000000..6250f54bc17b
--- /dev/null
+++ b/sci-biology/kalign/Manifest
@@ -0,0 +1 @@
+DIST kalign_2.03.orig.tar.gz 114022 SHA256 710318fea8e3091da6fdedd16d6f94b9de069846afa502f4fe00d5d6b07511c0
diff --git a/sci-biology/kalign/kalign-2.03-r1.ebuild b/sci-biology/kalign/kalign-2.03-r1.ebuild
new file mode 100644
index 000000000000..4422bad730c0
--- /dev/null
+++ b/sci-biology/kalign/kalign-2.03-r1.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit toolchain-funcs
+
+DESCRIPTION="Global and progressive multiple sequence alignment"
+HOMEPAGE="http://msa.cgb.ki.se/"
+SRC_URI="mirror://debian/pool/main/k/kalign/${PN}_${PV}.orig.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+S="${WORKDIR}"/${PN}
+
+src_prepare() {
+	sed \
+		-e "s/\$(CFLAGS) \$(OBJECTS)/\$(LDFLAGS) &/" \
+		-i Makefile.in || die
+}
+
+src_compile() {
+	emake CC="$(tc-getCC)" CFLAGS="${CFLAGS}"
+}
+
+src_install() {
+	dobin ${PN}
+	dodoc README
+}
diff --git a/sci-biology/kalign/kalign-2.03.ebuild b/sci-biology/kalign/kalign-2.03.ebuild
new file mode 100644
index 000000000000..3862e49eaf7f
--- /dev/null
+++ b/sci-biology/kalign/kalign-2.03.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+DESCRIPTION="Global and progressive multiple sequence alignment"
+HOMEPAGE="http://msa.cgb.ki.se/"
+SRC_URI="mirror://debian/pool/main/k/kalign/${PN}_${PV}.orig.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}/${PN}"
+
+src_unpack() {
+	unpack ${A}
+	sed -i 's/^CFLAGS.*= -O9/CFLAGS := ${CFLAGS} -O3/' "${S}"/Makefile.in
+}
+
+src_install() {
+	dobin kalign
+	dodoc README
+}
diff --git a/sci-biology/kalign/metadata.xml b/sci-biology/kalign/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/kalign/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+</pkgmetadata>