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

1 files changed, 58 insertions, 0 deletions

diff --git a/sci-biology/mummer/mummer-3.20.ebuild b/sci-biology/mummer/mummer-3.20.ebuild
new file mode 100644
index 000000000000..2f566667ceca
--- /dev/null
+++ b/sci-biology/mummer/mummer-3.20.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+inherit eutils
+
+MY_P="MUMmer${PV}"
+DESCRIPTION="A rapid whole genome aligner"
+HOMEPAGE="http://mummer.sourceforge.net/"
+SRC_URI="mirror://sourceforge/mummer/${MY_P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE="doc"
+KEYWORDS="amd64 x86"
+
+DEPEND=""
+RDEPEND="app-shells/tcsh"
+
+S="${WORKDIR}/${MY_P}"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+	epatch "${FILESDIR}"/${P}-gcc43.patch
+	# Warning: package uses CPPFLAGS on c in addition to cpp, despite the name
+	sed -i -e 's/CPPFLAGS =/CPPFLAGS = ${CFLAGS} /' \
+		-e 's/LDFLAGS  =$//' "${S}/Makefile"
+}
+
+src_compile() {
+	emake || die "emake failed"
+
+	sed -i -e 's|\($AUX_BIN_DIR = "\).*"|\1/usr/bin"|' \
+		-e 's|\($BIN_DIR = "\).*"|\1/usr/bin"|' \
+		-e 's|\($SCRIPT_DIR = "\).*"|\1/usr/share/'${PN}'/lib"|' \
+		-e 's|\(set bindir = \).*|\1/usr/bin|' \
+		-e 's|\(set scriptdir = \).*|\1/usr/share/'${PN}'/scripts|' \
+		-e 's|\(use lib "\).*"|\1/usr/share/'${PN}'/lib"|' \
+		scripts/* exact-tandems mapview mummerplot nucmer promer run-mummer{1,3} || die "Failed to replace paths"
+	sed -i 's|$bindir/annotate|$bindir/mummer-annotate|' run-mummer1 scripts/run-mummer1.csh
+}
+
+src_install() {
+	dobin nucmer2xfig show-coords mapview show-snps run-mummer{1,3} \
+		exact-tandems promer repeat-match show-aligns gaps mummer \
+		show-tiling mgaps nucmer mummerplot delta-filter combineMUMs aux_bin/* || die
+	newbin annotate mummer-annotate || die
+
+	insinto /usr/share/${PN}/scripts
+	doins scripts/{*.awk,*.csh,*.pl}
+	insinto /usr/share/${PN}/lib
+	doins scripts/Foundation.pm || die
+
+	dodoc ACKNOWLEDGEMENTS ChangeLog README
+	insinto /usr/share/doc/${PF}
+	use doc && doins -r docs
+}