New package from sunrise, bug 169793

Package-Manager: portage-2.1.5.2

4 files changed, 70 insertions, 0 deletions

diff --git a/sci-biology/mummer/ChangeLog b/sci-biology/mummer/ChangeLog
new file mode 100644
index 000000000000..00ee55828b1c
--- /dev/null
+++ b/sci-biology/mummer/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/mummer
+# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mummer/ChangeLog,v 1.1 2008/05/24 04:10:30 weaver Exp $
+
+*mummer-3.20 (24 May 2008)
+
+  24 May 2008; weaver <weaver@gentoo.org> +metadata.xml,
+  +mummer-3.20.ebuild:
+  Initial commit. New package from sunrise, bug 169793
+
diff --git a/sci-biology/mummer/Manifest b/sci-biology/mummer/Manifest
new file mode 100644
index 000000000000..44e883e753da
--- /dev/null
+++ b/sci-biology/mummer/Manifest
@@ -0,0 +1,4 @@
+DIST MUMmer3.20.tar.gz 3155446 RMD160 7e5fefef359c6a6ee49f2ebf14dc18caa19f48fb SHA1 68d6742de93d8524236ccf538f32ba8bb4edf7cc SHA256 9c7880b4ce25ef3c6bed9ccdc26f1c4d7e74eb0ef1ce403907790c0f96c0f260
+EBUILD mummer-3.20.ebuild 1525 RMD160 24ed4921348b56f0d0c8062ed00289645c6265ca SHA1 407dd44ed6692f139ca59e906a49f4a6a5e8929c SHA256 177d07a92a1ba7891549c7474670a27a2c5c3363ca78d9881af93f1eb513492a
+MISC ChangeLog 373 RMD160 60d5bdc9de309160d45167f4aff0c913e30bba5a SHA1 fabd66d870bffff0f858034732239d2e7bbaa8bd SHA256 81818fde3ced89fe8ad2068dd287efc3b01803a1b0385c4c864131979dc34c77
+MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
diff --git a/sci-biology/mummer/metadata.xml b/sci-biology/mummer/metadata.xml
new file mode 100644
index 000000000000..3302123e5718
--- /dev/null
+++ b/sci-biology/mummer/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer>
+		<email>weaver@gentoo.org</email>
+		<name>Andrey Kislyuk</name>
+	</maintainer>
+	<herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/mummer/mummer-3.20.ebuild b/sci-biology/mummer/mummer-3.20.ebuild
new file mode 100644
index 000000000000..11cf40d66f48
--- /dev/null
+++ b/sci-biology/mummer/mummer-3.20.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mummer/mummer-3.20.ebuild,v 1.1 2008/05/24 04:10:30 weaver Exp $
+
+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="~x86"
+
+DEPEND=""
+RDEPEND=""
+
+S=${WORKDIR}/${MY_P}
+
+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|$bindir/mummer-annotate|' run-mummer1 scripts/run-mummer1.csh
+}
+
+src_install() {
+	dobin nucmer2xfig show-coords mapview show-snps run-mummer{1,3} \
+		exact-tandems promer repeat-match show-aligns gaps mummer \
+		show-tiling mgaps nucmer mummerplot delta-filter combineMUMs aux_bin/*
+	newbin annotate mummer-annotate
+
+	insinto /usr/share/${PN}/scripts
+	doins scripts/{*.awk,*.csh,*.pl}
+	insinto /usr/share/${PN}/lib
+	doins scripts/Foundation.pm
+
+	dodoc ACKNOWLEDGEMENTS ChangeLog README
+	insinto /usr/share/doc/${PF}
+	use doc && doins -r docs
+}