sci-biology/mummer: New package, Bug 169793

svn path=/sunrise/; revision=3173

5 files changed, 85 insertions, 0 deletions

diff --git a/sci-biology/mummer/ChangeLog b/sci-biology/mummer/ChangeLog
new file mode 100644
index 000000000..794ba996c
--- /dev/null
+++ b/sci-biology/mummer/ChangeLog
@@ -0,0 +1,8 @@
+# ChangeLog for sci-biology/mummer
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  07 Mar 2007; AK <gentoo@horizon.ath.cx> +mummer-3.19.ebuild,
+  +metadata.xml:
+  New package, Bug 169793
+
diff --git a/sci-biology/mummer/Manifest b/sci-biology/mummer/Manifest
new file mode 100644
index 000000000..88aa94137
--- /dev/null
+++ b/sci-biology/mummer/Manifest
@@ -0,0 +1,16 @@
+DIST MUMmer3.19.tar.gz 3141991 RMD160 54f3c692efb8bde7762c48186919754f2a8c178c SHA1 8906bab6bd43b307461de8b5f44122a115799533 SHA256 c590264e0def7de9259083de085f589ea39dc729d7f491790340b6b0abf3d6ab
+EBUILD mummer-3.19.ebuild 1506 RMD160 c2d50b31197c9f21daaef78ef305049342935123 SHA1 6322c7378a082e253d1c9f0e18324603964e2d00 SHA256 7dd700bd807528a4afc48db0652aa934e8f3d5b00a6d7e53ed50a97a8bf007ff
+MD5 8bfc1908db1986c230d6c31e72d975c7 mummer-3.19.ebuild 1506
+RMD160 c2d50b31197c9f21daaef78ef305049342935123 mummer-3.19.ebuild 1506
+SHA256 7dd700bd807528a4afc48db0652aa934e8f3d5b00a6d7e53ed50a97a8bf007ff mummer-3.19.ebuild 1506
+MISC ChangeLog 226 RMD160 180e47334584e00a715f8205b0eda1c9e04eff66 SHA1 f514d4e34cbaae11f9a637822c3cdb5c58361b0c SHA256 4b825f4d217b994d07b9c150799c682931d98e87437e7f970bd42513284901f0
+MD5 29904921da51d1264fd54d4219295da8 ChangeLog 226
+RMD160 180e47334584e00a715f8205b0eda1c9e04eff66 ChangeLog 226
+SHA256 4b825f4d217b994d07b9c150799c682931d98e87437e7f970bd42513284901f0 ChangeLog 226
+MISC metadata.xml 170 RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 SHA1 ac7f48a14fec325926f9ce1be8fbf1f311b4f2e4 SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42
+MD5 1e678929a9fec6632e227bdf2262e9a1 metadata.xml 170
+RMD160 645927a396fdc21cdeb089fe42c5397332420ea6 metadata.xml 170
+SHA256 d797a2ec6f9dc516c9f9c1a758ee87ad3e8c43101b5dc76c2f872d5bd4639b42 metadata.xml 170
+MD5 aecc1fc23d65ba16769fc4b9cd7661f1 files/digest-mummer-3.19 235
+RMD160 579c3b585978eb4b23bdb2029556279eb7b7f1a7 files/digest-mummer-3.19 235
+SHA256 03a7db30ce80070d11adee5be808e1752dccd73cbffc5b73c4b131430b63ecc3 files/digest-mummer-3.19 235
diff --git a/sci-biology/mummer/files/digest-mummer-3.19 b/sci-biology/mummer/files/digest-mummer-3.19
new file mode 100644
index 000000000..52ef1125f
--- /dev/null
+++ b/sci-biology/mummer/files/digest-mummer-3.19
@@ -0,0 +1,3 @@
+MD5 7e0aa1c7da68c31b66fda9687171d9ff MUMmer3.19.tar.gz 3141991
+RMD160 54f3c692efb8bde7762c48186919754f2a8c178c MUMmer3.19.tar.gz 3141991
+SHA256 c590264e0def7de9259083de085f589ea39dc729d7f491790340b6b0abf3d6ab MUMmer3.19.tar.gz 3141991
diff --git a/sci-biology/mummer/metadata.xml b/sci-biology/mummer/metadata.xml
new file mode 100644
index 000000000..7e3286984
--- /dev/null
+++ b/sci-biology/mummer/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>maintainer-wanted</herd>
+</pkgmetadata>
diff --git a/sci-biology/mummer/mummer-3.19.ebuild b/sci-biology/mummer/mummer-3.19.ebuild
new file mode 100644
index 000000000..b34950bf1
--- /dev/null
+++ b/sci-biology/mummer/mummer-3.19.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+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/'${PN}'/scripts|' \
+		scripts/* exact-tandems mapview mummerplot nucmer promer run-mummer{1,3} || die "Failed to replace paths"
+	sed -i 's|$bindir/annotate|$bindir/mummer-annotate|' run-mummer1 scripts/run-mummer1.csh
+}
+
+src_install() {
+	dobin nucmer2xfig show-coords mapview show-snps run-mummer{1,3} \
+		exact-tandems promer repeat-match show-aligns gaps mummer \
+		show-tiling mgaps nucmer mummerplot delta-filter combineMUMs aux_bin/*
+	newbin annotate mummer-annotate
+
+	dodir /usr/share/${PN}/{lib,scripts}
+	insinto /usr/share/${PN}/scripts
+	doins scripts/{*.awk,*.csh,*.pl}
+	insinto /usr/share/${PN}/lib
+	doins scripts/Foundation.pm
+
+	cat > 99${PN} <<EOF
+COLON_SEPARATED=PERL5LIB
+PERL5LIB="/usr/share/${PN}/lib"
+EOF
+	doenvd 99${PN}
+
+	dodoc ACKNOWLEDGEMENTS ChangeLog README
+	insinto /usr/share/doc/${PF}
+	use doc && doins -r docs
+}