Mass import from sunrise

git-svn-id: http://overlays.gentoo.org/svn/proj/science/overlay@577 32389bae-6d03-0410-99cf-db05cde120eb

4 files changed, 74 insertions, 0 deletions

diff --git a/sci-biology/mummer/ChangeLog b/sci-biology/mummer/ChangeLog
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+++ b/sci-biology/mummer/ChangeLog
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+# ChangeLog for sci-biology/mummer
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +mummer-3.19.ebuild:
+  Mass import from sunrise
+
+  07 Mar 2007; Andrey Kislyuk <weaver@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
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index 000000000..3aeec3a21
--- /dev/null
+++ b/sci-biology/mummer/Manifest
@@ -0,0 +1,12 @@
+DIST MUMmer3.19.tar.gz 3141991 RMD160 54f3c692efb8bde7762c48186919754f2a8c178c SHA1 8906bab6bd43b307461de8b5f44122a115799533 SHA256 c590264e0def7de9259083de085f589ea39dc729d7f491790340b6b0abf3d6ab
+EBUILD mummer-3.19.ebuild 1462 RMD160 5f8b0b879579bbb191e127ff8502cf85ad24a1d6 SHA1 4fe7b3203592abf4fef23576225389304983102a SHA256 a4b07705f9363862d0a22418b3afbf90a1170653b3417f6217d69febf0ea70a5
+MD5 6e44430e8985e9ae0c49344af52c4d8d mummer-3.19.ebuild 1462
+RMD160 5f8b0b879579bbb191e127ff8502cf85ad24a1d6 mummer-3.19.ebuild 1462
+SHA256 a4b07705f9363862d0a22418b3afbf90a1170653b3417f6217d69febf0ea70a5 mummer-3.19.ebuild 1462
+MISC ChangeLog 341 RMD160 3af940375849fd821b9a26f495ec4dfe0d0e43d2 SHA1 343e404673256e84eaa87aab34f23c2fd0e10677 SHA256 fba592d098848186f7e54967015b44ca01753a11251c505add0bd83d361364eb
+MD5 583803d6dae0bbc9e2aa180ea0886f9a ChangeLog 341
+RMD160 3af940375849fd821b9a26f495ec4dfe0d0e43d2 ChangeLog 341
+SHA256 fba592d098848186f7e54967015b44ca01753a11251c505add0bd83d361364eb ChangeLog 341
+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/mummer-3.19.ebuild b/sci-biology/mummer/mummer-3.19.ebuild
new file mode 100644
index 000000000..a6b3e4c0c
--- /dev/null
+++ b/sci-biology/mummer/mummer-3.19.ebuild
@@ -0,0 +1,48 @@
+# 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|' \
+		-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|$bindir/mummer-annotate|' run-mummer1 scripts/run-mummer1.csh
+}
+
+src_install() {
+	dobin nucmer2xfig show-coords mapview show-snps run-mummer{1,3} \
+		exact-tandems promer repeat-match show-aligns gaps mummer \
+		show-tiling mgaps nucmer mummerplot delta-filter combineMUMs aux_bin/*
+	newbin annotate mummer-annotate
+
+	dodir /usr/share/${PN}/{lib,scripts}
+	insinto /usr/share/${PN}/scripts
+	doins scripts/{*.awk,*.csh,*.pl}
+	insinto /usr/share/${PN}/lib
+	doins scripts/Foundation.pm
+
+	dodoc ACKNOWLEDGEMENTS ChangeLog README
+	insinto /usr/share/doc/${PF}
+	use doc && doins -r docs
+}