New multiple sequence alignment package. Provides a great tradeoff between runtime and quality for global alignments; quite a bit worse on local alignments.

Package-Manager: portage-2.1_pre4-r1

5 files changed, 74 insertions, 0 deletions

diff --git a/sci-biology/muscle/ChangeLog b/sci-biology/muscle/ChangeLog
new file mode 100644
index 000000000000..b867b380d10f
--- /dev/null
+++ b/sci-biology/muscle/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-biology/muscle
+# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/muscle/ChangeLog,v 1.1 2006/02/21 20:06:10 spyderous Exp $
+
+*muscle-3.6 (21 Feb 2006)
+
+  21 Feb 2006; Donnie Berkholz <spyderous@gentoo.org>; +metadata.xml,
+  +muscle-3.6.ebuild:
+  New multiple sequence alignment package. Provides a great tradeoff between
+  runtime and quality for global alignments; quite a bit worse on local
+  alignments.
+
diff --git a/sci-biology/muscle/Manifest b/sci-biology/muscle/Manifest
new file mode 100644
index 000000000000..42ce7f6fac4d
--- /dev/null
+++ b/sci-biology/muscle/Manifest
@@ -0,0 +1,12 @@
+MD5 487d4ea255595305e50c6aeea5da2e60 ChangeLog 495
+RMD160 f08f953d139aec3d9c8ae33e860af02b5f73c1a8 ChangeLog 495
+SHA256 64e405b92b1adef1b8a352968253d466940465e062360f7e7fc33db078c464dd ChangeLog 495
+MD5 2ce7fc1feec78dd7428b1bfb6dca6f48 files/digest-muscle-3.6 241
+RMD160 00cdfc0a67940e555cae9b2917a3e59e4a880f44 files/digest-muscle-3.6 241
+SHA256 ff5d1ffa1cd22ba1ee71b8af23f4f92d25ae80f8fa88bf0ed303d0d8c3799cbd files/digest-muscle-3.6 241
+MD5 af1bfbb0777267a03e889b08173f2757 metadata.xml 248
+RMD160 6488d9f1ef3e05e6ac5a29ddcc818e5ead0a5230 metadata.xml 248
+SHA256 de0ad7dc383b462c407cae015684d27c090455eac87c6f0f9ff581ef6e0b5b27 metadata.xml 248
+MD5 d4b707c55d629eb80ed7aa0150780017 muscle-3.6.ebuild 817
+RMD160 b6bef3e305bf2176b5d08e661ea40e9770f5b14f muscle-3.6.ebuild 817
+SHA256 f8bc874d9f960fec4a5d42005a1b712bf133e9e2b8de85d536326d9863ec999f muscle-3.6.ebuild 817
diff --git a/sci-biology/muscle/files/digest-muscle-3.6 b/sci-biology/muscle/files/digest-muscle-3.6
new file mode 100644
index 000000000000..343f62ae80b5
--- /dev/null
+++ b/sci-biology/muscle/files/digest-muscle-3.6
@@ -0,0 +1,3 @@
+MD5 e721d0859da9feec3cedeb42dcee9f59 muscle3.6_src.tar.gz 185267
+RMD160 4afda92b982ec2b05853a582479c61a7d8814f51 muscle3.6_src.tar.gz 185267
+SHA256 32b818a51f421e1d687f513dc31374a330470950151a5e7df961e64781699431 muscle3.6_src.tar.gz 185267
diff --git a/sci-biology/muscle/metadata.xml b/sci-biology/muscle/metadata.xml
new file mode 100644
index 000000000000..211b8bd0f0a4
--- /dev/null
+++ b/sci-biology/muscle/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+<email>spyderous@gentoo.org</email>
+<name>Donnie Berkholz</name>
+</maintainer>
+</pkgmetadata>
diff --git a/sci-biology/muscle/muscle-3.6.ebuild b/sci-biology/muscle/muscle-3.6.ebuild
new file mode 100644
index 000000000000..68c6ed8eb2ad
--- /dev/null
+++ b/sci-biology/muscle/muscle-3.6.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/muscle/muscle-3.6.ebuild,v 1.1 2006/02/21 20:06:10 spyderous Exp $
+
+inherit toolchain-funcs
+
+MY_P="${PN}${PV}_src"
+DESCRIPTION="Multiple sequence comparison by log-expectation"
+HOMEPAGE="http://www.drive5.com/muscle/"
+SRC_URI="http://www.drive5.com/muscle/downloads${PV}/${MY_P}.tar.gz"
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+RDEPEND=""
+DEPEND="${RDEPEND}"
+S="${WORKDIR}/${MY_P}"
+
+src_unpack() {
+	unpack ${A}
+	sed -i \
+		"s:-static::g" \
+		${S}/Makefile
+	sed -i \
+		"/strip/d" \
+		${S}/Makefile
+}
+
+src_compile() {
+	emake \
+		GPP="$(tc-getCXX)" \
+		CFLAGS="${CXXFLAGS}" \
+		|| die "make failed"
+}
+
+src_install() {
+	DESTTREE="/usr" dobin muscle
+}