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

(Portage version: 2.1_pre4-r1)

5 files changed, 89 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..172eb1a4ec4d
--- /dev/null
+++ b/sci-biology/muscle/Manifest
@@ -0,0 +1,27 @@
+MD5 74eaf8b13786493ed6220c0c33e09b28 files/add-libint-error-message.patch 722
+RMD160 526e57d715b65fedc763069be30f7e49e52dcbb8 files/add-libint-error-message.patch 722
+SHA256 63715cab509893817c7cfb22422c3724fd02a4d0fa5065bbb5a477d8d8a23390 files/add-libint-error-message.patch 722
+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 09ec4c47c33e46e812d1c8a09f00a91a files/digest-probcons-1.10 241
+RMD160 2d5910f5cca5eb03d3d6e7ca83954774d4080051 files/digest-probcons-1.10 241
+SHA256 6dcaf5dcb70c5db87bebfb7d61342cc1f56758d67fc2db674ae900bc685406ef files/digest-probcons-1.10 241
+MD5 dbaa3f7804f89cfbc6b41a8fceeec0ca files/digest-psi-3.2.3 232
+RMD160 36c9c50c4c7e2ef156f0f0334b2b330435968e9b files/digest-psi-3.2.3 232
+SHA256 e9a1506870d5bf1fdfb1aee4740fc584343f0e716afe52c19411d115adf0bc4c files/digest-psi-3.2.3 232
+MD5 285e67094e0841a79a32c9301c023b39 files/dont-build-libint.patch 355
+RMD160 c3b00a7edb9af349f2321fcbbdc286168d5d6db3 files/dont-build-libint.patch 355
+SHA256 57513d9f897776055dfbe14e717761de314e79409def91ccc27563a613a66e18 files/dont-build-libint.patch 355
+MD5 9ec964134fe443be4a6d6760278bea87 files/try-more-compilers.patch 401
+RMD160 550151b01cc4362d70c3e79d250a2fb2e36af64f files/try-more-compilers.patch 401
+SHA256 cb3b404ad7725700840df7602686d651f38f3d7623857af63e3556d1317aaf08 files/try-more-compilers.patch 401
+MD5 f73030c473338710e13e3dfe3ce59463 files/try-pthread-for-blas-lapack.patch 1489
+RMD160 092e0613b7184b065bb5ffa2288ce342e84d9483 files/try-pthread-for-blas-lapack.patch 1489
+SHA256 09cf2f5bc6835697322501280de3027b932416dd939d04d0d25a9790fe02eaa5 files/try-pthread-for-blas-lapack.patch 1489
+MD5 6dc1efc685dfc6994c972eed20daf18c files/use-external-libint.patch 1359
+RMD160 560598e6d7c99d901d97dd6037480bd57c82433f files/use-external-libint.patch 1359
+SHA256 41faa20ba804e98a81cb6809c789c643fd17458b6f6bc95dbe6311dd2fb16713 files/use-external-libint.patch 1359
+MD5 5d75567eec90190cf000570cfd16c228 muscle-3.6.ebuild 813
+RMD160 7643cca1df0e58199700e15b87ac081d5b1f72b8 muscle-3.6.ebuild 813
+SHA256 8776ce3cc6abdfe998619b6be801e55f039ecfefef34f2fbe24ce6ba736812da muscle-3.6.ebuild 813
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
+}