New multiple sequence alignment package. Perhaps the most accurate and fastest local aligner.

(Portage version: 2.1_pre4-r1)

5 files changed, 92 insertions, 0 deletions

diff --git a/sci-biology/dialign-t/ChangeLog b/sci-biology/dialign-t/ChangeLog
new file mode 100644
index 000000000000..8d05a1c56b83
--- /dev/null
+++ b/sci-biology/dialign-t/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-biology/dialign-t
+# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/dialign-t/ChangeLog,v 1.1 2006/02/21 20:50:32 spyderous Exp $
+
+*dialign-t-0.2.1 (21 Feb 2006)
+
+  21 Feb 2006; Donnie Berkholz <spyderous@gentoo.org>; +metadata.xml,
+  +dialign-t-0.2.1.ebuild:
+  New multiple sequence alignment package. Perhaps the most accurate and
+  fastest local aligner.
+
diff --git a/sci-biology/dialign-t/Manifest b/sci-biology/dialign-t/Manifest
new file mode 100644
index 000000000000..d5e89309e647
--- /dev/null
+++ b/sci-biology/dialign-t/Manifest
@@ -0,0 +1,30 @@
+MD5 745cc89f4cd095bf146de4ba73af1033 dialign-t-0.2.1.ebuild 1031
+RMD160 8ff474cb2eb40316fe7d7ce8da021bfaae507e1d dialign-t-0.2.1.ebuild 1031
+SHA256 20de1a581bf9d370b7dbeea53889f24a930548685607576861422dcc90fb8588 dialign-t-0.2.1.ebuild 1031
+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 20a9e61f87048ee301d0cb690b890ede files/digest-dialign-t-0.2.1 250
+RMD160 9d920eafc14c5c82bb7f59a0589570c52ce5e292 files/digest-dialign-t-0.2.1 250
+SHA256 13b80f9063a8294da8e20803cd0ab7ac56a38eb1ba5548885f52000103db8795 files/digest-dialign-t-0.2.1 250
+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
diff --git a/sci-biology/dialign-t/dialign-t-0.2.1.ebuild b/sci-biology/dialign-t/dialign-t-0.2.1.ebuild
new file mode 100644
index 000000000000..0eea4e6dff6b
--- /dev/null
+++ b/sci-biology/dialign-t/dialign-t-0.2.1.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/dialign-t/dialign-t-0.2.1.ebuild,v 1.1 2006/02/21 20:50:32 spyderous Exp $
+
+inherit multilib toolchain-funcs
+
+MY_P="DIALIGN-T_${PV}"
+DESCRIPTION="An improved algorithm for segment-based multiple sequence alignment"
+HOMEPAGE="http://dialign-t.gobics.de/"
+SRC_URI="http://dialign-t.gobics.de/${MY_P}.tar.gz"
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+RDEPEND=""
+DEPEND="${RDEPEND}"
+S="${WORKDIR}/${MY_P}"
+
+src_compile() {
+	cd ${S}/source
+	emake clean
+	emake \
+		CPPFLAGS="${CFLAGS}" \
+		|| die "make failed"
+}
+
+src_install() {
+	DESTTREE="/usr" dobin ${S}/source/dialign-t
+	dohtml ${S}/doc/html/*
+	dodoc ${S}/doc/user_guide*
+	insinto /usr/$(get_libdir)/${PN}/conf
+	doins ${S}/conf/*
+}
+
+pkg_postinst() {
+	ewarn "The configuration directory is"
+	ewarn "${ROOT}usr/$(get_libdir)/${PN}/conf"
+	ewarn "You will need to pass this to ${PN} on every run."
+}
diff --git a/sci-biology/dialign-t/files/digest-dialign-t-0.2.1 b/sci-biology/dialign-t/files/digest-dialign-t-0.2.1
new file mode 100644
index 000000000000..fd423eb5e37f
--- /dev/null
+++ b/sci-biology/dialign-t/files/digest-dialign-t-0.2.1
@@ -0,0 +1,3 @@
+MD5 d1d4fc381a009c68387e159b78b33801 DIALIGN-T_0.2.1.tar.gz 1635888
+RMD160 a43807668354120b873cad0120a7691b6860ca28 DIALIGN-T_0.2.1.tar.gz 1635888
+SHA256 2249bf9007588e891525b4edc085285f1390c2bf8d42ce327aa9217130d7e930 DIALIGN-T_0.2.1.tar.gz 1635888
diff --git a/sci-biology/dialign-t/metadata.xml b/sci-biology/dialign-t/metadata.xml
new file mode 100644
index 000000000000..211b8bd0f0a4
--- /dev/null
+++ b/sci-biology/dialign-t/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>