New multiple sequence alignment package. Probably the best global aligner, although it runs slower. Takes 5-10 times longer than clustalw, but about half as long as t-coffee.

(Portage version: 2.1_pre4-r1)

6 files changed, 116 insertions, 0 deletions

diff --git a/sci-biology/probcons/ChangeLog b/sci-biology/probcons/ChangeLog
new file mode 100644
index 000000000000..044374da44e0
--- /dev/null
+++ b/sci-biology/probcons/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-biology/probcons
+# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/probcons/ChangeLog,v 1.1 2006/02/21 20:27:27 spyderous Exp $
+
+*probcons-1.10 (21 Feb 2006)
+
+  21 Feb 2006; Donnie Berkholz <spyderous@gentoo.org>;
+  +files/1.10-fix-cxxflags.patch, +metadata.xml, +probcons-1.10.ebuild:
+  New multiple sequence alignment package. Probably the best global aligner,
+  although it runs slower. Takes 5-10 times longer than clustalw, but about
+  half as long as t-coffee.
+
diff --git a/sci-biology/probcons/Manifest b/sci-biology/probcons/Manifest
new file mode 100644
index 000000000000..8f4dd746a9d1
--- /dev/null
+++ b/sci-biology/probcons/Manifest
@@ -0,0 +1,27 @@
+MD5 bcc20b9c5e249f07fb535f0744f816e2 files/1.10-fix-cxxflags.patch 845
+RMD160 1e04c84b35c245623619c6d5a7128a8ab1c880af files/1.10-fix-cxxflags.patch 845
+SHA256 73a298114996b5d879b9ec3253d104464cb456d19382668cdf75bfe9f93f11de files/1.10-fix-cxxflags.patch 845
+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 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 dfce50503ba4abc4c4d4845cef79faef probcons-1.10.ebuild 1238
+RMD160 6fe62998a1b18aa4700deb574d9edc2c99dd8025 probcons-1.10.ebuild 1238
+SHA256 abb10a9fea1636935526bb6cdaa195a4c17b3ba38e7554c460a746afff68b657 probcons-1.10.ebuild 1238
diff --git a/sci-biology/probcons/files/1.10-fix-cxxflags.patch b/sci-biology/probcons/files/1.10-fix-cxxflags.patch
new file mode 100644
index 000000000000..bf76e77b36c1
--- /dev/null
+++ b/sci-biology/probcons/files/1.10-fix-cxxflags.patch
@@ -0,0 +1,21 @@
+diff -urN probcons.orig/Makefile probcons/Makefile
+--- probcons.orig/Makefile	2006-02-21 12:14:37.000000000 -0800
++++ probcons/Makefile	2006-02-21 12:15:15.000000000 -0800
+@@ -15,6 +15,8 @@
+ #    c) RELEASE mode
+ ################################################################################
+ 
++OPT_CXXFLAGS = -O3 -W -Wall -pedantic -funroll-loops
++
+ OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.10"
+ 
+ # debug mode    
+@@ -25,7 +27,7 @@
+ 
+ # release mode
+ #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer 
+-CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops
++CXXFLAGS = $(OPT_CXXFLAGS) -DNDEBUG $(OTHERFLAGS)
+ 
+ ################################################################################
+ # 3) Dependencies
diff --git a/sci-biology/probcons/files/digest-probcons-1.10 b/sci-biology/probcons/files/digest-probcons-1.10
new file mode 100644
index 000000000000..e49b2933d04c
--- /dev/null
+++ b/sci-biology/probcons/files/digest-probcons-1.10
@@ -0,0 +1,3 @@
+MD5 c7938b95732a85c35225bafd4b5b174f probcons_v1_10.tar.gz 43004
+RMD160 ba7caa3cadd702c3dc00c20f01bfb22416435784 probcons_v1_10.tar.gz 43004
+SHA256 f7a775ac4ba3b3261c0bbe5d2c203c96fc2551e67448aefbac83b461c931b518 probcons_v1_10.tar.gz 43004
diff --git a/sci-biology/probcons/metadata.xml b/sci-biology/probcons/metadata.xml
new file mode 100644
index 000000000000..211b8bd0f0a4
--- /dev/null
+++ b/sci-biology/probcons/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/probcons/probcons-1.10.ebuild b/sci-biology/probcons/probcons-1.10.ebuild
new file mode 100644
index 000000000000..2128a8505739
--- /dev/null
+++ b/sci-biology/probcons/probcons-1.10.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/probcons/probcons-1.10.ebuild,v 1.1 2006/02/21 20:27:27 spyderous Exp $
+
+inherit eutils toolchain-funcs
+
+MY_P="${PN}_v${PV/./_}"
+DESCRIPTION="Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences"
+HOMEPAGE="http://probcons.stanford.edu/"
+SRC_URI="http://probcons.stanford.edu/${MY_P}.tar.gz"
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+# Gnuplot is explicitly runtime-only, it's run using system()
+RDEPEND="sci-visualization/gnuplot"
+DEPEND=""
+S="${WORKDIR}/${PN}"
+
+src_unpack() {
+	unpack ${A}
+	epatch ${FILESDIR}/${PV}-fix-cxxflags.patch
+}
+
+src_compile() {
+	emake \
+		CXX="$(tc-getCXX)" \
+		OPT_CXXFLAGS="${CXXFLAGS}" \
+		|| die "make failed"
+}
+
+src_install() {
+	DESTTREE="/usr" dobin probcons project makegnuplot
+	# Overlap with imagemagick
+	DESTTREE="/usr" newbin compare compare-probcons
+	dodoc README
+}
+
+pkg_postinst() {
+	ewarn "The 'compare' binary is installed as 'compare-probcons'"
+	ewarn "to avoid overlap with other packages."
+	einfo "You may also want to download the user manual"
+	einfo "from http://probcons.stanford.edu/manual.pdf"
+}