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.

Package-Manager: portage-2.1_pre4-r1

6 files changed, 104 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..c114d7fe7237
--- /dev/null
+++ b/sci-biology/probcons/Manifest
@@ -0,0 +1,15 @@
+MD5 2142bd7824940065a60d5024e3fd6e8b ChangeLog 555
+RMD160 4869d11c827be891be11672e4b2b5f7443eaca77 ChangeLog 555
+SHA256 2f910cb76d04fa4761b6bccfc410081b16f4c9e683c46615d24a1c475251a9cb ChangeLog 555
+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 09ec4c47c33e46e812d1c8a09f00a91a files/digest-probcons-1.10 241
+RMD160 2d5910f5cca5eb03d3d6e7ca83954774d4080051 files/digest-probcons-1.10 241
+SHA256 6dcaf5dcb70c5db87bebfb7d61342cc1f56758d67fc2db674ae900bc685406ef files/digest-probcons-1.10 241
+MD5 af1bfbb0777267a03e889b08173f2757 metadata.xml 248
+RMD160 6488d9f1ef3e05e6ac5a29ddcc818e5ead0a5230 metadata.xml 248
+SHA256 de0ad7dc383b462c407cae015684d27c090455eac87c6f0f9ff581ef6e0b5b27 metadata.xml 248
+MD5 7e0f62f3e3c56d54ca75a5ce26d80374 probcons-1.10.ebuild 1237
+RMD160 1557442a1dfe780629d4b69111617beb29110e28 probcons-1.10.ebuild 1237
+SHA256 66ade2e4c472cd457bf1e3c8d64904cb5ec148e8e81cb652cc0927c87939c5d4 probcons-1.10.ebuild 1237
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"
+}