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

1 files changed, 44 insertions, 0 deletions

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"
+}