Initial import, see bug #45938

5 files changed, 72 insertions, 0 deletions

diff --git a/app-sci/tree-puzzle/ChangeLog b/app-sci/tree-puzzle/ChangeLog
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+# ChangeLog for app-sci/tree-puzzle
+# Copyright 2000-2004 Gentoo Technologies, Inc.; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/app-sci/tree-puzzle/ChangeLog,v 1.1 2004/05/17 11:54:19 phosphan Exp $
+
+  17 May 2004; Patrick Kursawe <phosphan@gentoo.org> :
+  Initial import, ebuild by Olivier Fisette <olivier.fisette@sympatico.ca> in
+  bug #45938
+
diff --git a/app-sci/tree-puzzle/Manifest b/app-sci/tree-puzzle/Manifest
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index 000000000000..49abd0196255
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+++ b/app-sci/tree-puzzle/Manifest
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+MD5 ef9c9879454d97c43479cbc3c6e421a2 tree-puzzle-5.1.ebuild 807
+MD5 b3b353ea8c6ac55d3918c4c09b785dd8 metadata.xml 1451
+MD5 432840347efef142f52c23eb03c21e89 files/digest-tree-puzzle-5.1 67
diff --git a/app-sci/tree-puzzle/files/digest-tree-puzzle-5.1 b/app-sci/tree-puzzle/files/digest-tree-puzzle-5.1
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index 000000000000..cea399f56f67
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+++ b/app-sci/tree-puzzle/files/digest-tree-puzzle-5.1
@@ -0,0 +1 @@
+MD5 5c33d8c0d2c5da21f246e9bf6a0c3513 tree-puzzle-5.1.tar.gz 612216
diff --git a/app-sci/tree-puzzle/metadata.xml b/app-sci/tree-puzzle/metadata.xml
new file mode 100644
index 000000000000..d7499f40c396
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+++ b/app-sci/tree-puzzle/metadata.xml
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+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci</herd>
+	<longdescription>
+		TREE-PUZZLE is a computer program to reconstruct phylogenetic trees
+		from molecular sequence data by maximum likelihood. It implements a
+		fast tree search algorithm, quartet puzzling, that allows analysis of
+		large data sets and automatically assigns estimations of support to
+		each internal branch. TREE-PUZZLE also computes pairwise maximum
+		likelihood distances as well as branch lengths for user specified
+		trees. Branch lengths can be calculated under the clock-assumption. In
+		addition, TREE-PUZZLE offers a novel method, likelihood mapping, to
+		investigate the support of a hypothesized internal branch without
+		computing an overall tree and to visualize the phylogenetic content of
+		a sequence alignment. TREE-PUZZLE also conducts a number of statistical
+		tests on the data set (chi-square test for homogeneity of base
+		composition, likelihood ratio clock test, Kishino-Hasegawa test). The
+		models of substitution provided by TREE-PUZZLE are TN, HKY, F84, SH for
+		nucleotides, Dayhoff, JTT, mtREV24, VT, WAG, BLOSUM 62 for amino acids,
+		and F81 for two-state data. Rate heterogeneity is modeled by a discrete
+		Gamma distribution and by allowing invariable sites. The corresponding
+		parameters can be inferred from the data set.
+	</longdescription>
+</pkgmetadata>
diff --git a/app-sci/tree-puzzle/tree-puzzle-5.1.ebuild b/app-sci/tree-puzzle/tree-puzzle-5.1.ebuild
new file mode 100644
index 000000000000..095511bb5b0c
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+++ b/app-sci/tree-puzzle/tree-puzzle-5.1.ebuild
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+# Copyright 1999-2004 Gentoo Technologies, Inc.
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/app-sci/tree-puzzle/tree-puzzle-5.1.ebuild,v 1.1 2004/05/17 11:54:19 phosphan Exp $
+
+DESCRIPTION="Maximum likelihood analysis for nucleotide, amino acid, and two-state data."
+HOMEPAGE="http://www.tree-puzzle.de"
+SRC_URI="http://www.tree-puzzle.de/${P}.tar.gz"
+
+LICENSE="GPL-1"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+
+src_compile() {
+	econf || die "Configuration failed."
+	emake || die "Compilation failed."
+}
+
+src_install() {
+	make DESTDIR=${D} install || die
+	dodoc AUTHORS ChangeLog COPYING README
+
+	# User manual
+	dohtml doc/{*.html,*.gif}
+	insinto /usr/share/doc/${PF}/pdf
+	doins doc/*.pdf
+
+	# Example data files
+	insinto /usr/share/${PN}/data
+	doins data/{*.3trees,*.a,*.b,*.phy,*.n}
+
+	# Program logos
+	insinto /usr/share/${PN}/graphics
+	doins doc/{*.png,*.eps}
+}