Moved from app-sci/tree-puzzle to sci-biology/tree-puzzle.

7 files changed, 158 insertions, 0 deletions

diff --git a/sci-biology/tree-puzzle/ChangeLog b/sci-biology/tree-puzzle/ChangeLog
new file mode 100644
index 000000000000..34690720ccb3
--- /dev/null
+++ b/sci-biology/tree-puzzle/ChangeLog
@@ -0,0 +1,37 @@
+# ChangeLog for app-sci/tree-puzzle
+# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/tree-puzzle/ChangeLog,v 1.1 2004/12/23 18:14:07 ribosome Exp $
+
+*tree-puzzle-5.2 (23 Dec 2004)
+
+  23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+  +tree-puzzle-5.1.ebuild, +tree-puzzle-5.2.ebuild:
+  Moved from app-sci/tree-puzzle to sci-biology/tree-puzzle.
+
+  14 Oct 2004; Hasan Khalil <gongloo@gentoo.org> tree-puzzle-5.1.ebuild:
+  Keyworded ~ppc-macos.
+
+  14 Oct 2004; Olivier Fisette <ribosome@gentoo.org> tree-puzzle-5.1.ebuild,
+  tree-puzzle-5.2.ebuild:
+  Added to x86. Use gcc-getCC from gcc.eclass rather than ${CC}.
+
+  23 Jul 2004; Jon Hood <squinky86@gentoo.org> tree-puzzle-5.2.ebuild:
+  Change virtual/glibc -> virtual/libc.
+
+*tree-puzzle-5.2 (20 Jul 2004)
+
+  20 Jul 2004; Olivier Fisette <ribosome@gentoo.org>
+  tree-puzzle-5.2.ebuild, metadata.xml:
+  New version and an updated ebuild supporting the compilation of the
+  parallelized version of the program (ppuzzle).
+  Set myself as maintainer.
+
+*tree-puzzle-5.1 (08 Jun 2004)
+
+  08 Jun 2004; David Holm <dholm@gentoo.org> tree-puzzle-5.1.ebuild:
+  Added to ~ppc.
+
+  17 May 2004; Patrick Kursawe <phosphan@gentoo.org> :
+  Initial import, ebuild by Olivier Fisette <olivier.fisette@sympatico.ca> in
+  bug #45938
+
diff --git a/sci-biology/tree-puzzle/Manifest b/sci-biology/tree-puzzle/Manifest
new file mode 100644
index 000000000000..686b8762be19
--- /dev/null
+++ b/sci-biology/tree-puzzle/Manifest
@@ -0,0 +1,6 @@
+MD5 045662b656ba3ff5f6f317604f1c5185 ChangeLog 1130
+MD5 d034503a05e54849a282d5baca880756 metadata.xml 1548
+MD5 37fd72859f823608b1d25b8d714e6081 tree-puzzle-5.2.ebuild 1343
+MD5 050406af0280d0ffc7a247df6a0bc6bc tree-puzzle-5.1.ebuild 919
+MD5 432840347efef142f52c23eb03c21e89 files/digest-tree-puzzle-5.1 67
+MD5 91165e7d2ebcd4a70e55b5e8bea21e43 files/digest-tree-puzzle-5.2 67
diff --git a/sci-biology/tree-puzzle/files/digest-tree-puzzle-5.1 b/sci-biology/tree-puzzle/files/digest-tree-puzzle-5.1
new file mode 100644
index 000000000000..cea399f56f67
--- /dev/null
+++ b/sci-biology/tree-puzzle/files/digest-tree-puzzle-5.1
@@ -0,0 +1 @@
+MD5 5c33d8c0d2c5da21f246e9bf6a0c3513 tree-puzzle-5.1.tar.gz 612216
diff --git a/sci-biology/tree-puzzle/files/digest-tree-puzzle-5.2 b/sci-biology/tree-puzzle/files/digest-tree-puzzle-5.2
new file mode 100644
index 000000000000..fa411d8fcefb
--- /dev/null
+++ b/sci-biology/tree-puzzle/files/digest-tree-puzzle-5.2
@@ -0,0 +1 @@
+MD5 20fa9606434ddc789670e681d98fe68f tree-puzzle-5.2.tar.gz 875142
diff --git a/sci-biology/tree-puzzle/metadata.xml b/sci-biology/tree-puzzle/metadata.xml
new file mode 100644
index 000000000000..ee5ea99507eb
--- /dev/null
+++ b/sci-biology/tree-puzzle/metadata.xml
@@ -0,0 +1,29 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer>
+		<email>ribosome@gentoo.org</email>
+		<name>Olivier Fisette</name>
+	</maintainer>
+	<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/sci-biology/tree-puzzle/tree-puzzle-5.1.ebuild b/sci-biology/tree-puzzle/tree-puzzle-5.1.ebuild
new file mode 100644
index 000000000000..1e7df801683a
--- /dev/null
+++ b/sci-biology/tree-puzzle/tree-puzzle-5.1.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2004 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/tree-puzzle/tree-puzzle-5.1.ebuild,v 1.1 2004/12/23 18:14:07 ribosome 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/${P}.tar.gz"
+
+LICENSE="GPL-1"
+SLOT="0"
+KEYWORDS="x86 ~ppc ~ppc-macos"
+IUSE=""
+
+src_compile() {
+	econf || die "Configuration failed."
+	emake || die "Compilation failed."
+}
+
+src_install() {
+	make DESTDIR=${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}
+}
diff --git a/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild b/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild
new file mode 100644
index 000000000000..baeb97170c3f
--- /dev/null
+++ b/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2004 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild,v 1.1 2004/12/23 18:14:07 ribosome Exp $
+
+inherit gcc
+
+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-2"
+
+SLOT="0"
+KEYWORDS="x86"
+IUSE="mpi"
+
+DEPEND="virtual/libc
+	mpi? ( sys-cluster/lam-mpi )"
+
+pkg_setup () {
+	use mpi && [ $(gcc-getCC) = icc ] && die "The parallelized version of tree-puzzle cannot be compiled using icc.
+	Either disable the \"mpi\" USE flag to compile only the non-parallelized
+	version of the program, or use gcc as your compiler (CC=\"gcc\")."
+}
+
+src_compile() {
+	econf || die
+	cd ${S}/src
+	if ! use mpi; then
+		sed -i -e 's:bin_PROGRAMS = puzzle$(EXEEXT) ppuzzle:bin_PROGRAMS = puzzle :' Makefile
+		sed -i -e 's:DIST_SOURCES = $(ppuzzle_SOURCES) $(puzzle_SOURCES):DIST_SOURCES = $(puzzle_SOURCES):' Makefile
+	fi
+	cd {S}
+	emake || die
+}
+
+src_install() {
+	dobin src/puzzle
+	use mpi && dobin src/ppuzzle
+	dodoc AUTHORS ChangeLog README
+
+	# User manual
+	insinto /usr/share/doc/${PF}
+	doins doc/tree-puzzle.pdf
+
+	# Example data files
+	insinto /usr/share/${PN}/data
+	rm data/Makefile*
+	doins data/*
+}