+++ /dev/null
-# ChangeLog for app-sci/tree-puzzle
-# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/tree-puzzle/ChangeLog,v 1.7 2004/10/14 19:12:21 gongloo Exp $
-
- 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
-
+++ /dev/null
-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
+++ /dev/null
-MD5 5c33d8c0d2c5da21f246e9bf6a0c3513 tree-puzzle-5.1.tar.gz 612216
+++ /dev/null
-MD5 20fa9606434ddc789670e681d98fe68f tree-puzzle-5.2.tar.gz 875142
+++ /dev/null
-<?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>
+++ /dev/null
-# Copyright 1999-2004 Gentoo Foundation
-# 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 1.5 2004/10/14 19:12:21 gongloo 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}
-}
+++ /dev/null
-# Copyright 1999-2004 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/tree-puzzle/tree-puzzle-5.2.ebuild,v 1.4 2004/10/14 15:02:34 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/*
-}
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