From 11049003f131f463ac9c6fc4180d3068b9c86710 Mon Sep 17 00:00:00 2001 From: Olivier Fisette Date: Thu, 23 Dec 2004 18:13:11 +0000 Subject: [PATCH] Moving to sci-biology/tree-puzzle --- app-sci/tree-puzzle/ChangeLog | 31 ------------ app-sci/tree-puzzle/Manifest | 6 --- .../tree-puzzle/files/digest-tree-puzzle-5.1 | 1 - .../tree-puzzle/files/digest-tree-puzzle-5.2 | 1 - app-sci/tree-puzzle/metadata.xml | 29 ----------- app-sci/tree-puzzle/tree-puzzle-5.1.ebuild | 35 ------------- app-sci/tree-puzzle/tree-puzzle-5.2.ebuild | 49 ------------------- 7 files changed, 152 deletions(-) delete mode 100644 app-sci/tree-puzzle/ChangeLog delete mode 100644 app-sci/tree-puzzle/Manifest delete mode 100644 app-sci/tree-puzzle/files/digest-tree-puzzle-5.1 delete mode 100644 app-sci/tree-puzzle/files/digest-tree-puzzle-5.2 delete mode 100644 app-sci/tree-puzzle/metadata.xml delete mode 100644 app-sci/tree-puzzle/tree-puzzle-5.1.ebuild delete mode 100644 app-sci/tree-puzzle/tree-puzzle-5.2.ebuild diff --git a/app-sci/tree-puzzle/ChangeLog b/app-sci/tree-puzzle/ChangeLog deleted file mode 100644 index 28b2a3239d9c..000000000000 --- a/app-sci/tree-puzzle/ChangeLog +++ /dev/null @@ -1,31 +0,0 @@ -# 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 tree-puzzle-5.1.ebuild: - Keyworded ~ppc-macos. - - 14 Oct 2004; Olivier Fisette 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 tree-puzzle-5.2.ebuild: - Change virtual/glibc -> virtual/libc. - -*tree-puzzle-5.2 (20 Jul 2004) - - 20 Jul 2004; Olivier Fisette - 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 tree-puzzle-5.1.ebuild: - Added to ~ppc. - - 17 May 2004; Patrick Kursawe : - Initial import, ebuild by Olivier Fisette in - bug #45938 - diff --git a/app-sci/tree-puzzle/Manifest b/app-sci/tree-puzzle/Manifest deleted file mode 100644 index 686b8762be19..000000000000 --- a/app-sci/tree-puzzle/Manifest +++ /dev/null @@ -1,6 +0,0 @@ -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/app-sci/tree-puzzle/files/digest-tree-puzzle-5.1 b/app-sci/tree-puzzle/files/digest-tree-puzzle-5.1 deleted file mode 100644 index cea399f56f67..000000000000 --- a/app-sci/tree-puzzle/files/digest-tree-puzzle-5.1 +++ /dev/null @@ -1 +0,0 @@ -MD5 5c33d8c0d2c5da21f246e9bf6a0c3513 tree-puzzle-5.1.tar.gz 612216 diff --git a/app-sci/tree-puzzle/files/digest-tree-puzzle-5.2 b/app-sci/tree-puzzle/files/digest-tree-puzzle-5.2 deleted file mode 100644 index fa411d8fcefb..000000000000 --- a/app-sci/tree-puzzle/files/digest-tree-puzzle-5.2 +++ /dev/null @@ -1 +0,0 @@ -MD5 20fa9606434ddc789670e681d98fe68f tree-puzzle-5.2.tar.gz 875142 diff --git a/app-sci/tree-puzzle/metadata.xml b/app-sci/tree-puzzle/metadata.xml deleted file mode 100644 index ee5ea99507eb..000000000000 --- a/app-sci/tree-puzzle/metadata.xml +++ /dev/null @@ -1,29 +0,0 @@ - - - - - ribosome@gentoo.org - Olivier Fisette - - sci - - 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. - - diff --git a/app-sci/tree-puzzle/tree-puzzle-5.1.ebuild b/app-sci/tree-puzzle/tree-puzzle-5.1.ebuild deleted file mode 100644 index 1be30c93de80..000000000000 --- a/app-sci/tree-puzzle/tree-puzzle-5.1.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# 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} -} diff --git a/app-sci/tree-puzzle/tree-puzzle-5.2.ebuild b/app-sci/tree-puzzle/tree-puzzle-5.2.ebuild deleted file mode 100644 index 40adabbf686c..000000000000 --- a/app-sci/tree-puzzle/tree-puzzle-5.2.ebuild +++ /dev/null @@ -1,49 +0,0 @@ -# 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/* -} -- 2.26.2