reinit the tree, so we can have metadata

4 files changed, 104 insertions, 0 deletions

diff --git a/sci-biology/tree-puzzle/Manifest b/sci-biology/tree-puzzle/Manifest
new file mode 100644
index 000000000000..33758246557c
--- /dev/null
+++ b/sci-biology/tree-puzzle/Manifest
@@ -0,0 +1,6 @@
+AUX tree-puzzle-impl-dec.patch 380 SHA256 0d0941cb6030e089e224a2390a28193ec848c4b2aabf021888292e41df1a1f50 SHA512 092743fff8a305a41ef55afde3e058c1892d9c608bd05cb87de38a451c2b9cafc7749825347d5c245f1c6b1e84cf9d28b63bd4e7389440da5604766412290110 WHIRLPOOL d12a213adb3aefff795814859c02d9e8ed925b37bae31ad95d39344c6bc6514c05a3d03ef080ac9b8e7aff33f3a55d637c79c8df754c3ba6105e430b88b58282
+DIST tree-puzzle-5.2.tar.gz 875142 SHA256 3396d3b80b03b0600afb479dc33f0bd3e5631298337295a4fa454211ac44c3fb SHA512 5b9a729b120cba59f59ba426acd439cf396826ea01e75361b23387ccb9baf295d2512f21af96071a5f7b7507db4ff4d6b135cf6c5b6233a8b438532d31abe751 WHIRLPOOL 145afdfc266809638d7b049beb65cdfc8fb6c108ecba831ba36fae938d58edd141fdf1762d9ce86269f0098043e7314b0ddefaa5e7f9b11cc6fd56a480b54d61
+EBUILD tree-puzzle-5.2.ebuild 1355 SHA256 ce039a7b96e3715546fee972f598d1836bcd132ef417fd59e73e7d3071cb7527 SHA512 44c268b736aa1769c4b85170094d620bdd12798e8d194d4d991f5a2078641d29a19216bb733636052337b93863dec386b0cf2bc3544401059c566205d6d5fe7d WHIRLPOOL 9ff0e12d871e78efd79f2744d3ca3a16f564de758ddcf5e265439ed70cb9c868f65503c43a9a0f0668fe4baf91b5ddf9b5904db955d7a088f018e3e41688e98c
+MISC ChangeLog 2473 SHA256 51b8e8509bc9e744a8f35bdd17615cce04f51e49757600adf2bd5ca0bbb16c8d SHA512 467af996c4275a463e6dd2bf035ff537973704bed42f7cbf27e8dcbe358431b9cba5e3761c67da55b27280e91abc48f5452d5c5876a7f90b56a8bc6f11a2bf32 WHIRLPOOL ad40efb66a62171b0be1f3f8415f587a7a99c1cf68ac08a190b84adf4e5266a381d680da21c25cf7371931597ab4e1fb01261945f6c1c41f2bd2ed734d5b4b55
+MISC ChangeLog-2015 3415 SHA256 73662fc7bcbd74f8b2da79455934d8b6b40267e0b403c92d33866f6ceb156bfe SHA512 f9547f4a6f63a55aa98c0703d269a222a4cea38b4c7ac32dfc9965467b14f4e0be0fd0e502cb33b003cd6099c44dfed1c1ab5a49f2bf31a1777890d644d6a0a3 WHIRLPOOL 76a2553e06efafdf9864d87a2a774b05d48b3d13f2ad50bbcc20cc1f4cc54f841e5c3c1af97f43b6d9e4a76c60f1852ec71604cb73379f99ba1b70db3b20bf6d
+MISC metadata.xml 1555 SHA256 d67ff8bb601bd9dd1950082180043e1e7991b177d1cebca4798484a401377fca SHA512 d74b3243cb62071c16a1728cb14e4c226644b8116dc032ac2d74a928260a252334583d1867ec3663533f36fa1bb746270f1d33f6fb4bae220af86eba668307b8 WHIRLPOOL 44a04284aa8e3216f620fe8efa6c327fb1fc689d15ce2be88639db23d98dae76c8f14854c1b1eccb34430c83f49181fa2ac735ae840e8b3e809f77cc016eac0c
diff --git a/sci-biology/tree-puzzle/files/tree-puzzle-impl-dec.patch b/sci-biology/tree-puzzle/files/tree-puzzle-impl-dec.patch
new file mode 100644
index 000000000000..93b960f5c2b4
--- /dev/null
+++ b/sci-biology/tree-puzzle/files/tree-puzzle-impl-dec.patch
@@ -0,0 +1,14 @@
+ src/sprng/primes-lcg64.c |    1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/src/sprng/primes-lcg64.c b/src/sprng/primes-lcg64.c
+index 8e5a7c9..fb04373 100644
+--- a/src/sprng/primes-lcg64.c
++++ b/src/sprng/primes-lcg64.c
+@@ -1,5 +1,6 @@
+ #include <stdio.h>
+ #include <stdlib.h>
++#include <string.h>
+ #include "primes-lcg64.h"
+ #include "primelist-lcg64.h"
+ 
diff --git a/sci-biology/tree-puzzle/metadata.xml b/sci-biology/tree-puzzle/metadata.xml
new file mode 100644
index 000000000000..4a34df848e3a
--- /dev/null
+++ b/sci-biology/tree-puzzle/metadata.xml
@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<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-5.2.ebuild b/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild
new file mode 100644
index 000000000000..27dd0bc2212f
--- /dev/null
+++ b/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+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/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc x86 ~amd64-linux ~x86-linux ~ppc-macos"
+IUSE="mpi"
+
+DEPEND="mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+RESTRICT="test"
+
+pkg_setup () {
+	use mpi && [ $(tc-getCC) = icc ] && die "The parallelized version of tree-puzzle cannot be compiled using icc.
+	Either disable the \"mpi\" USE flag to compile only the non-parallelized
+	version of the program, or use gcc as your compiler (CC=\"gcc\")."
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PN}-impl-dec.patch
+}
+
+src_configure() {
+	default
+
+	if ! use mpi; then
+			sed \
+				-e 's:bin_PROGRAMS = puzzle$(EXEEXT) ppuzzle:bin_PROGRAMS = puzzle :' \
+				-e 's:DIST_SOURCES = $(ppuzzle_SOURCES) $(puzzle_SOURCES):DIST_SOURCES = $(puzzle_SOURCES):' \
+				-i "${S}"/src/Makefile || die
+	fi
+}
+
+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/*
+}