reinit the tree, so we can have metadata

5 files changed, 177 insertions, 0 deletions

diff --git a/sci-biology/mrbayes/Manifest b/sci-biology/mrbayes/Manifest
new file mode 100644
index 000000000000..4a7a73623659
--- /dev/null
+++ b/sci-biology/mrbayes/Manifest
@@ -0,0 +1,7 @@
+AUX mb_readline_312.patch 1108 SHA256 6d7566cbe59eee9881b41a21ea561fd610816df768bb8fda42ef4435c84f5f22 SHA512 0a169b8560853dbff87c983bf8220384dcf22f53106ce5711bf3b1fc76d8a9adbf1860618176dde65a8657abe3ad888521bf5485fc00d4014adf1acb7ba3f114 WHIRLPOOL 925581e97278d36cdbfa4c53ab47a331640cf0d57c912eee7567d28805875a15e677a283f7a941c851783057cd606165ebccd6360e4f705eae53b2bf8df0fa89
+DIST mrbayes-3.1.2.tar.gz 545968 SHA256 c60253de1980c9f0a0eb684fffe7ba428fda7c39a3edcb6acf384b5e1443f2f4 SHA512 2fb0ee7224cbb69c1acf2ffb0c6c8974f63002cda4f39a626eadf80fad9cfc23861f8c03f5545970f3a81e02093d62b6a0549ab7d7f7080557e91e21b2c3ee14 WHIRLPOOL 45c9750a1e3e3ac85a1085bcaf8fc5c108b730a3dfa2f9e8d81cea8720bd6f02815c3145c19ee6c369a43f4565c2b234ec81cd5721672abded17186264de2e3f
+EBUILD mrbayes-3.1.2-r1.ebuild 1008 SHA256 4ed3c0c65258e1bdabac5a3a461660862faecd809a0d7d4fb7eea219c0b0eb6d SHA512 5fcbdd396c7b035ecc0b596a9866fdc3544cf8993fd60efa0a5ab41f7cd4271c437626e3c131d9d07759cecef3cb8700a0b5b761ec87cbcbf12b9d206543f918 WHIRLPOOL 65d442f033f1eea5e6ee4dc89f9514e6e9738996b8da169c850b31baa8a5b8a09aa133d29456768190e9a6d838a944056e962ae7c454e7fa021aee42e9a15404
+EBUILD mrbayes-3.1.2-r2.ebuild 1347 SHA256 ace0ceab6ce36430d74c70d4bae913053aa13978f51c0b148b8f391caa587dfa SHA512 c8655ecaf9933a963b072a242e44c156f89c635fae00fa135262911e2588beb623764a92634c27a16dcdac4fb70c16b88a428aa154a56ea816fd9b9ff2418037 WHIRLPOOL 57a34def5ab5c89fa72153b5e93b1d16cacafd0ad2404dfdf47aa2d3ba91627eea0cc9a0bfac83a17202494fdfbb26b05482fc036773b0222f9de5909e713140
+MISC ChangeLog 2658 SHA256 dcb2547bd0d07004b50e6e8a8ef179e3ce5e9c07b2f91c4783394d33d7f93112 SHA512 1be3d35c10b13c4f0fbd7f38a41678001133e58eef4436efbb6083002bd0a695f4823647bb4553142ddf182d83f60f49e0528614a5ff1fd929ba1fbc9feb12aa WHIRLPOOL 54940fc6251c4cebd53f07623a3dc0213de8c9d948b6922e1a2918e4615857037089e7a3605cb55dad7104a32d807bc56ba3acbd52005217c67ba3a280b5ada3
+MISC ChangeLog-2015 3659 SHA256 624f09b69c5d303e7dbcceae7cf41a0a0961a8affdea23e3a70ee4e5c10142af SHA512 68cb1b6c4177abf3ed1dd339edbff99c87bb70e16d637588f9d76ef798ca501a148a0a6b751c3fcc5df9b1b28305379a3b4e157973e6bbbce7bb10eb5c9dbdf3 WHIRLPOOL bd446c6d7ee8dba16098c97f203a52450ef924862838ffad53b75db387a8547c258f43dc65a81fc576699d5c99239736f7837e46518c5c7e8a656119111fd1b4
+MISC metadata.xml 916 SHA256 44be6660a7e4d632ae6a0bc88f8a4850beb6865e21634a75a0746a0e67849bb9 SHA512 ab6be2e4111088bc13e6da5f65d11437dc05dbcdeab83e5d3899b913ff9ad3dc1f22ec81f2fe73f60bf991d01f0a8691eaa124ba24bd7ebb17d995fdd271bfef WHIRLPOOL 208fdc5fc49d67b4124d4dfcf7ae678c5646f67734c543e7c922b3bde17568815caad894df954ce4f1b549118b552a60524a7871cd539b32b3cba95aac4b5db3
diff --git a/sci-biology/mrbayes/files/mb_readline_312.patch b/sci-biology/mrbayes/files/mb_readline_312.patch
new file mode 100644
index 000000000000..2f8bab1e7665
--- /dev/null
+++ b/sci-biology/mrbayes/files/mb_readline_312.patch
@@ -0,0 +1,37 @@
+Index: Makefile
+===================================================================
+RCS file: /cvsroot/mrbayes/mrbayes/Makefile,v
+retrieving revision 3.23
+retrieving revision 3.24
+diff -U2 -r3.23 -r3.24
+--- Makefile	22 Dec 2005 16:13:06 -0000	3.23
++++ Makefile	3 Jan 2006 16:43:13 -0000	3.24
+@@ -50,4 +50,5 @@
+ ifeq  ($(strip $(USEREADLINE)),yes)
+     CFLAGS += -DUSE_READLINE
++#   CFLAGS += -DCOMPLETIONMATCHES
+ 	LIBS += -lncurses -lreadline 
+ endif
+Index: bayes.c
+===================================================================
+RCS file: /cvsroot/mrbayes/mrbayes/bayes.c,v
+retrieving revision 3.39
+retrieving revision 3.40
+diff -U2 -r3.39 -r3.40
+--- bayes.c	23 Dec 2005 16:26:28 -0000	3.39
++++ bayes.c	3 Jan 2006 16:43:13 -0000	3.40
+@@ -382,9 +382,11 @@
+ char **readline_completion(const char *text, int start, int stop) {
+ 	char **matches = (char **) NULL;
+-	
++
++#ifdef COMPLETIONMATCHES	
+ 	if(start == 0)
+-    	matches = rl_completion_matches (text, command_generator);
++    		matches = rl_completion_matches (text, command_generator);
++#endif
+ 
+-  return (matches);	
++	return (matches);	
+ }
+ #endif
diff --git a/sci-biology/mrbayes/metadata.xml b/sci-biology/mrbayes/metadata.xml
new file mode 100644
index 000000000000..ca6afd95a12e
--- /dev/null
+++ b/sci-biology/mrbayes/metadata.xml
@@ -0,0 +1,21 @@
+<?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>
+MrBayes is a program for the Bayesian estimation of phylogeny.
+Bayesian inference of phylogeny is based upon a quantity called the
+posterior probability distribution of trees, which is the probability of a
+tree conditioned on the observations. The conditioning is accomplished using
+Bayes's theorem. The posterior probability distribution of trees is
+impossible to calculate analytically; instead, MrBayes uses a simulation
+technique called Markov chain Monte Carlo (or MCMC) to approximate the
+posterior probabilities of trees.
+</longdescription>
+  <upstream>
+    <remote-id type="sourceforge">mrbayes</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild b/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild
new file mode 100644
index 000000000000..b67b4b228f9b
--- /dev/null
+++ b/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Bayesian Inference of Phylogeny"
+HOMEPAGE="http://mrbayes.csit.fsu.edu/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="debug mpi readline"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+
+DEPEND="
+	sys-libs/ncurses
+	mpi? ( virtual/mpi )
+	readline? ( sys-libs/readline:0 )"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	use readline && epatch "${FILESDIR}"/mb_readline_312.patch
+	sed -e 's:-ggdb::g' -i Makefile || die
+}
+
+src_compile() {
+	local myconf mycc
+
+	if use mpi; then
+		mycc=mpicc
+	else
+		mycc=$(tc-getCC)
+	fi
+
+	use mpi && myconf="MPI=yes"
+	use readline || myconf="${myconf} USEREADLINE=no"
+	use debug && myconf="${myconf} DEBUG=yes"
+	emake \
+		OPTFLAGS="${CFLAGS}" \
+		LDFLAGS="${LDFLAGS}" \
+		CC=${mycc} \
+		${myconf}
+}
+
+src_install() {
+	dobin mb
+	insinto /usr/share/${PN}
+	doins *.nex
+}
diff --git a/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild b/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild
new file mode 100644
index 000000000000..ebe9926212c9
--- /dev/null
+++ b/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Bayesian Inference of Phylogeny"
+HOMEPAGE="http://mrbayes.csit.fsu.edu/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+IUSE="debug mpi readline"
+
+DEPEND="
+	sys-libs/ncurses:0=
+	mpi? ( virtual/mpi )
+	readline? ( sys-libs/readline:0= )"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	if use mpi; then
+		sed -e "s:MPI ?= no:MPI=yes:" -i Makefile || die "Patching MPI support."
+	fi
+	if ! use readline; then
+		sed -e "s:USEREADLINE ?= yes:USEREADLINE=no:" \
+			-i Makefile || die "Patching readline support."
+	else
+		# Only needed for OSX with an old (4.x) version of
+		# libreadline, but it doesn't hurt for other distributions.
+		epatch "${FILESDIR}"/mb_readline_312.patch
+	fi
+	sed -e 's:-ggdb::g' -i Makefile || die
+}
+
+src_compile() {
+	local myconf mycc
+
+	if use mpi; then
+		mycc=mpicc
+	else
+		mycc=$(tc-getCC)
+	fi
+
+	use mpi && myconf="MPI=yes"
+	use readline || myconf="${myconf} USEREADLINE=no"
+	use debug && myconf="${myconf} DEBUG=yes"
+	emake \
+		OPTFLAGS="${CFLAGS}" \
+		LDFLAGS="${LDFLAGS}" \
+		CC=${mycc} \
+		${myconf}
+}
+
+src_install() {
+	dobin mb
+	insinto /usr/share/${PN}
+	doins *.nex
+}