Import changes from science overlay

(Portage version: 2.2.18/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

4 files changed, 75 insertions, 8 deletions

diff --git a/sci-biology/mrbayes/ChangeLog b/sci-biology/mrbayes/ChangeLog
index 6e131881219e..38863e55c8f8 100644
--- a/sci-biology/mrbayes/ChangeLog
+++ b/sci-biology/mrbayes/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/mrbayes
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mrbayes/ChangeLog,v 1.26 2011/12/21 09:05:28 jlec Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mrbayes/ChangeLog,v 1.27 2015/04/17 06:49:59 jlec Exp $
+
+*mrbayes-3.1.2-r2 (17 Apr 2015)
+
+  17 Apr 2015; Justin Lecher <jlec@gentoo.org> +mrbayes-3.1.2-r2.ebuild,
+  metadata.xml, mrbayes-3.1.2-r1.ebuild:
+  Import changes from science overlay
 
   21 Dec 2011; Justin Lecher <jlec@gentoo.org> -mrbayes-3.1.2.ebuild:
   Cleaned old
@@ -96,4 +102,3 @@
 
   19 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> :
   Initial commit
-
diff --git a/sci-biology/mrbayes/metadata.xml b/sci-biology/mrbayes/metadata.xml
index d33282dbbb50..9b0503f3a779 100644
--- a/sci-biology/mrbayes/metadata.xml
+++ b/sci-biology/mrbayes/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-biology</herd>
-<longdescription>
+  <herd>sci-biology</herd>
+  <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
diff --git a/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild b/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild
index 69b7d11509bf..1e74c5fb27f8 100644
--- a/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild
+++ b/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild,v 1.5 2011/12/21 08:59:32 phajdan.jr Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild,v 1.6 2015/04/17 06:49:59 jlec Exp $
 
 EAPI=4
 
@@ -18,7 +18,7 @@ KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
 DEPEND="
 	sys-libs/ncurses
 	mpi? ( virtual/mpi )
-	readline? ( sys-libs/readline )"
+	readline? ( sys-libs/readline:0 )"
 RDEPEND="${DEPEND}"
 
 src_prepare() {
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..c60f61a93433
--- /dev/null
+++ b/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild
@@ -0,0 +1,62 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild,v 1.1 2015/04/17 06:49:59 jlec Exp $
+
+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
+	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
+}