Moved from sci-biology/MrBayes to sci-biology/mrbayes.

5 files changed, 80 insertions, 0 deletions

diff --git a/sci-biology/mrbayes/ChangeLog b/sci-biology/mrbayes/ChangeLog
new file mode 100644
index 000000000000..a12a0e6d0910
--- /dev/null
+++ b/sci-biology/mrbayes/ChangeLog
@@ -0,0 +1,17 @@
+# ChangeLog for sci-biology/MrBayes
+# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mrbayes/ChangeLog,v 1.1 2005/02/03 02:20:37 j4rg0n Exp $
+
+*mrbayes-3.0 (02 Feb 2005)
+
+  02 Feb 2005; <burgundy@gentoo.org> +metadata.xml, +mrbayes-3.0.ebuild:
+  Moved from sci-biology/MrBayes to sci-biology/mrbayes.
+
+*MrBayes-3.0 (30 Jan 2005)
+
+  30 Jan 2005; Olivier Fisette <ribosome@gentoo.org> MrBayes-3.0.ebuild:
+  Check for "sed" exit code.
+
+  19 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> :
+  Initial commit
+
diff --git a/sci-biology/mrbayes/Manifest b/sci-biology/mrbayes/Manifest
new file mode 100644
index 000000000000..a6fd168d4d5f
--- /dev/null
+++ b/sci-biology/mrbayes/Manifest
@@ -0,0 +1,4 @@
+MD5 f464ab228b7479f5821cec0105927b05 MrBayes-3.0.ebuild 841
+MD5 f3b54ff169e97f1f03375bd80dac4c0e ChangeLog 413
+MD5 3fd56e7547b0f35a37db19dd45932fef metadata.xml 792
+MD5 98b5d381ba0621a27ffce26bf40da031 files/digest-MrBayes-3.0 64
diff --git a/sci-biology/mrbayes/files/digest-mrbayes-3.0 b/sci-biology/mrbayes/files/digest-mrbayes-3.0
new file mode 100644
index 000000000000..f79cf0de2b89
--- /dev/null
+++ b/sci-biology/mrbayes/files/digest-mrbayes-3.0
@@ -0,0 +1 @@
+MD5 be98da64334732b9b12dde1da2907850 MrBayes-3.0.tar.bz2 300352
diff --git a/sci-biology/mrbayes/metadata.xml b/sci-biology/mrbayes/metadata.xml
new file mode 100644
index 000000000000..eade7f81070b
--- /dev/null
+++ b/sci-biology/mrbayes/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-biology</herd>
+<maintainer>
+  <email>j4rg0n@gentoo.org</email>
+</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>
+</pkgmetadata>
diff --git a/sci-biology/mrbayes/mrbayes-3.0.ebuild b/sci-biology/mrbayes/mrbayes-3.0.ebuild
new file mode 100644
index 000000000000..90516b6e5398
--- /dev/null
+++ b/sci-biology/mrbayes/mrbayes-3.0.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mrbayes/mrbayes-3.0.ebuild,v 1.1 2005/02/03 02:20:37 j4rg0n Exp $
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Bayesian Inference of Phylogeny"
+HOMEPAGE="http://morphbank.ebc.uu.se/mrbayes/"
+SRC_URI="mirror://gentoo/MrBayes-3.0.tar.bz2"
+
+LICENSE="as-is"
+SLOT="0"
+KEYWORDS="~x86 ~ppc-macos"
+IUSE=""
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+
+	# TODO: Implement MPI-aware ebuild/use flags, etc. to use Makefile-Mpi
+
+	# Fix the non-standard Makefile.
+	sed -i \
+		-e "s:-O4:${CFLAGS}:" \
+		-e "s:gcc:${CC}:" \
+		Makefile || die
+}
+
+src_compile() {
+	emake \
+		CC="$(tc-getCC)" \
+		CXX="$(tc-getCXX)" \
+		|| die "emake failed"
+}
+
+src_install() {
+	# Non-standard manual install
+	into /usr
+	dobin mb
+}