diff options
Diffstat (limited to 'sci-biology/mrbayes')
| -rw-r--r-- | sci-biology/mrbayes/ChangeLog | 17 | ||||
| -rw-r--r-- | sci-biology/mrbayes/Manifest | 4 | ||||
| -rw-r--r-- | sci-biology/mrbayes/files/digest-mrbayes-3.0 | 1 | ||||
| -rw-r--r-- | sci-biology/mrbayes/metadata.xml | 18 | ||||
| -rw-r--r-- | sci-biology/mrbayes/mrbayes-3.0.ebuild | 40 |
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 +} |