commit: e95dd20d9eaea3e8fa32f9337c8b3beb7ba5eddb Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> AuthorDate: Thu Jan 27 16:33:02 2022 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> CommitDate: Thu Jan 27 16:37:38 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e95dd20d
sci-biology/mrbayes: add version 3.2.7 Closes: https://bugs.gentoo.org/521510 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> sci-biology/mrbayes/Manifest | 1 + sci-biology/mrbayes/metadata.xml | 19 +++++++------- sci-biology/mrbayes/mrbayes-3.2.7.ebuild | 45 ++++++++++++++++++++++++++++++++ 3 files changed, 56 insertions(+), 9 deletions(-) diff --git a/sci-biology/mrbayes/Manifest b/sci-biology/mrbayes/Manifest index 799aafc484a4..3d68a52ee87a 100644 --- a/sci-biology/mrbayes/Manifest +++ b/sci-biology/mrbayes/Manifest @@ -1 +1,2 @@ DIST mrbayes-3.1.2.tar.gz 545968 BLAKE2B f4c5bbdde765fb9e596c17d5fd890b168c22cefb0d24b67c1c68623e1dcfa4df716a896fe120f7a1cac4234125b6ed524973506e47492ba3ec26e389783d618a SHA512 2fb0ee7224cbb69c1acf2ffb0c6c8974f63002cda4f39a626eadf80fad9cfc23861f8c03f5545970f3a81e02093d62b6a0549ab7d7f7080557e91e21b2c3ee14 +DIST mrbayes-3.2.7.tar.gz 9787214 BLAKE2B 2d0ebbc376712e15fc1ed146053d977ad1af96f44c31b8fd0fdbd47ef9bafc41cbb8904db94bc8d30c753c0267a1dcce0d08c73d8b35c20e0f15206bc8fef6ff SHA512 4dc869cd07cf384b3a3945ac8d91a7cc2982e8c5cd8d1f097b46a479a071cb71e71c60e152aa4fc01b0bb296295c5fa9f5a48aa8e913b920c33e30cbb3a6ed37 diff --git a/sci-biology/mrbayes/metadata.xml b/sci-biology/mrbayes/metadata.xml index 348542381e73..2fbcd4fa4f98 100644 --- a/sci-biology/mrbayes/metadata.xml +++ b/sci-biology/mrbayes/metadata.xml @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd";> <pkgmetadata> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> + <maintainer type="project"> + <email>[email protected]</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 @@ -14,8 +14,9 @@ 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> + </longdescription> + <upstream> + <remote-id type="sourceforge">mrbayes</remote-id> + <remote-id type="github">NBISweden/MrBayes</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/mrbayes/mrbayes-3.2.7.ebuild b/sci-biology/mrbayes/mrbayes-3.2.7.ebuild new file mode 100644 index 000000000000..ad87554eb31e --- /dev/null +++ b/sci-biology/mrbayes/mrbayes-3.2.7.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DESCRIPTION="Bayesian Inference of Phylogeny" +HOMEPAGE="https://nbisweden.github.io/MrBayes/"; +SRC_URI="https://github.com/NBISweden/MrBayes/releases/download/v${PV}/${P}.tar.gz"; + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" +IUSE="debug mpi readline" +# --with-readline was given, but MPI support requires readline to be disabled. +REQUIRED_USE="mpi? ( !readline )" + +DEPEND=" + sys-libs/ncurses:= + mpi? ( virtual/mpi ) + readline? ( sys-libs/readline:= ) +" +RDEPEND="${DEPEND}" + +src_configure() { + econf \ + "$(use_with mpi)" \ + "$(use_with readline)" \ + "$(use_enable debug )" \ + # configure checks cpuid and enables fma{3,4}, sse{1..4} if detected. + # Configure options only allow disabling the auto-detection, but do not + # actually allow toggling the individual cpu instruction sets. The only + # way to guarantee that cross-compiling and binpkgs will work on machines + # other than the host is to unconditionally disable sse/fma/avx. + #"$(use_enable cpu_flags_x86_sse sse )" \ + #"$(use_enable cpu_flags_x86_avx avx )" \ + #"$(use_enable cpu_flags_x86_fma3 fma )" \ + # Has optional support for sci-biology/beagle::science + # "$(use_with beagle)" +} + +src_compile() { + # The --disable options for the cpu instruction sets don't actually work so + # we override it here and also set the user specified CFLAGS. + emake SIMD_FLAGS= CPUEXT_FLAGS= CFLAGS="${CFLAGS}" +}
