From c19ce2e6e51a4c7d1edb2cccc1da8aa6696f7b36 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Thu, 6 Jun 2013 06:20:05 +0000 Subject: sci-biology/mafft: Version Bump (Portage version: 2.2.0_alpha177/cvs/Linux x86_64, signed Manifest commit with key 8009D6F070EB7916) --- sci-biology/mafft/ChangeLog | 7 ++++- sci-biology/mafft/mafft-7.045.ebuild | 61 ++++++++++++++++++++++++++++++++++++ 2 files changed, 67 insertions(+), 1 deletion(-) create mode 100644 sci-biology/mafft/mafft-7.045.ebuild (limited to 'sci-biology') diff --git a/sci-biology/mafft/ChangeLog b/sci-biology/mafft/ChangeLog index 957be58e800c..b4ec5b5ec13a 100644 --- a/sci-biology/mafft/ChangeLog +++ b/sci-biology/mafft/ChangeLog @@ -1,6 +1,11 @@ # ChangeLog for sci-biology/mafft # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/ChangeLog,v 1.14 2013/05/26 11:12:15 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/ChangeLog,v 1.15 2013/06/06 06:20:05 jlec Exp $ + +*mafft-7.045 (06 Jun 2013) + + 06 Jun 2013; Justin Lecher +mafft-7.045.ebuild: + Version Bump 26 May 2013; Justin Lecher mafft-7.043.ebuild: Use append-cppflags for preprocessor flags diff --git a/sci-biology/mafft/mafft-7.045.ebuild b/sci-biology/mafft/mafft-7.045.ebuild new file mode 100644 index 000000000000..209ae84cf352 --- /dev/null +++ b/sci-biology/mafft/mafft-7.045.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/mafft-7.045.ebuild,v 1.1 2013/06/06 06:20:05 jlec Exp $ + +EAPI=5 + +inherit eutils flag-o-matic multilib toolchain-funcs + +EXTENSIONS="-without-extensions" + +DESCRIPTION="Multiple sequence alignments using a variety of algorithms" +HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html" +SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~x64-macos ~x86-macos" +IUSE="threads" + +S="${WORKDIR}"/${P}${EXTENSIONS} + +src_prepare() { + epatch "${FILESDIR}"/${PN}-7.037-respect.patch + use threads && append-cppflags -Denablemultithread + sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile || die + sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed" +} + +src_compile() { + pushd core > /dev/null || die + emake \ + $(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \ + PREFIX="${EPREFIX}"/usr \ + CC="$(tc-getCC)" \ + CFLAGS="${CFLAGS}" + popd > /dev/null || die +} + +src_test() { + export MAFFT_BINARIES="${S}"/core + cd test || die + bash ../core/mafft sample > test.fftns2 || die + bash ../core/mafft --maxiterate 100 sample > test.fftnsi || die + bash ../core/mafft --globalpair sample > test.gins1 || die + bash ../core/mafft --globalpair --maxiterate 100 sample > test.ginsi || die + bash ../core/mafft --localpair sample > test.lins1 || die + bash ../core/mafft --localpair --maxiterate 100 sample > test.linsi || die + + diff test.fftns2 sample.fftns2 || die + diff test.fftnsi sample.fftnsi || die + diff test.gins1 sample.gins1 || die + diff test.ginsi sample.ginsi || die + diff test.lins1 sample.lins1 || die +} + +src_install() { + pushd core + emake PREFIX="${ED}usr" install + popd + dodoc readme +} -- cgit v1.2.3-65-gdbad