[gentoo-commits] gentoo-x86 commit in sci-biology/mafft: ChangeLog mafft-7.050.ebuild mafft-6.707.ebuild mafft-7.046.ebuild mafft-7.047.ebuild mafft-7.045.ebuild mafft-7.043.ebuild mafft-6.240-r1.ebuild mafft-6.811.ebuild mafft-7.040.ebuild mafft-7.037.ebuild

[gentoo-commits] gentoo-x86 commit in sci-biology/mafft: ChangeLog mafft-7.050.ebuild mafft-6.707.ebuild mafft-7.046.ebuild mafft-7.047.ebuild mafft-7.045.ebuild mafft-7.043.ebuild mafft-6.240-r1.ebuild mafft-6.811.ebuild mafft-7.040.ebuild mafft-7.037.ebuild

[Justin Lecher (jlec)]

jlec        13/07/03 07:17:58

  Modified:             ChangeLog
  Added:                mafft-7.050.ebuild
  Removed:              mafft-6.707.ebuild mafft-7.046.ebuild
                        mafft-7.047.ebuild mafft-7.045.ebuild
                        mafft-7.043.ebuild mafft-6.240-r1.ebuild
                        mafft-6.811.ebuild mafft-7.040.ebuild
                        mafft-7.037.ebuild
  Log:
  sci-biology/mafft: Drop old; Bump version
  
  (Portage version: 2.2.0_alpha186/cvs/Linux x86_64, signed Manifest commit with key 8009D6F070EB7916)

Revision  Changes    Path
1.19                 sci-biology/mafft/ChangeLog

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mafft/ChangeLog?rev=1.19&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mafft/ChangeLog?rev=1.19&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mafft/ChangeLog?r1=1.18&r2=1.19

Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/mafft/ChangeLog,v
retrieving revision 1.18
retrieving revision 1.19
diff -u -r1.18 -r1.19
--- ChangeLog	24 Jun 2013 09:53:38 -0000	1.18
+++ ChangeLog	3 Jul 2013 07:17:58 -0000	1.19
@@ -1,6 +1,14 @@
 # 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 1.18 2013/06/24 09:53:38 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/ChangeLog,v 1.19 2013/07/03 07:17:58 jlec Exp $
+
+*mafft-7.050 (03 Jul 2013)
+
+  03 Jul 2013; Justin Lecher <jlec@gentoo.org> -mafft-6.240-r1.ebuild,
+  -mafft-6.707.ebuild, -mafft-6.811.ebuild, -mafft-7.037.ebuild,
+  -mafft-7.040.ebuild, -mafft-7.043.ebuild, -mafft-7.045.ebuild,
+  -mafft-7.046.ebuild, -mafft-7.047.ebuild, +mafft-7.050.ebuild:
+  Drop old; Bump version
 
 *mafft-7.047 (24 Jun 2013)
 



1.1                  sci-biology/mafft/mafft-7.050.ebuild

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mafft/mafft-7.050.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mafft/mafft-7.050.ebuild?rev=1.1&content-type=text/plain

Index: mafft-7.050.ebuild
===================================================================
# 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-7.050.ebuild,v 1.1 2013/07/03 07:17:58 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
}