commit: 3e3bd5f1361f0c4c02446b4fac67b9869d1ef8ad Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Mon Nov 10 14:39:09 2014 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Mon Nov 10 14:39:09 2014 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3e3bd5f1
sci-biology/mavid: Bump EAPI Package-Manager: portage-2.2.14 --- sci-biology/mavid/ChangeLog | 6 +++++- sci-biology/mavid/mavid-2.0.4.ebuild | 31 +++++++++++++++++++++++-------- sci-biology/mavid/metadata.xml | 10 +++++----- 3 files changed, 33 insertions(+), 14 deletions(-) diff --git a/sci-biology/mavid/ChangeLog b/sci-biology/mavid/ChangeLog index 713a8e2..320e337 100644 --- a/sci-biology/mavid/ChangeLog +++ b/sci-biology/mavid/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/mavid -# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 10 Nov 2014; Justin Lecher <j...@gentoo.org> mavid-2.0.4.ebuild, + metadata.xml: + Bump EAPI + 08 Jul 2008; weaver <wea...@gentoo.org> +metadata.xml, +mavid-2.0.4.ebuild: New ebuild, bug 207250 diff --git a/sci-biology/mavid/mavid-2.0.4.ebuild b/sci-biology/mavid/mavid-2.0.4.ebuild index 40d2737..79bead6 100644 --- a/sci-biology/mavid/mavid-2.0.4.ebuild +++ b/sci-biology/mavid/mavid-2.0.4.ebuild @@ -2,6 +2,10 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ +EAPI=5 + +inherit toolchain-funcs + DESCRIPTION="Multiple alignment of large DNA sequences" HOMEPAGE="http://baboon.math.berkeley.edu/mavid/"; SRC_URI="http://bio.math.berkeley.edu/mavid/download/mavid-package-${PV}.tar.gz"; @@ -9,22 +13,33 @@ SRC_URI="http://bio.math.berkeley.edu/mavid/download/mavid-package-${PV}.tar.gz"; LICENSE="mavid" SLOT="0" IUSE="" -KEYWORDS="~x86" +KEYWORDS="~amd64 ~x86" DEPEND="" -RDEPEND="sci-biology/clustalw +RDEPEND=" + sci-biology/clustalw sci-biology/fastdnaml" -S="${WORKDIR}/mavid-package-${PV}" +S="${WORKDIR}"/${PN}-package-${PV} + +src_prepare() { + sed \ + -e 's:OPT_CPP_OPTIONS =:OPT_CPP_OPTIONS ?=:g' \ + -e 's:DEBUG_CPP_OPTIONS =:DEBUG_CPP_OPTIONS ?=:g' \ + -i $(find -type f -name Makefile) || die +} + +src_compile() { + emake \ + CPP=$(tc-getCXX) \ + BASE_CPP_OPTIONS="${CXXFLAGS}" \ + DEBUG_CPP_OPTIONS="${CXXFLAGS}" \ + OPT_CPP_OPTIONS="${CXXFLAGS}" -src_unpack() { - unpack ${A} - sed -i 's/\(OPT_CPP_OPTIONS =\)/\1 ${CFLAGS} /' "${S}"/{bioc,mavid}/Makefile || die - sed -i 's/\(CPP_OPTIONS =\) -O4/\1 ${CFLAGS} -O4/' "${S}"/utils/*/Makefile || die - sed -i 's/$.*_DIRECTORY\///' "${S}"/mavid/mavid.pl || die } src_install() { + local i dobin mavid/{mavid,mavid.pl} for i in checkfasta cut_alignment extract_seq extract_tree fasta2phylip phylip2fasta project_alignment randtree root_tree tree_dists; do dobin utils/$i/$i diff --git a/sci-biology/mavid/metadata.xml b/sci-biology/mavid/metadata.xml index 3302123..fc7c769 100644 --- a/sci-biology/mavid/metadata.xml +++ b/sci-biology/mavid/metadata.xml @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> <pkgmetadata> - <maintainer> - <email>wea...@gentoo.org</email> - <name>Andrey Kislyuk</name> - </maintainer> - <herd>sci-biology</herd> + <maintainer> + <email>wea...@gentoo.org</email> + <name>Andrey Kislyuk</name> + </maintainer> + <herd>sci-biology</herd> </pkgmetadata>
