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# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
MIRA_3RDPARTY_PV="06-07-2012"
MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat)
inherit autotools eutils multilib
DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler"
HOMEPAGE="http://www.chevreux.org/projects_mira.html"
SRC_URI="
http://sourceforge.net/projects/mira-assembler/files/MIRA/development/"${PN}"-"${MY_PV}".tar.bz2
mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
# http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2
# http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2
# mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
S="${WORKDIR}"/"${PN}"-"${MY_PV}"
SLOT="0"
LICENSE="GPL-2"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
IUSE="doc"
CDEPEND="
dev-libs/boost
dev-util/google-perftools"
DEPEND="${CDEPEND}
app-editors/vim-core
dev-libs/expat"
RDEPEND="${CDEPEND}"
#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED
# THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf )
DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS )
# mira 4.9.x requires C++14 standard compliant compiler, so >=gcc-4.9.1
src_prepare() {
find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
epatch \
"${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch \
"${FILESDIR}"/${P}-cout.patch \
"${FILESDIR}"/${P}-fix-miramer-symlink-error.patch
sed \
-e "s:-O[23]::g" \
-e "s:-funroll-loops::g" \
-i configure.ac || die
eautoreconf
}
src_configure() {
econf \
--with-boost="${EPREFIX}/usr/$(get_libdir)" \
--with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \
--with-boost-thread=boost_thread-mt
}
#src_compile() {
# base_src_compile
# # TODO: resolve docbook incompatibility for building docs
# if use doc; then emake -C doc clean docs || die; fi
#}
src_install() {
default
dodoc ${DOCS[@]}
dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta}
# if sci-biology/staden is installed, ideally use configprotect?
if [ -e "${ED}"/usr/share/staden/etc/GTAGDB ]; then
if [ `grep -c HAF "${ED}"/usr/share/staden/etc/GTAGDB` -eq 0 ]; then
cat "${ED}"/usr/share/staden/etc/GTAGDB "${S}"/src/support/GTAGDB > "${WORKDIR}"/GTAGDB || die
insinto /usr/share/staden/etc/
doins "${WORKDIR}"/GTAGDB
fi
fi
if [ -e "/etc/consedrc/" ]; then
insinto /etc/consedrc
doins "${S}"/src/support/consedtaglib.txt
fi
}
pkg_postinst() {
einfo "Documentation is no longer built, you can find it at:"
einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html"
}
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