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# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
MIRA_3RDPARTY_PV="06-07-2012"
MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat)
inherit autotools multilib
DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Illumina"
HOMEPAGE="http://www.chevreux.org/projects_mira.html"
SRC_URI="
https://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2
mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
# https://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}"-"${MY_PV}"
SLOT="0"
LICENSE="GPL-2"
KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
IUSE="doc"
CDEPEND="
dev-libs/boost:=[threads(+)]
dev-util/google-perftools"
DEPEND="${CDEPEND}
sys-devel/flex
app-editors/vim-core
dev-libs/expat"
RDEPEND="${CDEPEND}"
#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED
# THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf )
DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS )
PATCHES=(
"${FILESDIR}/${PN}-4.0.2-boost-1.50.patch"
"${FILESDIR}/${PN}-4.0.2-cout.patch"
"${FILESDIR}/${PN}-4.0.2-cmath.patch"
)
src_prepare() {
find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
default
sed \
-e "s:-O[23]::g" \
-e "s:-funroll-loops::g" \
-i configure.ac || die
eautoreconf
# Remove C++ source files that upstream built with flex.
local f
local PREBUILT_CXX_LEXER_FILES=(
"${S}"/src/caf/caf_flexer.cc
"${S}"/src/io/exp_flexer.cc
"${S}"/src/mira/parameters_flexer.cc
)
for f in "${PREBUILT_CXX_LEXER_FILES[@]}"; do
if [[ -f ${f} ]] ; then
rm "${f}" || die "Failed to remove ${f}"
else
die "${f} not found"
fi
done
}
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
# use doc && emake -C doc clean docs
#}
src_install() {
default
dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta}
}
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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