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# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
PYTHON_COMPAT=( python2_7 )
PERL_EXPORT_PHASE_FUNCTIONS=no
inherit perl-module eutils toolchain-funcs autotools flag-o-matic python-single-r1 qmake-utils
AUTOTOOLS_AUTORECONF=true
inherit autotools-utils git-r3
DESCRIPTION="Whole genome assembler, Hawkeye and AMOScmp to compare multiple assemblies"
HOMEPAGE="http://sourceforge.net/projects/amos"
SRC_URI=""
EGIT_REPO_URI="git://amos.git.sourceforge.net/gitroot/amos/amos"
LICENSE="Artistic"
SLOT="0"
KEYWORDS=""
IUSE="mpi qt5 X"
DEPEND="
mpi? ( virtual/mpi )
dev-libs/boost
qt5? ( dev-qt/qtcore:5 )
sci-biology/blat
sci-biology/jellyfish:1"
RDEPEND="${DEPEND}
dev-perl/DBI
dev-perl/Statistics-Descriptive
sci-biology/mummer"
# $ gap-links
# ERROR: Could not open file LIBGUESTFS_PATH=/usr/share/guestfs/appliance/
# $
src_prepare() {
epatch "${FILESDIR}"/"${P}"-fix-include-paths.patch
epatch "${FILESDIR}"/amos-3.1.0-rename_to_jellyfish1.patch
sh ./bootstrap || die
default
eautoreconf
# prevent GCC 6 log pollution due to hash_map deprecation in C++11
# shutdown gcc-8.2.0 messages too
append-cxxflags -Wno-cpp -Wno-narrowing
}
src_configure() {
local myconf
use X && myconf+=( --with-x )
econf ${myconf[@]} --with-jellyfish="${EPREFIX}"/usr/include --with-Boost-dir="${EPREFIX}"/usr/include --with-qmake-qt4=qmake --enable-all
}
src_install() {
default
python_replicate_script "${ED}"/usr/bin/goBambus2
# bambus needs TIGR::FASTAreader.pm and others
# configure --libdir sadly copies both *.a files and *.pm into /usr/lib64/AMOS/ and /usr/lib64/TIGR/, work around it
perl_set_version
insinto ${VENDOR_LIB}/AMOS
doins "${D}"/usr/lib64/AMOS/*.pm
insinto ${VENDOR_LIB}/TIGR
doins "${D}"/usr/lib64/TIGR/*.pm
# move also /usr/lib64/AMOS/AMOS.py to /usr/bin
mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die
# zap the mis-placed files ('make install' is at fault)
rm -f "${D}"/usr/lib64/AMOS/*.pm
rm -rf "${D}"/usr/lib64/TIGR
echo AMOSCONF="${EPREFIX}"/etc/amos.acf > "${S}"/99amos || die
mkdir -p "${ED}"/etc || die
touch "${ED}"/etc/amos.acf || die
doenvd "${S}/99amos"
}
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