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# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
PYTHON_COMPAT=( python2_7 )
inherit autotools python-r1 toolchain-funcs
DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
HOMEPAGE="http://www.htslib.org/"
SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
IUSE="examples"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
RDEPEND="sys-libs/ncurses:0=
=sci-libs/htslib-${PV}*
dev-lang/perl"
DEPEND="${RDEPEND}
virtual/pkgconfig"
PATCHES=(
"${FILESDIR}/${P}-buildsystem.patch"
"${FILESDIR}/${P}-ncurses.patch"
)
src_prepare() {
default
# unbundle libs
find htslib-* -delete || die
sed -i -e 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
sed -i -e '/htslib.mk/d' -i Makefile || die
tc-export CC AR
rm -f aclocal.m4 || die
eautoreconf
}
src_compile() {
local mymakeargs=(
LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
HTSDIR="${EPREFIX}/usr/include"
HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
BAMLIB="libbam.so"
libdir=/usr/$(get_libdir)
)
emake "${mymakeargs[@]}"
}
src_test() {
local mymakeargs=(
LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
HTSDIR="${EPREFIX}/usr/include"
HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
BAMLIB="libbam.so"
)
LD_LIBRARY_PATH="${S}" emake "${mymakeargs[@]}" test
}
src_install() {
dobin samtools $(find misc -type f -executable)
python_replicate_script "${ED}"usr/bin/varfilter.py
# fix perl shebangs
pushd "${ED}"usr/bin/ >> /dev/null
local i
for i in plot-bamstats *.pl; do
sed -e '1s:.*:#!/usr/bin/env perl:' -i "${i}" || die
done
# remove lua scripts
rm -f r2plot.lua vcfutils.lua || die
popd >> /dev/null
dolib.so libbam.so*
insinto /usr/include/bam
doins *.h
doman ${PN}.1
dodoc AUTHORS NEWS README
if use examples; then
insinto /usr/share/${PN}
doins -r examples
fi
}
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