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# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
PYTHON_COMPAT=( python2_7 )
inherit eutils multilib python-r1 toolchain-funcs
DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
HOMEPAGE="http://samtools.sourceforge.net/"
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="${PYTHON_REQUIRED_USE}"
CDEPEND="sys-libs/ncurses:0="
RDEPEND="${CDEPEND}
dev-lang/lua
dev-lang/perl
${PYTHON_DEPS}"
DEPEND="${CDEPEND}
virtual/pkgconfig"
src_prepare() {
epatch "${FILESDIR}"/${P}-buildsystem.patch
sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
tc-export CC AR
}
src_compile() {
local _ncurses="$($(tc-getPKG_CONFIG) --libs ncurses)"
emake dylib LIBCURSES="${_ncurses}"
emake LIBCURSES="${_ncurses}"
}
src_install() {
dobin samtools $(find bcftools misc -type f -executable)
python_replicate_script "${ED}"/usr/bin/varfilter.py
dolib.so libbam$(get_libname 1)
dosym libbam$(get_libname 1) /usr/$(get_libdir)/libbam$(get_libname)
insinto /usr/include/bam
doins *.h
doman ${PN}.1
dodoc AUTHORS NEWS
if use examples; then
insinto /usr/share/${PN}
doins -r examples
fi
}
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