82 lines
1.6 KiB
Bash
82 lines
1.6 KiB
Bash
# Copyright 1999-2016 Gentoo Foundation
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# Distributed under the terms of the GNU General Public License v2
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EAPI=5
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PYTHON_COMPAT=( python2_7 )
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inherit eutils multilib python-r1 toolchain-funcs
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DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
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HOMEPAGE="http://www.htslib.org/"
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SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
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LICENSE="MIT"
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SLOT="0"
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KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
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IUSE="examples"
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REQUIRED_USE="${PYTHON_REQUIRED_USE}"
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CDEPEND="
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sys-libs/ncurses:0=
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~sci-libs/htslib-${PV}"
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RDEPEND="${CDEPEND}
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dev-lang/lua
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dev-lang/perl"
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DEPEND="${CDEPEND}
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virtual/pkgconfig"
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src_prepare() {
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find htslib-* -delete || die
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sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
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epatch "${FILESDIR}"/${P}-buildsystem.patch
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tc-export CC AR
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sed \
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-e '/htslib.mk/d' \
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-i Makefile || die
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}
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src_compile() {
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local mymakeargs=(
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LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
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HTSDIR="${EPREFIX}/usr/include"
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HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
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BAMLIB="libbam.so"
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)
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emake "${mymakeargs[@]}"
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}
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src_test() {
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local mymakeargs=(
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LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
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HTSDIR="${EPREFIX}/usr/include"
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HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
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BAMLIB="libbam.so"
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)
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emake "${mymakeargs[@]}" test
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}
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src_install() {
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dobin samtools $(find misc -type f -executable)
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python_replicate_script "${ED}"/usr/bin/varfilter.py
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dolib.so libbam.so*
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insinto /usr/include/bam
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doins *.h
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doman ${PN}.1
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dodoc AUTHORS NEWS README
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if use examples; then
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insinto /usr/share/${PN}
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doins -r examples
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fi
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}
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