| # Copyright 1999-2015 Gentoo Foundation |
| # Distributed under the terms of the GNU General Public License v2 |
| # $Id$ |
| |
| EAPI=5 |
| |
| PYTHON_COMPAT=( python2_7 ) |
| |
| inherit eutils multilib python-r1 toolchain-funcs |
| |
| DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments" |
| 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="${PYTHON_REQUIRED_USE}" |
| |
| CDEPEND=" |
| sys-libs/ncurses |
| sci-libs/htslib" |
| |
| RDEPEND="${CDEPEND} |
| dev-lang/lua |
| dev-lang/perl" |
| DEPEND="${CDEPEND} |
| virtual/pkgconfig" |
| |
| src_prepare() { |
| find htslib-1.0 -delete || die |
| |
| sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die |
| |
| epatch "${FILESDIR}"/${P}-buildsystem.patch |
| |
| tc-export CC AR |
| |
| sed \ |
| -e '/htslib.mk/d' \ |
| -i Makefile || die |
| |
| } |
| |
| src_compile() { |
| local mymakeargs=( |
| LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" |
| HTSDIR="${EPREFIX}/usr/include" |
| HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) |
| BAMLIB="libbam.so" |
| ) |
| emake "${mymakeargs[@]}" |
| } |
| |
| src_install() { |
| dobin samtools $(find misc -type f -executable) |
| |
| python_replicate_script "${ED}"/usr/bin/varfilter.py |
| 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 |
| } |
