# Copyright 1999-2014 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-1.0.ebuild,v 1.2 2014/09/24 08:12:27 jlec Exp $ 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 tc-export CC AR sed \ -e '/htslib.mk/d' \ -i Makefile || die } src_compile() { local mymakeargs=( LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" CC="$(tc-getCC)" LDFLAGS="${LDFLAGS}" CFLAGS="${CFLAGS}" HTSDIR="${EPREFIX}/usr/include" HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) ) emake "${mymakeargs[@]}" } src_install() { dobin samtools $(find misc -type f -executable) python_replicate_script "${ED}"/usr/bin/varfilter.py doman ${PN}.1 dodoc AUTHORS NEWS README if use examples; then insinto /usr/share/${PN} doins -r examples fi }