69 lines
1.5 KiB
Bash
69 lines
1.5 KiB
Bash
# Copyright 1999-2014 Gentoo Foundation
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# Distributed under the terms of the GNU General Public License v2
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# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-1.0.ebuild,v 1.2 2014/09/24 08:12:27 jlec Exp $
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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 SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
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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="${PYTHON_REQUIRED_USE}"
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CDEPEND="
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sys-libs/ncurses
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sci-libs/htslib"
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RDEPEND="${CDEPEND}
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dev-lang/lua
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dev-lang/perl"
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DEPEND="${CDEPEND}
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virtual/pkgconfig"
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src_prepare() {
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find htslib-1.0 -delete || die
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sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
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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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CC="$(tc-getCC)"
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LDFLAGS="${LDFLAGS}"
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CFLAGS="${CFLAGS}"
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HTSDIR="${EPREFIX}/usr/include"
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HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
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)
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emake "${mymakeargs[@]}"
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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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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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