sci-biology/samtools/samtools-0.1.19-r2.ebuild


1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61

# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.19-r2.ebuild,v 1.3 2015/04/08 18:20:42 mgorny 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://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"
RDEPEND="${CDEPEND}
	dev-lang/lua
	dev-lang/perl"
DEPEND="${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
}