blob: 04211ba9e4e35b6fd11f3dc9e8fee48056a5cefa (
plain)
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
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
|
# 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-1.1.ebuild,v 1.1 2015/01/06 12:57:48 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="${PYTHON_REQUIRED_USE}"
CDEPEND="
sys-libs/ncurses
~sci-libs/htslib-${PV}"
RDEPEND="${CDEPEND}
dev-lang/lua
dev-lang/perl"
DEPEND="${CDEPEND}
virtual/pkgconfig"
src_prepare() {
find htslib-* -delete || die
sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
epatch "${FILESDIR}"/${P}-buildsystem.patch
epatch "${FILESDIR}"/${P}-rmdup.patch
tc-export CC AR
sed \
-e '/htslib.mk/d' \
-i Makefile || die
}
src_compile() {
local mymakeargs=(
LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
HTSDIR="${EPREFIX}/usr/include"
HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
BAMLIB="libbam.so"
)
emake "${mymakeargs[@]}"
}
src_test() {
local mymakeargs=(
LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
HTSDIR="${EPREFIX}/usr/include"
HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
BAMLIB="libbam.so"
)
emake "${mymakeargs[@]}" test
}
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
}
|
GitWeb