/[gentoo-x86]/sci-biology/samtools/samtools-0.1.18-r2.ebuild
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Contents of /sci-biology/samtools/samtools-0.1.18-r2.ebuild

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Revision 1.1 - (show annotations) (download)
Sun Jan 27 18:09:51 2013 UTC (19 months ago) by jlec
Branch: MAIN
sci-biology/samtools: Add missing deps and correct sed lines, #454134; thanks Torsten Veller

(Portage version: 2.2.0_alpha161/cvs/Linux x86_64, signed Manifest commit with key 8009D6F070EB7916)

1 # Copyright 1999-2013 Gentoo Foundation
2 # Distributed under the terms of the GNU General Public License v2
3 # $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.18-r1.ebuild,v 1.1 2013/01/23 10:51:13 jlec Exp $
4
5 EAPI=5
6
7 inherit multilib toolchain-funcs
8
9 DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
10 HOMEPAGE="http://samtools.sourceforge.net/"
11 SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
12
13 LICENSE="MIT"
14 SLOT="0"
15 IUSE="examples"
16 KEYWORDS="~amd64 ~x86 ~x64-macos"
17
18 RDEPEND="sys-libs/ncurses"
19 DEPEND="${RDEPEND}
20 virtual/pkgconfig"
21
22 src_prepare() {
23 sed \
24 -e '/^CC/s:=:?=:g' \
25 -e "/^LIBCURSES/s:=.*$:= $(pkg-config --libs ncurses):g" \
26 -e '/^CFLAGS=/s:=:?=:' \
27 -e "s/\$(CC) \$(CFLAGS)/& \$(LDFLAGS)/g" \
28 -e "s/-shared/& \$(LDFLAGS)/" \
29 -i "${S}"/{Makefile,misc/Makefile} || die #358563
30 sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
31
32 tc-export CC
33 }
34
35 src_compile() {
36 emake dylib
37 emake
38 }
39
40 src_install() {
41 dobin samtools $(find misc -type f -executable)
42
43 dolib.so libbam.so.1
44 dosym libbam.so.1 /usr/$(get_libdir)/libbam.so
45
46 insinto /usr/include/bam
47 doins bam.h bgzf.h faidx.h kaln.h khash.h kprobaln.h kseq.h ksort.h sam.h
48
49 doman ${PN}.1
50 dodoc AUTHORS ChangeLog NEWS
51
52 if use examples; then
53 insinto /usr/share/${PN}
54 doins -r examples
55 fi
56 }

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