sci-biology/samtools/samtools-0.1.18-r2.ebuild

# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $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 $

EAPI=5

inherit multilib 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"
IUSE="examples"
KEYWORDS="~amd64 ~x86 ~x64-macos"

RDEPEND="sys-libs/ncurses"
DEPEND="${RDEPEND}
        virtual/pkgconfig"

src_prepare() {
        sed \
                -e '/^CC/s:=:?=:g' \
                -e "/^LIBCURSES/s:=.*$:= $(pkg-config --libs ncurses):g" \
                -e '/^CFLAGS=/s:=:?=:' \
                -e "s/\$(CC) \$(CFLAGS)/& \$(LDFLAGS)/g" \
                -e "s/-shared/& \$(LDFLAGS)/" \
                -i "${S}"/{Makefile,misc/Makefile} || die #358563
        sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die

        tc-export CC
}

src_compile() {
        emake dylib
        emake
}

src_install() {
        dobin samtools $(find misc -type f -executable)

        dolib.so libbam.so.1
        dosym libbam.so.1 /usr/$(get_libdir)/libbam.so

        insinto /usr/include/bam
        doins bam.h bgzf.h faidx.h kaln.h khash.h kprobaln.h kseq.h ksort.h sam.h

        doman ${PN}.1
        dodoc AUTHORS ChangeLog NEWS

        if use examples; then
                insinto /usr/share/${PN}
                doins -r examples
        fi
}
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	}