blob: dcc441acfb4168dfe1f4b7f91990acdfcdc35eba (
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
85
86
87
88
89
90
91
92
93
94
95
96
|
# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.8.5.ebuild,v 1.7 2011/12/21 08:24:41 phajdan.jr Exp $
EAPI="3"
PYTHON_DEPEND="python? 2"
SUPPORT_PYTHON_ABIS="1"
inherit autotools distutils multilib perl-module toolchain-funcs
DESCRIPTION="RNA secondary structure prediction and comparison"
HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/"
SRC_URI="http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-${PV}.tar.gz"
LICENSE="vienna-rna"
SLOT="0"
IUSE="python static-libs"
KEYWORDS="amd64 ~ppc x86"
DEPEND="
dev-lang/perl
media-libs/gd
python? ( dev-lang/swig )"
RDEPEND="${DEPEND}"
S="${WORKDIR}/ViennaRNA-${PV}"
PATCHES=(
"${FILESDIR}"/${PN}-1.6.5-c-fixes.patch
"${FILESDIR}"/${PN}-1.7.2-LDFLAGS.patch
"${FILESDIR}"/${PN}-1.8.3-gcc4.3.patch
"${FILESDIR}"/${PN}-1.8.3-disable-gd.patch
"${FILESDIR}"/${PN}-1.8.4-jobserver-fix.patch
"${FILESDIR}"/${PN}-1.8.4-bindir.patch
"${FILESDIR}"/${PN}-1.8.4-overflows.patch
"${FILESDIR}"/${PN}-1.8.4-implicits.patch
)
src_prepare() {
base_src_prepare
sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die
sed -i 's/@PerlCmd@ Makefile.PL/& INSTALLDIRS=vendor/' Perl/Makefile.am || die
eautoreconf
cd RNAforester && eautoreconf
use python && cp "${FILESDIR}"/${P}-setup.py "${S}"/setup.py
}
src_configure() {
econf --with-cluster
sed -e "s:LIBDIR = /usr/lib:LIBDIR = ${D}/usr/$(get_libdir):" \
-e "s:INCDIR = /usr/include:INCDIR = ${D}/usr/include:" \
-i RNAforester/g2-0.70/Makefile \
|| die "Failed patching RNAForester build system."
sed -e "s:CC=cc:CC=$(tc-getCC):" -e "s:CFLAGS=:CFLAGS=${CFLAGS}:" \
-i Readseq/Makefile || die "Failed patching readseq Makefile."
}
src_compile() {
emake clean || die
emake || die
emake -C Readseq || die "Failed to compile readseq."
# TODO: Add (optional?) support for the NCBI toolkit.
if use python; then
pushd Perl > /dev/null
mv RNA_wrap.c{,-perl}
swig -python RNA.i
popd > /dev/null
distutils_src_compile
mv Perl/RNA_wrap.c{-perl,}
fi
}
src_test() {
cd "${S}"/Perl && emake check || die "Perl tests failed"
cd "${S}"/Readseq && emake test || die "Readseq tests failed"
}
src_install() {
emake DESTDIR="${D}" install || die
if ! use static-libs; then
rm -f "${ED}"/usr/$(get_libdir)/*.a || die
fi
dodoc AUTHORS ChangeLog NEWS README THANKS || die
newbin Readseq/readseq readseq-vienna || die
dodoc Readseq/Readseq.help || die
newdoc Readseq/Readme README.readseq || die
newdoc Readseq/Formats Formats.readseq || die
# remove perlocal.pod to avoid file collisions (see #240358)
fixlocalpod || die "Failed to remove perlocal.pod"
use python && distutils_src_install
}
|
GitWeb