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# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
PYTHON_COMPAT=( python2_7 )
DISTUTILS_OPTIONAL=true
AUTOTOOLS_AUTORECONF=true
AUTOTOOLS_IN_SOURCE_BUILD=1
inherit autotools-utils distutils-r1 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/~ronny/RNA/ViennaRNA-${PV}.tar.gz"
SLOT="0"
LICENSE="vienna-rna"
KEYWORDS="amd64 ppc x86"
IUSE="doc openmp python static-libs"
REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
RDEPEND="
dev-lang/perl
media-libs/gd
doc? ( dev-texlive/texlive-latex )
python? ( ${PYTHON_DEPS} )"
DEPEND="${RDEPEND}
python? ( dev-lang/swig:0 )"
S="${WORKDIR}/ViennaRNA-${PV}"
PATCHES=(
"${FILESDIR}"/${P}-bindir.patch
"${FILESDIR}"/${P}-prll.patch
"${FILESDIR}"/${P}-impl-decl.patch
)
src_prepare() {
sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die
sed -i 's/@PerlCmd@ Makefile.PL/& INSTALLDIRS=vendor/' Perl/Makefile.am || die
autotools-utils_src_prepare
if use python; then
cp "${FILESDIR}"/${P}-setup.py "${S}"/setup.py || die
PATCHES=()
distutils-r1_src_prepare
fi
}
src_configure() {
local myeconfargs=(
--with-cluster
$(use_enable openmp) )
use doc || \
myeconfargs+=(
--without-doc-pdf
--without-doc-html
--without-doc
)
autotools-utils_src_configure
sed \
-e "s:LIBDIR = /usr/lib:LIBDIR = ${D}/usr/$(get_libdir):" \
-e "s:INCDIR = /usr/include:INCDIR = ${D}/usr/include:" \
-i RNAforester/g2-0.70/Makefile || die
sed \
-e "s:CC=gcc:CC=$(tc-getCC):" \
-e "s:^CFLAGS=:CFLAGS=${CFLAGS}:" \
-i Readseq/Makefile || die
use python && distutils-r1_src_configure
}
src_compile() {
autotools-utils_src_compile
autotools-utils_src_compile -C Readseq build CC=$(tc-getCC)
# TODO: Add (optional?) support for the NCBI toolkit.
if use python; then
pushd Perl > /dev/null
mv RNA_wrap.c{,-perl} || die
swig -python RNA.i || die
popd > /dev/null
distutils-r1_src_compile
mv Perl/RNA_wrap.c{-perl,} || die
fi
}
src_test() {
autotools-utils_src_compile -C Perl check
autotools-utils_src_compile -C Readseq test
}
src_install() {
autotools-utils_src_install
if ! use static-libs; then
rm -f "${ED}"/usr/$(get_libdir)/*.a || die
fi
newbin Readseq/readseq readseq-vienna
dodoc Readseq/Readseq.help
newdoc Readseq/Readme README.readseq
newdoc Readseq/Formats Formats.readseq
# remove perlocal.pod to avoid file collisions (see #240358)
perl_delete_localpod || die "Failed to remove perlocal.pod"
use python && distutils-r1_src_install
}
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