sci-biology/meme: Version bump to 4.11.2_p2

Gentoo-bug: 599860
* EAPI=6
* Install documentation and examples correctly
* Install perl and python modules correctly
* Add missing perl runtime dependencies

Package-Manager: portage-2.3.2

1 files changed, 111 insertions, 0 deletions

diff --git a/sci-biology/meme/meme-4.11.2_p2.ebuild b/sci-biology/meme/meme-4.11.2_p2.ebuild
new file mode 100644
index 000000000000..4eb826065500
--- /dev/null
+++ b/sci-biology/meme/meme-4.11.2_p2.ebuild
@@ -0,0 +1,111 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit autotools perl-functions python-single-r1 versionator
+
+MY_PV=$(get_version_component_range 1-3)
+MY_P=${PN}_${MY_PV}
+
+DESCRIPTION="The MEME/MAST system - Motif discovery and search"
+HOMEPAGE="http://meme-suite.org/tools/meme"
+SRC_URI="http://meme-suite.org/meme-software/${MY_PV}/${MY_P}.tar.gz"
+
+LICENSE="meme"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="debug doc examples mpi"
+
+RDEPEND="
+	${PYTHON_DEPS}
+	app-shells/tcsh
+	dev-libs/libxml2:2
+	dev-libs/libxslt
+	sys-libs/zlib
+	app-text/ghostscript-gpl
+	media-gfx/imagemagick
+	dev-lang/perl:=
+	dev-perl/HTML-Parser
+	dev-perl/HTML-Template
+	dev-perl/Log-Log4perl
+	dev-perl/Math-CDF
+	dev-perl/XML-Compile-SOAP
+	dev-perl/XML-Compile-WSDL11
+	dev-perl/XML-Parser
+	dev-perl/XML-Simple
+	virtual/perl-Data-Dumper
+	virtual/perl-Exporter
+	virtual/perl-File-Path
+	virtual/perl-File-Spec
+	virtual/perl-File-Temp
+	virtual/perl-Getopt-Long
+	virtual/perl-Scalar-List-Utils
+	virtual/perl-Time-HiRes
+	mpi? ( virtual/mpi )"
+DEPEND="${RDEPEND}"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+S="${WORKDIR}/${MY_P}"
+PATCHES=(
+	"${FILESDIR}"/${PN}-4.11.2_p2-patch1.patch
+	"${FILESDIR}"/${PN}-4.11.2_p2-patch2.patch
+	"${FILESDIR}"/${PN}-4.11.2_p2-fix-build-system.patch
+)
+
+pkg_setup() {
+	python-single-r1_pkg_setup
+	perl_set_version
+}
+
+src_prepare() {
+	default
+	eautoreconf
+}
+
+src_configure() {
+	econf \
+		--sysconfdir="${EPREFIX}"/etc/${PN} \
+		--with-logs="${EPREFIX}"/var/log/${PN} \
+		--with-perl=perl \
+		--with-convert=convert \
+		--with-gs=gs \
+		--disable-build-libxml2 \
+		--disable-build-libxslt \
+		$(use_enable debug) \
+		$(use_enable doc) \
+		$(use_enable examples) \
+		$(use_enable !mpi serial) \
+		--with-perl-dir="${VENDOR_LIB#${EPREFIX}/usr}" \
+		PYTHON="${EPYTHON}"
+
+	# delete bundled libs, just to be sure. These need
+	# to be removed after econf, else AC_OUTPUT will fail
+	rm -r src/{libxml2,lib{,e}xslt} || die
+}
+
+src_test() {
+	# bug #297070
+	emake -j1 test
+}
+
+src_install() {
+	default
+	docompress -x /usr/share/doc/${PF}/examples
+
+	# prefix all binaries with 'meme-', in order
+	# to prevent collisions, bug 455010
+	cd "${ED%/}"/usr/bin/ || die
+	local i
+	for i in *; do
+		if [[ $i != meme-* ]]; then
+			mv {,meme-}"${i}" || die
+		fi
+	done
+
+	diropts -m ugo+rwxt -o root
+	keepdir /var/log/meme
+}