1 files changed, 89 insertions, 0 deletions
diff --git a/sci-biology/meme/meme-3.5.7.ebuild b/sci-biology/meme/meme-3.5.7.ebuild
new file mode 100644
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--- /dev/null
+++ b/sci-biology/meme/meme-3.5.7.ebuild
@@ -0,0 +1,89 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $
+
+inherit autotools eutils toolchain-funcs
+
+DESCRIPTION="The MEME/MAST system - Motif discovery and search"
+HOMEPAGE="http://meme.sdsc.edu/meme"
+SRC_URI="http://meme.nbcr.net/downloads/${PN}_${PV}.tar.gz"
+LICENSE="meme"
+
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+# Other possible USE flags include "debug", "client", "server", "web",
+# "queue". Other variables must be set at compile time, but only when
+# the Web server is built. Right now, Web server and client are disabled.
+IUSE="mpi"
+
+DEPEND=">=dev-lang/perl-5.6.1
+	mpi? ( virtual/mpi )"
+
+S="${WORKDIR}/${PN}_${PV}"
+
+src_unpack() {
+	unpack ${A}
+
+	cd "${S}"
+	epatch "${FILESDIR}/${P}-Makefile.am.patch"
+#	epatch "${FILESDIR}/${P}-patch1.patch"
+#	epatch "${FILESDIR}/${P}-patch2.patch"
+	einfo "Regenerating autotools files..."
+	eautoreconf
+}
+
+src_compile() {
+	local EXTRA_CONF
+	# Build system is too bugy to make the programs use standard locations.
+	# Put everything in "/opt" instead.
+	EXTRA_CONF="${EXTRA_CONF} --prefix=/opt/${PN}"
+	EXTRA_CONF="${EXTRA_CONF} --with-logs=/var/log/${PN}"
+	# Connect hyperlinks to official Web site.
+	EXTRA_CONF="${EXTRA_CONF} --with-url=http://meme.nbcr.net/meme"
+	# Disable Web server, client and Web site.
+	EXTRA_CONF="${EXTRA_CONF} --disable-server --disable-client --disable-web"
+	# Parallel implementation
+	if ! use mpi; then
+		EXTRA_CONF="${EXTRA_CONF} --enable-serial"
+	fi
+
+	./configure ${EXTRA_CONF} || die "Configure failed."
+	CC="$(tc-getCC)" ac_cc_opt="${CFLAGS}"  make -e || die "Make failed."
+
+# Install parallel files only on x86, otherwise the install fails with the error:
+# i386 architecture of input file `mp.o' is incompatible with i386:x86-64 output
+	if [[ "${ARCH}" == "x86" ]] ; then
+		if use mpi; then
+			cd src/parallel
+			make || die "Parallel make failed."
+		fi
+	fi
+}
+
+src_install() {
+	make install DESTDIR="${D}" || die "Failed to install program files."
+	exeinto "/opt/${PN}/bin"
+	if [[ "${ARCH}" == "x86" ]] ; then
+		if use mpi; then
+		doexe "${S}/src/parallel/${PN}_p" || \
+			die "Failed to install parallel MEME implementation."
+		fi
+	fi
+	keepdir "/var/log/${PN}"
+	fperms 777 "/var/log/${PN}"
+}
+
+pkg_postinst() {
+	echo
+	einfo 'Prior to using MEME/MAST, you should source "/opt/meme/etc/meme.sh"'
+	einfo '(or "/opt/meme/etc/meme.csh" if you use a csh-style shell). To do'
+	einfo 'this automatically with bash, add the following statement to your'
+	einfo '"~/.bashrc" file (without the quotes): "source /opt/meme/etc/meme.sh".'
+	echo
+	einfo 'Log files are produced in the "/var/log/meme" directory.'
+	echo
+}
+
+src_test() {
+	make test || die "Regression tests failed."
+}