Version bump.

Package-Manager: portage-2.2_rc8/cvs/Linux 2.6.26-SENTINEL-2 i686

3 files changed, 105 insertions, 2 deletions

diff --git a/sci-biology/meme/ChangeLog b/sci-biology/meme/ChangeLog
index 3a2bd73cd55e..c68755fbb494 100644
--- a/sci-biology/meme/ChangeLog
+++ b/sci-biology/meme/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/meme
 # Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/ChangeLog,v 1.7 2008/06/14 12:34:50 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/ChangeLog,v 1.8 2008/09/12 14:06:53 markusle Exp $
+
+*meme-3.5.7 (12 Sep 2008)
+
+  12 Sep 2008; Markus Dittrich <markusle@gentoo.org> +meme-3.5.7.ebuild:
+  Version bump.
 
   14 Jun 2008; Markus Dittrich <markusle@gentoo.org> -meme-3.5.4.ebuild:
   Removed old ebuild with bad autotools usage (fixes bug #226609).
diff --git a/sci-biology/meme/Manifest b/sci-biology/meme/Manifest
index 185d785a6762..25aaf5828bd7 100644
--- a/sci-biology/meme/Manifest
+++ b/sci-biology/meme/Manifest
@@ -2,6 +2,8 @@ AUX meme-3.5.4-Makefile.am.patch 377 RMD160 a8d4551bcb53b66044ded24421cd2a17bf93
 AUX meme-3.5.4-patch1.patch 7443 RMD160 6d72e74d6139d8c29bfcda9da750dc454f08ef0a SHA1 336c91ad5ecd44d49de0e940bb18315b62569a2b SHA256 306cee9c3c831494cf264ded84d248e5773c9a56d259a02e8da9c6dc31457f04
 AUX meme-3.5.4-patch2.patch 2074 RMD160 56520122dd1d35afa444414ea57199924e8492b5 SHA1 29edf295100721006aea8b76ff4c5bdfb9312020 SHA256 bf74f09bcd6c247f464f15b17e3a0e8f95149fdc5b92d8f17d06ede430d2d7be
 DIST meme_3.5.4.tar.gz 1045501 RMD160 063a804c18f07349e95f4aba2a3c97cb025ed2a8 SHA1 d780dba0b900f840a599cf69cfeba4eefd4856b4 SHA256 b753ee276bc5eafeab8ff310e6d938977da11f466d26cfd3ae9c0f0a7a91de86
+DIST meme_3.5.7.tar.gz 1101383 RMD160 ab2c38873d30490933151520b09bec0644d2c492 SHA1 f04f233be63a75a78ea878d025a0476099e496cd SHA256 b5d84d969f69dbe02f2636e2161c53212f7c9a5b141ae2ed759f99a322f221a9
 EBUILD meme-3.5.4-r1.ebuild 2830 RMD160 7d22f826e65582135face95b90cafefbd1cd97d0 SHA1 100a2254ec137006e75c2758ee6ba2457ded0935 SHA256 9c1604a7d2067b6bcf14ddb81f78fa609c6055ca8e6399fa866e7fae6b670cfd
-MISC ChangeLog 1287 RMD160 61bad967bf36b391e688ae28389725f5d086bbe5 SHA1 41835da193974387db3c7d85c50e3e4010085553 SHA256 ef11e901ac420ae60c86492832d2dc6624d714d49f2579481b982d1939c3de45
+EBUILD meme-3.5.7.ebuild 2974 RMD160 ef63c37b71c75134c6cb8249c0a83ade93c159b5 SHA1 b77c4959b727b95607dba37005b9251112b3bfc4 SHA256 a4500c42a62dc9cb4110671ed1a154f28d3de6cf0c6e2afc4943e80ef9c01b01
+MISC ChangeLog 1404 RMD160 a7837842aaead26624982ece9561318b4d0733a3 SHA1 ba5df26472f2ed6ac9d2b414a09c4428fbad98d8 SHA256 0d3528e6b027d85f01681e96122abe483fd4d94fd7f5c0cb7626ba52bf58738e
 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
diff --git a/sci-biology/meme/meme-3.5.7.ebuild b/sci-biology/meme/meme-3.5.7.ebuild
new file mode 100644
index 000000000000..4ab0643740ca
--- /dev/null
+++ b/sci-biology/meme/meme-3.5.7.ebuild
@@ -0,0 +1,96 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/meme-3.5.7.ebuild,v 1.1 2008/09/12 14:06:53 markusle Exp $
+
+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"
+
+# Works only with LAM-MPI.
+DEPEND=">=dev-lang/perl-5.6.1
+	mpi? ( sys-cluster/lam-mpi )"
+
+S="${WORKDIR}/${PN}_${PV}"
+
+pkg_setup() {
+	# generate meme group to restrict logging to 
+	# /var/log/meme
+	enewgroup meme
+}
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+	epatch "${FILESDIR}/${PN}-3.5.4-Makefile.am.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/${PN}_p" || \
+			die "Failed to install parallel MEME implementation."
+		fi
+	fi
+
+	# allow logging only for members of meme group
+	diropts -m 0770 -g meme -o root
+	keepdir "/var/log/${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. Users'
+	einfo 'need to be part of the meme group to use this facility.'
+	echo
+}
+
+src_test() {
+	make test || die "Regression tests failed."
+}