Initial import.

Package-Manager: portage-2.1.2.2

diff --git a/sci-biology/meme/ChangeLog b/sci-biology/meme/ChangeLog
new file mode 100644 (file)
index 0000000..5d7e68b
--- /dev/null
+++ b/sci-biology/meme/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/meme
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/ChangeLog,v 1.1 2007/04/24 20:44:01 ribosome Exp $
+
+*meme-3.5.4 (24 Apr 2007)
+
+  24 Apr 2007; Olivier Fisette <ribosome@gentoo.org>
+  +files/meme-3.5.4-Makefile.am.patch, +metadata.xml, +meme-3.5.4.ebuild:
+  Initial import.
+

diff --git a/sci-biology/meme/Manifest b/sci-biology/meme/Manifest
new file mode 100644 (file)
index 0000000..e2cf3a8
--- /dev/null
+++ b/sci-biology/meme/Manifest
@@ -0,0 +1,20 @@
+AUX meme-3.5.4-Makefile.am.patch 377 RMD160 a8d4551bcb53b66044ded24421cd2a17bf93b3ad SHA1 96530d5a58b8c01c99ae2b5463b7448758d7fb3d SHA256 ef3f0d8ccca728325d9f9b4f485e8cd4db2ced50fc975f8b66f3b76fcf17b5e8
+MD5 1340a30b4b010637181605a11e78a950 files/meme-3.5.4-Makefile.am.patch 377
+RMD160 a8d4551bcb53b66044ded24421cd2a17bf93b3ad files/meme-3.5.4-Makefile.am.patch 377
+SHA256 ef3f0d8ccca728325d9f9b4f485e8cd4db2ced50fc975f8b66f3b76fcf17b5e8 files/meme-3.5.4-Makefile.am.patch 377
+DIST meme_3.5.4.tar.gz 1045501 RMD160 063a804c18f07349e95f4aba2a3c97cb025ed2a8 SHA1 d780dba0b900f840a599cf69cfeba4eefd4856b4 SHA256 b753ee276bc5eafeab8ff310e6d938977da11f466d26cfd3ae9c0f0a7a91de86
+EBUILD meme-3.5.4.ebuild 2522 RMD160 91306d472533051cbe7ccb08594a0c527be86d5d SHA1 ca5cc1df4a8fadd2456423231cba5e2168a4eef3 SHA256 1a2e88d01b7183d530d1796b144fc0e4de6f3f0b0faa138e5552ba9a65f9c188
+MD5 f2a6ac226bbcea335120135f8a490df8 meme-3.5.4.ebuild 2522
+RMD160 91306d472533051cbe7ccb08594a0c527be86d5d meme-3.5.4.ebuild 2522
+SHA256 1a2e88d01b7183d530d1796b144fc0e4de6f3f0b0faa138e5552ba9a65f9c188 meme-3.5.4.ebuild 2522
+MISC ChangeLog 380 RMD160 8a57ff4a858b07340d524de06454d283b74779a3 SHA1 23f8d9f0fe0f9310f6443d6496604f8f59ea3504 SHA256 84f7ebf236107ba251b7f33776a75976670ae89615f006d8c95128071d4c7dd6
+MD5 b156e44c571a255e6e9bff163fd6433b ChangeLog 380
+RMD160 8a57ff4a858b07340d524de06454d283b74779a3 ChangeLog 380
+SHA256 84f7ebf236107ba251b7f33776a75976670ae89615f006d8c95128071d4c7dd6 ChangeLog 380
+MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
+MD5 aec0225cc3c4bc9490275e897849b449 metadata.xml 165
+RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 metadata.xml 165
+SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 metadata.xml 165
+MD5 1eaad7de1310f43b70c0414c120687f6 files/digest-meme-3.5.4 235
+RMD160 ed97244306a01084ca6973c50c49726724212632 files/digest-meme-3.5.4 235
+SHA256 98b3e51f5544aa86ee4cfed70da0b3d9068cd677c3744e750b4f0bee2be5be8b files/digest-meme-3.5.4 235

diff --git a/sci-biology/meme/files/digest-meme-3.5.4 b/sci-biology/meme/files/digest-meme-3.5.4
new file mode 100644 (file)
index 0000000..01fad30
--- /dev/null
+++ b/sci-biology/meme/files/digest-meme-3.5.4
@@ -0,0 +1,3 @@
+MD5 9a8b3d21c6094616cc7b9b424352c697 meme_3.5.4.tar.gz 1045501
+RMD160 063a804c18f07349e95f4aba2a3c97cb025ed2a8 meme_3.5.4.tar.gz 1045501
+SHA256 b753ee276bc5eafeab8ff310e6d938977da11f466d26cfd3ae9c0f0a7a91de86 meme_3.5.4.tar.gz 1045501

diff --git a/sci-biology/meme/files/meme-3.5.4-Makefile.am.patch b/sci-biology/meme/files/meme-3.5.4-Makefile.am.patch
new file mode 100644 (file)
index 0000000..1293de0
--- /dev/null
+++ b/sci-biology/meme/files/meme-3.5.4-Makefile.am.patch
@@ -0,0 +1,17 @@
+--- Makefile.am.old    2007-04-24 10:36:50.000000000 -0400
++++ Makefile.am        2007-04-24 10:37:37.000000000 -0400
+@@ -57,11 +57,11 @@
+ endif
+ 
+ dbdir:
+-      mkdir -p $(MEME_DB)
++      mkdir -p $(DESTDIR)$(MEME_DB)
+ 
+ install-data-local:
+-      mkdir -p $(MEME_LOGS)
+-      chmod a+w $(MEME_LOGS)
++      mkdir -p $(DESTDIR)$(MEME_LOGS)
++      chmod a+w $(DESTDIR)$(MEME_LOGS)
+ 
+ distdir = $(PACKAGE)_$(VERSION)
+ 

diff --git a/sci-biology/meme/meme-3.5.4.ebuild b/sci-biology/meme/meme-3.5.4.ebuild
new file mode 100644 (file)
index 0000000..fd350c4
--- /dev/null
+++ b/sci-biology/meme/meme-3.5.4.ebuild
@@ -0,0 +1,81 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/meme-3.5.4.ebuild,v 1.1 2007/04/24 20:44:01 ribosome Exp $
+
+inherit 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}"
+
+src_unpack() {
+       unpack ${A}
+
+       cd "${S}"
+       epatch "${FILESDIR}/${P}-Makefile.am.patch"
+       einfo "Regenerating autotools files..."
+       autoconf || die "autoconf failed"
+       automake || die "automake failed"
+}
+
+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="${CFLAGS}"  make -e || die "Make failed."
+
+       if use mpi; then
+               cd src/parallel
+               make || die "Parallel make failed."
+       fi
+}
+
+src_install() {
+       make install DESTDIR="${D}" || die "Failed to install program files."
+       exeinto "/opt/${PN}/bin"
+       doexe "${S}/src/parallel/${PN}_p" || \
+                       die "Failed to install parallel MEME implementation."
+       keepdir "/var/log/${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."
+}

diff --git a/sci-biology/meme/metadata.xml b/sci-biology/meme/metadata.xml
new file mode 100644 (file)
index 0000000..d464821
--- /dev/null
+++ b/sci-biology/meme/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+       <herd>sci-biology</herd>
+</pkgmetadata>