From: Olivier Fisette Date: Tue, 24 Apr 2007 20:44:01 +0000 (+0000) Subject: Initial import. X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=6bb808e855bde0054164d6630ba8552002d997ac;p=gentoo.git 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 index 000000000000..5d7e68bbe252 --- /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 + +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 index 000000000000..e2cf3a81f26b --- /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 index 000000000000..01fad3060d81 --- /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 index 000000000000..1293de0ea080 --- /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 index 000000000000..fd350c487554 --- /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 index 000000000000..d4648212cbad --- /dev/null +++ b/sci-biology/meme/metadata.xml @@ -0,0 +1,5 @@ + + + + sci-biology +