From ce7512f6240216a7f6c9468af3cfbf95d92c029a Mon Sep 17 00:00:00 2001 From: Jeffrey Gardner Date: Thu, 26 Jun 2008 16:43:32 +0000 Subject: try relying on virtual/mpi svn path=/; revision=230 --- sci-biology/meme/Manifest | 25 ++-------- sci-biology/meme/meme-3.5.4-r1.ebuild | 90 +++++++++++++++++++++++++++++++++++ sci-biology/meme/meme-3.5.4.ebuild | 89 ---------------------------------- 3 files changed, 93 insertions(+), 111 deletions(-) create mode 100644 sci-biology/meme/meme-3.5.4-r1.ebuild delete mode 100644 sci-biology/meme/meme-3.5.4.ebuild (limited to 'sci-biology') diff --git a/sci-biology/meme/Manifest b/sci-biology/meme/Manifest index 42e9a66..75d2b28 100644 --- a/sci-biology/meme/Manifest +++ b/sci-biology/meme/Manifest @@ -1,28 +1,9 @@ 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 AUX meme-3.5.4-patch1.patch 8019 RMD160 c443da2f16552c488b77e897bdae543839a0738d SHA1 d37473061f4294d342521570729d65421ead0d99 SHA256 7f42f3de330e19630ab5eb335043749afd94652b8d2b1564ce8cd6856acf81e6 -MD5 491211c1a3d87abd057280406f95220c files/meme-3.5.4-patch1.patch 8019 -RMD160 c443da2f16552c488b77e897bdae543839a0738d files/meme-3.5.4-patch1.patch 8019 -SHA256 7f42f3de330e19630ab5eb335043749afd94652b8d2b1564ce8cd6856acf81e6 files/meme-3.5.4-patch1.patch 8019 AUX meme-3.5.4-patch2.patch 2496 RMD160 1d492e01a9e06aa0564e2c15235eb49f28f4d2b7 SHA1 cbc691788e2d30cde438f15d94a97f637fdce4a5 SHA256 2571bff727505cddfe59aefa931f2b2436ed2a2daf1e35b5a1d6c6014a753a21 -MD5 7b0765e479af87218368f29ae7041fb8 files/meme-3.5.4-patch2.patch 2496 -RMD160 1d492e01a9e06aa0564e2c15235eb49f28f4d2b7 files/meme-3.5.4-patch2.patch 2496 -SHA256 2571bff727505cddfe59aefa931f2b2436ed2a2daf1e35b5a1d6c6014a753a21 files/meme-3.5.4-patch2.patch 2496 +AUX meme_3.5.4.patch_1 7443 RMD160 6d72e74d6139d8c29bfcda9da750dc454f08ef0a SHA1 336c91ad5ecd44d49de0e940bb18315b62569a2b SHA256 306cee9c3c831494cf264ded84d248e5773c9a56d259a02e8da9c6dc31457f04 +AUX meme_3.5.4.patch_2 2074 RMD160 56520122dd1d35afa444414ea57199924e8492b5 SHA1 29edf295100721006aea8b76ff4c5bdfb9312020 SHA256 bf74f09bcd6c247f464f15b17e3a0e8f95149fdc5b92d8f17d06ede430d2d7be DIST meme_3.5.4.tar.gz 1045501 RMD160 063a804c18f07349e95f4aba2a3c97cb025ed2a8 SHA1 d780dba0b900f840a599cf69cfeba4eefd4856b4 SHA256 b753ee276bc5eafeab8ff310e6d938977da11f466d26cfd3ae9c0f0a7a91de86 -EBUILD meme-3.5.4.ebuild 2778 RMD160 db6f29dd51ecf5bac56f064c75d788b36f56a83a SHA1 cebab3898c38b9396b2cf591f8ac49ff6ddc106b SHA256 05bd30158cc5b79c2de4f2e97c523f9cff48131965c992f24137bb2e36e006e0 -MD5 c71dbb29f70e8dfa3bc3ab607c33f226 meme-3.5.4.ebuild 2778 -RMD160 db6f29dd51ecf5bac56f064c75d788b36f56a83a meme-3.5.4.ebuild 2778 -SHA256 05bd30158cc5b79c2de4f2e97c523f9cff48131965c992f24137bb2e36e006e0 meme-3.5.4.ebuild 2778 +EBUILD meme-3.5.4-r1.ebuild 2822 RMD160 2855f8b8c529002cb498639f51779294d0d4f41e SHA1 ea3e3b23dce7ce2b3bbca1ea3b393fb3da283e1e SHA256 c3370cf5ad110a7a3e4a5b0c53ed8823c4b9e151dcf79aa3a46f8a5a0e80b0c7 MISC ChangeLog 566 RMD160 74f3916e717ce84e593217bd53c0b99eb10a14c9 SHA1 799df7e3146993c26d897dd8224f302fd0970fcc SHA256 909bde96179b1488d0bcd854d9cd2d3a37a6e55c6c9756623fae0e77e8562dff -MD5 233146864b46de91b59ff4a506da21d7 ChangeLog 566 -RMD160 74f3916e717ce84e593217bd53c0b99eb10a14c9 ChangeLog 566 -SHA256 909bde96179b1488d0bcd854d9cd2d3a37a6e55c6c9756623fae0e77e8562dff ChangeLog 566 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/meme-3.5.4-r1.ebuild b/sci-biology/meme/meme-3.5.4-r1.ebuild new file mode 100644 index 0000000..f2e9e8d --- /dev/null +++ b/sci-biology/meme/meme-3.5.4-r1.ebuild @@ -0,0 +1,90 @@ +# 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-3.5.4-r1.ebuild,v 1.4 2008/06/14 12:34:50 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? ( 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." +} diff --git a/sci-biology/meme/meme-3.5.4.ebuild b/sci-biology/meme/meme-3.5.4.ebuild deleted file mode 100644 index 1932bd7..0000000 --- a/sci-biology/meme/meme-3.5.4.ebuild +++ /dev/null @@ -1,89 +0,0 @@ -# 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-r1.ebuild,v 1.1 2007/09/17 02:41:56 je_fro 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" - epatch "${FILESDIR}/${P}-patch1.patch" - epatch "${FILESDIR}/${P}-patch2.patch" - 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." -} -- cgit v1.2.3-65-gdbad