diff options
| -rw-r--r-- | sci-biology/meme/ChangeLog | 8 | ||||
| -rw-r--r-- | sci-biology/meme/Manifest | 31 | ||||
| -rw-r--r-- | sci-biology/meme/files/digest-meme-3.5.4-r1 | 3 | ||||
| -rw-r--r-- | sci-biology/meme/meme-3.5.4-r1.ebuild | 90 |
4 files changed, 119 insertions, 13 deletions
diff --git a/sci-biology/meme/ChangeLog b/sci-biology/meme/ChangeLog index 28e5a6febb17..086d6e8d4c57 100644 --- a/sci-biology/meme/ChangeLog +++ b/sci-biology/meme/ChangeLog @@ -1,6 +1,12 @@ # 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 1.3 2007/09/17 06:00:16 je_fro Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/ChangeLog,v 1.4 2007/09/17 14:11:13 je_fro Exp $ + +*meme-3.5.4-r1 (17 Sep 2007) + + 17 Sep 2007; <jeff@gentoo.org> files/meme-3.5.4-patch1.patch, + files/meme-3.5.4-patch2.patch, +meme-3.5.4-r1.ebuild: + Once again, remove parallel install for amd64 boxes, and add upstream patches. 17 Sep 2007; <jeff@gentoo.org> -meme-3.5.4-r1.ebuild: Whoa...this version worked in my overlay. Pulling until I figure out what diff --git a/sci-biology/meme/Manifest b/sci-biology/meme/Manifest index 68d1c1b9e698..bbff97cd1874 100644 --- a/sci-biology/meme/Manifest +++ b/sci-biology/meme/Manifest @@ -2,23 +2,27 @@ AUX meme-3.5.4-Makefile.am.patch 377 RMD160 a8d4551bcb53b66044ded24421cd2a17bf93 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-patch1.patch 8064 RMD160 28a81c1013ec6b064f597265ef78c7d29e95cbf5 SHA1 724f8baaa1f7183437116f5a5a0eae05ea869997 SHA256 a15d1283805fd1ce414f47aa7cb2095f2f6ac4f9b375bc0e3a63f9eed7c58a01 +MD5 763f02a29abf3835c8005f8c5432ad9e files/meme-3.5.4-patch1.patch 8064 +RMD160 28a81c1013ec6b064f597265ef78c7d29e95cbf5 files/meme-3.5.4-patch1.patch 8064 +SHA256 a15d1283805fd1ce414f47aa7cb2095f2f6ac4f9b375bc0e3a63f9eed7c58a01 files/meme-3.5.4-patch1.patch 8064 +AUX meme-3.5.4-patch2.patch 2526 RMD160 1fed3c07b38b1b0244c09e50f6c0c103d69a8268 SHA1 540bc56122e974ae9f1d2cf3ee28241786fc8b8f SHA256 c3eb7c56d769c13a62843d51da0b7c980089353ab97b789fce0bc8d34cc30ff7 +MD5 c0e790d6a390da2798d6effe809249d1 files/meme-3.5.4-patch2.patch 2526 +RMD160 1fed3c07b38b1b0244c09e50f6c0c103d69a8268 files/meme-3.5.4-patch2.patch 2526 +SHA256 c3eb7c56d769c13a62843d51da0b7c980089353ab97b789fce0bc8d34cc30ff7 files/meme-3.5.4-patch2.patch 2526 DIST meme_3.5.4.tar.gz 1045501 RMD160 063a804c18f07349e95f4aba2a3c97cb025ed2a8 SHA1 d780dba0b900f840a599cf69cfeba4eefd4856b4 SHA256 b753ee276bc5eafeab8ff310e6d938977da11f466d26cfd3ae9c0f0a7a91de86 +EBUILD meme-3.5.4-r1.ebuild 2828 RMD160 53c0031f0f8f02d92bb40e5014a4fdab42ad645a SHA1 2a1d3707b20e03980020662ae826789ab05524aa SHA256 dc252b0cf3cd0e450f5bcda22a6ccb620fa4f4084fad84d93343fbf7d4403a0a +MD5 8dfda51f16c86842a4e7a2743a38afea meme-3.5.4-r1.ebuild 2828 +RMD160 53c0031f0f8f02d92bb40e5014a4fdab42ad645a meme-3.5.4-r1.ebuild 2828 +SHA256 dc252b0cf3cd0e450f5bcda22a6ccb620fa4f4084fad84d93343fbf7d4403a0a meme-3.5.4-r1.ebuild 2828 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 713 RMD160 bf5b78869b6c9f4da082482075db25b10387b00b SHA1 20c2c4dde29b952b7a06787e5d8f291c6958a590 SHA256 986e970eb962a95df3fcc1b2c34d7a7a9808477962b5473707fa1ffdf8c6ad3b -MD5 de2cfd75223564ceb4ffb9888d2fa1a6 ChangeLog 713 -RMD160 bf5b78869b6c9f4da082482075db25b10387b00b ChangeLog 713 -SHA256 986e970eb962a95df3fcc1b2c34d7a7a9808477962b5473707fa1ffdf8c6ad3b ChangeLog 713 +MISC ChangeLog 945 RMD160 3e33164438e93a10b6b48a9ceb12db79b8c1109b SHA1 434af03eac11b1fc23881119bac378cec0741e69 SHA256 1f79b29f2747b0dcc6bae8b7048f8a29d7a61cde794505cacdd7fb384dc33425 +MD5 ad7e086bd3ccb54eff94f19527a9495d ChangeLog 945 +RMD160 3e33164438e93a10b6b48a9ceb12db79b8c1109b ChangeLog 945 +SHA256 1f79b29f2747b0dcc6bae8b7048f8a29d7a61cde794505cacdd7fb384dc33425 ChangeLog 945 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 MD5 aec0225cc3c4bc9490275e897849b449 metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 metadata.xml 165 @@ -26,3 +30,6 @@ SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 metadata 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 +MD5 1eaad7de1310f43b70c0414c120687f6 files/digest-meme-3.5.4-r1 235 +RMD160 ed97244306a01084ca6973c50c49726724212632 files/digest-meme-3.5.4-r1 235 +SHA256 98b3e51f5544aa86ee4cfed70da0b3d9068cd677c3744e750b4f0bee2be5be8b files/digest-meme-3.5.4-r1 235 diff --git a/sci-biology/meme/files/digest-meme-3.5.4-r1 b/sci-biology/meme/files/digest-meme-3.5.4-r1 new file mode 100644 index 000000000000..01fad3060d81 --- /dev/null +++ b/sci-biology/meme/files/digest-meme-3.5.4-r1 @@ -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/meme-3.5.4-r1.ebuild b/sci-biology/meme/meme-3.5.4-r1.ebuild new file mode 100644 index 000000000000..fe197fe6aba4 --- /dev/null +++ b/sci-biology/meme/meme-3.5.4-r1.ebuild @@ -0,0 +1,90 @@ +# 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 1.3 2007/09/17 14:11:13 je_fro 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}" + +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." +} |