From 4bfa45644434e16d40b41fc810a89d09daf9a40a Mon Sep 17 00:00:00 2001 From: Olivier Fisette Date: Fri, 9 Mar 2007 02:43:13 +0000 Subject: [PATCH] New upstream version. Package-Manager: portage-2.1.2.2 --- sci-biology/t-coffee/ChangeLog | 9 ++- sci-biology/t-coffee/Manifest | 26 ++++---- .../t-coffee/files/digest-t-coffee-4.96 | 3 + sci-biology/t-coffee/t-coffee-4.96.ebuild | 62 +++++++++++++++++++ 4 files changed, 84 insertions(+), 16 deletions(-) create mode 100644 sci-biology/t-coffee/files/digest-t-coffee-4.96 create mode 100644 sci-biology/t-coffee/t-coffee-4.96.ebuild diff --git a/sci-biology/t-coffee/ChangeLog b/sci-biology/t-coffee/ChangeLog index 25f8fa411b9f..1a630c6a439d 100644 --- a/sci-biology/t-coffee/ChangeLog +++ b/sci-biology/t-coffee/ChangeLog @@ -1,6 +1,11 @@ # ChangeLog for sci-biology/t-coffee -# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.16 2006/09/13 23:52:04 ribosome Exp $ +# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.17 2007/03/09 02:43:13 ribosome Exp $ + +*t-coffee-4.96 (09 Mar 2007) + + 09 Mar 2007; Olivier Fisette +t-coffee-4.96.ebuild: + New upstream version. *t-coffee-4.45 (13 Sep 2006) diff --git a/sci-biology/t-coffee/Manifest b/sci-biology/t-coffee/Manifest index 64e074224285..35c18c0a9b6b 100644 --- a/sci-biology/t-coffee/Manifest +++ b/sci-biology/t-coffee/Manifest @@ -1,8 +1,6 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - DIST T-COFFEE_distribution_Version_3.84.tar.gz 1625217 RMD160 cda295fd0c2c432c8f802739a3748fcb01f40389 SHA1 b1ddedc7a1d756c6265c20a870e101d75942a1aa SHA256 1c062fe67b1817570fdce8f57999ce637863cc91b4feb91053ef805cc3f48eab DIST T-COFFEE_distribution_Version_4.45.tar.gz 2735436 RMD160 f05110dff0d05c852b9a72be7247ebe527a4649c SHA1 85f2608f220376f4a9793d1b6be7f99247cafbb1 SHA256 256675fdb3e438839a179c2ca5019a14045fcb346836c9c9c54581e7694d4ca3 +DIST T-COFFEE_distribution_Version_4.96.tar.gz 2863327 RMD160 d6a7722f1fe3b2a8b186fad49e8bc136d812b610 SHA1 b8ae0be131ae470f5aa596369afa9fc9fbc18701 SHA256 49181acd69a5723fd5b11f579b1efe685b5289bf187985b25b40c514b0af0213 EBUILD t-coffee-3.84.ebuild 1814 RMD160 2f89d06ef91f1946a0cb0178caeff16924f35dd3 SHA1 89744ef5e82c61bf0f77cad88f09d0806245fd16 SHA256 aad58deacb8762799f5dc443a1b34be4fa06fb54c0b42980ec23cbf5e4736595 MD5 93fd7a0d063210749ad2817dca89df98 t-coffee-3.84.ebuild 1814 RMD160 2f89d06ef91f1946a0cb0178caeff16924f35dd3 t-coffee-3.84.ebuild 1814 @@ -11,10 +9,14 @@ EBUILD t-coffee-4.45.ebuild 1882 RMD160 63d60a1c6fd7de29f8c5b10de9f66249a0918d11 MD5 05d9b62a0da700a27a5b180ac4799b03 t-coffee-4.45.ebuild 1882 RMD160 63d60a1c6fd7de29f8c5b10de9f66249a0918d11 t-coffee-4.45.ebuild 1882 SHA256 1e6cb93c8839abe8823e90e59fbf24acad28a49784a3786fe17526244db4523d t-coffee-4.45.ebuild 1882 -MISC ChangeLog 2453 RMD160 f593bd30648ea2eecad3442122a1243924862b01 SHA1 0c28e79c7439cbe7f974dbdb062b02590be16639 SHA256 ed92cf41b3d41182cb0bc518e7d030418fd40986658998d35f4f7235869b8358 -MD5 23c6e62f85830d2e0a898972789db1b5 ChangeLog 2453 -RMD160 f593bd30648ea2eecad3442122a1243924862b01 ChangeLog 2453 -SHA256 ed92cf41b3d41182cb0bc518e7d030418fd40986658998d35f4f7235869b8358 ChangeLog 2453 +EBUILD t-coffee-4.96.ebuild 2005 RMD160 2d2fc3b8efac91c9701ef6324c9745d6eb77f194 SHA1 e1dbcaa2d1e1ca432f5e8301d30f410ec1debbdf SHA256 431fe23ac6bac5c85538658619041cbd7c2c7c5bd0e4381350323662d7f813b1 +MD5 e8914d250401ad84c7abdf9ba3907665 t-coffee-4.96.ebuild 2005 +RMD160 2d2fc3b8efac91c9701ef6324c9745d6eb77f194 t-coffee-4.96.ebuild 2005 +SHA256 431fe23ac6bac5c85538658619041cbd7c2c7c5bd0e4381350323662d7f813b1 t-coffee-4.96.ebuild 2005 +MISC ChangeLog 2584 RMD160 c1d40253336ab1809fb94a887b3f2076b7d38e0b SHA1 d800935c83b571df47cab77dccbfa3123b3e168a SHA256 bf4ec6936c46f6d7b662ef19dec1a26247e59c4891a17e5d8aeaf06b9e92e36e +MD5 e52ad059fd1f9a9f1788512592769b2f ChangeLog 2584 +RMD160 c1d40253336ab1809fb94a887b3f2076b7d38e0b ChangeLog 2584 +SHA256 bf4ec6936c46f6d7b662ef19dec1a26247e59c4891a17e5d8aeaf06b9e92e36e ChangeLog 2584 MISC metadata.xml 763 RMD160 1163b25c489923e806ccf77dd3b4b5a486da0c28 SHA1 9a6b86bfa165e9b7c0a9b8631990bbfb727fe410 SHA256 8ff6c199eb54e1a49903130ed1aebbe32a0c0b1698aaec2044530c27533270a2 MD5 d5530b7c0b5defb31d0e1ad80fad02d6 metadata.xml 763 RMD160 1163b25c489923e806ccf77dd3b4b5a486da0c28 metadata.xml 763 @@ -25,10 +27,6 @@ SHA256 6717825503db3a5cc4d64a2506dc81d25498dcc2625f37eb64c8df50c25462f9 files/di MD5 d81db5e2bd9495765fd8434602d640a7 files/digest-t-coffee-4.45 307 RMD160 511f979bf54572e7339a99d3b1f748c33667ba29 files/digest-t-coffee-4.45 307 SHA256 b3b5f1aca6ea37a586fd0763776d63b5c228b12c15630cbc6b3b8d0e444d5520 files/digest-t-coffee-4.45 307 ------BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.2 (GNU/Linux) - -iD8DBQFF3tSa/ejvha5XGaMRAnxFAKCD2fDtfgNi/BQXyir/3T/f1iLYtACgxa8p -srDjPM7JtOfQk9Iyl1LCqX0= -=7dcM ------END PGP SIGNATURE----- +MD5 f59bcfecf86c8b4729dc646cfe693047 files/digest-t-coffee-4.96 307 +RMD160 1813cba165d62ee51fcecbcc5f04fe587374a5c9 files/digest-t-coffee-4.96 307 +SHA256 2a6ffaf1bef9217315fb872171f49b5810002e900edb2ecc136d9a9f24503d7c files/digest-t-coffee-4.96 307 diff --git a/sci-biology/t-coffee/files/digest-t-coffee-4.96 b/sci-biology/t-coffee/files/digest-t-coffee-4.96 new file mode 100644 index 000000000000..d6f8c17360de --- /dev/null +++ b/sci-biology/t-coffee/files/digest-t-coffee-4.96 @@ -0,0 +1,3 @@ +MD5 ce40b2654663b7c22c1c8427fb5e32db T-COFFEE_distribution_Version_4.96.tar.gz 2863327 +RMD160 d6a7722f1fe3b2a8b186fad49e8bc136d812b610 T-COFFEE_distribution_Version_4.96.tar.gz 2863327 +SHA256 49181acd69a5723fd5b11f579b1efe685b5289bf187985b25b40c514b0af0213 T-COFFEE_distribution_Version_4.96.tar.gz 2863327 diff --git a/sci-biology/t-coffee/t-coffee-4.96.ebuild b/sci-biology/t-coffee/t-coffee-4.96.ebuild new file mode 100644 index 000000000000..ddc5809f988a --- /dev/null +++ b/sci-biology/t-coffee/t-coffee-4.96.ebuild @@ -0,0 +1,62 @@ +# Copyright 1999-2007 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/t-coffee-4.96.ebuild,v 1.1 2007/03/09 02:43:13 ribosome Exp $ + +inherit toolchain-funcs flag-o-matic + +DESCRIPTION="A multiple sequence alignment package" +LICENSE="t-coffee" +HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html" +SRC_URI="http://www.tcoffee.org/Packages/T-COFFEE_distribution_Version_${PV}.tar.gz" + +SLOT="0" +IUSE="" +KEYWORDS="~ppc ~x86" + +RESTRICT="nomirror" + +DEPEND="sci-biology/clustalw" + +TCDIR="${WORKDIR}/T-COFFEE_distribution_Version_${PV}" +S="${TCDIR}/t_coffee_source" + +src_unpack() { + unpack ${A} + cd "${S}" + sed -e "s/CC = cc/CC = $(tc-getCC) ${CFLAGS}/" -i makefile || die \ + "Failed to patch makefile." +} + +die_compile() { + echo + eerror "If you experience an internal compiler error (consult the above" + eerror "messages), try compiling t-coffee using very modest compiler flags." + eerror "See bug #114745 on the Gentoo Bugzilla for more details." + die "Compilation failed" +} + +src_compile() { + [[ $(gcc-version) == "3.4" ]] && append-flags -fno-unit-at-a-time + [[ $(gcc-version) == "4.1" ]] && append-flags -fno-unit-at-a-time + make all || die_compile +} + +src_install() { + dobin "${TCDIR}"/bin/t_coffee || die "Failed to install program." + + insinto /usr/share/${PN}/lib/html + doins "${TCDIR}"/html/* || die "Failed to install Web interface files." + + cd "${TCDIR}"/doc + dodoc aln_compare.doc.txt README4T-COFFEE seq_reformat.doc.txt \ + t_coffee_technical.txt t_coffee_tutorial.txt || die \ + "Failed to install text documentation." + dohtml t_coffee_technical.htm t_coffee_tutorial.htm || die \ + "Failed to install HTML documentation." + insinto /usr/share/doc/${PF} + doins t_coffee.pdf t_coffee_technical.doc t_coffee_tutorial.doc || die \ + "Failed to install DOC and PDF documentation." + + insinto /usr/share/${PN}/example + doins "${TCDIR}"/example/* || die "Failed to install example files." +} -- 2.26.2