New upstream version.

Package-Manager: portage-2.1.2.2

4 files changed, 84 insertions, 16 deletions

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 <ribosome@gentoo.org> +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."
+}