Bump to 7.54. Closes #258081.

Package-Manager: portage-2.2_rc23/cvs/Linux x86_64

3 files changed, 68 insertions, 3 deletions

diff --git a/sci-biology/t-coffee/ChangeLog b/sci-biology/t-coffee/ChangeLog
index 0cdccee89417..95ace70bc299 100644
--- a/sci-biology/t-coffee/ChangeLog
+++ b/sci-biology/t-coffee/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/t-coffee
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.34 2008/09/06 11:29:59 markusle Exp $
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.35 2009/03/01 17:15:20 patrick Exp $
+
+*t-coffee-7.54 (01 Mar 2009)
+
+  01 Mar 2009; Patrick Lauer <patrick@gentoo.org> +t-coffee-7.54.ebuild:
+  Bump to 7.54. Closes #258081.
 
 *t-coffee-6.82 (06 Sep 2008)
 
diff --git a/sci-biology/t-coffee/Manifest b/sci-biology/t-coffee/Manifest
index 588f8c387719..2a466adf5f44 100644
--- a/sci-biology/t-coffee/Manifest
+++ b/sci-biology/t-coffee/Manifest
@@ -1,8 +1,10 @@
 DIST T-COFFEE_distribution_Version_5.31.tar.gz 2857478 RMD160 95cb261c57fe31b3c26bdac85c10a4609692c2eb SHA1 dde68b94c26bb8727a9a667ecec0cd919ee14dc5 SHA256 43a38a6e9d0dc4bd663704b69c94c3aefd15608e5113703fad8d42f8fdc1a615
 DIST T-COFFEE_distribution_Version_5.65.tar.gz 2892013 RMD160 50c04dfbda649ebbf0e691a74bd62433bb1dbd14 SHA1 a8dc4bcc37eaa8237670c9daf1b260c8452fab89 SHA256 536cfe25648fbaf4d96baf36b3c8d4d2d81e97b2939e09e89880cae39893d0c6
 DIST T-COFFEE_distribution_Version_6.82.tar.gz 2377424 RMD160 01e7e43da5637114ded1f5509f3fae605ed4f08b SHA1 ea02ed7908a3628772ea72bc4226529586247580 SHA256 23329516078fa0d242a0160e807e71bbe221462323892f8ddcc62affa569628a
+DIST T-COFFEE_distribution_Version_7.54.tar.gz 3968725 RMD160 d11964db5232d137bf0db8101dfb75b1fde25936 SHA1 a302954a10860455bc23f924628598757c39eb12 SHA256 9d7d56abc000b61b48908fa4f93fb382a35df11c883966a0119605cd16aa668e
 EBUILD t-coffee-5.31.ebuild 1997 RMD160 7612d1f86bd8b702c196b0269f093fad63482be2 SHA1 bf6f4e8de8e451207d618de60b56926d5fd0b525 SHA256 f19291307534c6168cc046c0c8a74d622aa63197d07bdff756c18a6e9159bc55
 EBUILD t-coffee-5.65.ebuild 1999 RMD160 7ae18da2d689343547258b54f1de66f289f47114 SHA1 6518aae4c5e8b9bc55eaff6c0e763ae22995c393 SHA256 25d353182a9e946df52ad7dea404800a169067c77441c8d2456042b0cbea4d25
 EBUILD t-coffee-6.82.ebuild 1838 RMD160 79975b36ece635a8473b9843a04d19e7bdf16584 SHA1 6b0957b53cbcc8bfc945ea32613718dc8ff30fce SHA256 3ec2720e76effedc6f76d81c273de59a3ef1fe9aa16a4258923245b2543e0d2f
-MISC ChangeLog 4623 RMD160 fff7ad5226f6c27a9f3f2978774eb603978f9a83 SHA1 ada7a314e69531b15321a4c1500c66cb9eb9ab0f SHA256 bc68473b62e0b2d8587165481eb1f5480a2d04e93efcd01855037cdfd0094f13
+EBUILD t-coffee-7.54.ebuild 1857 RMD160 ee23165c9f4e40b608c960d6c14886b1a680a4e6 SHA1 eb77681d7a1facb7fdab7c0ca45fe6dc02b99e61 SHA256 3da47ef23cf41088177fe5c8b90f96627c0f29f777145e79bf28b7aab618f372
+MISC ChangeLog 4758 RMD160 39332b4fadae2d819ab3ab14ee507a67b9a8c011 SHA1 0334ae3ebe6ca981c5a5f9ae070e6a35f3bfe382 SHA256 21696484aa064a0f04a51bf6dbadfe250157557da736321409d7d5acf7b550cd
 MISC metadata.xml 763 RMD160 1163b25c489923e806ccf77dd3b4b5a486da0c28 SHA1 9a6b86bfa165e9b7c0a9b8631990bbfb727fe410 SHA256 8ff6c199eb54e1a49903130ed1aebbe32a0c0b1698aaec2044530c27533270a2
diff --git a/sci-biology/t-coffee/t-coffee-7.54.ebuild b/sci-biology/t-coffee/t-coffee-7.54.ebuild
new file mode 100644
index 000000000000..3dd596d3185b
--- /dev/null
+++ b/sci-biology/t-coffee/t-coffee-7.54.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/t-coffee-7.54.ebuild,v 1.1 2009/03/01 17:15:20 patrick Exp $
+
+inherit toolchain-funcs flag-o-matic
+
+DESCRIPTION="A multiple sequence alignment package"
+LICENSE="GPL-2"
+HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html"
+SRC_URI="http://www.tcoffee.org/Packages/T-COFFEE_distribution_Version_${PV}.tar.gz"
+
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~ppc ~x86"
+
+DEPEND="sci-biology/clustalw"
+RDEPEND="${DEPEND}"
+
+TCDIR="${WORKDIR}/T-COFFEE_distribution_Version_${PV}"
+S="${TCDIR}/t_coffee_source"
+
+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
+	[[ $(gcc-version) == "4.1" ]] && append-flags -fno-unit-at-a-time
+	CC="$(tc-getCC)" CFLAGS="${CFLAGS}" emake || die_compile
+}
+
+src_install() {
+	dobin t_coffee || die "Failed to install program."
+
+	insinto /usr/share/${PN}/lib/html
+	doins "${TCDIR}"/html/* \
+		|| die "Failed to install Web interface files."
+
+	cd "${TCDIR}"/doc
+	dodoc aln_compare.doc.txt 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/${PF}
+	doins t_coffee_technical.doc t_coffee_tutorial.doc \
+		|| die "Failed to install DOC documentation."
+
+	insinto /usr/share/${PN}/example
+	doins "${TCDIR}"/example/* \
+		|| die "Failed to install example files."
+}