sci-biology/t-coffee: Don't build TMalign, but depend on sci-chemistry/tm-align; fixes #451802 and #451804

(Portage version: 2.2.0_alpha151/cvs/Linux x86_64, signed Manifest commit with key 70EB7916)

3 files changed, 23 insertions, 14 deletions

diff --git a/sci-biology/t-coffee/ChangeLog b/sci-biology/t-coffee/ChangeLog
index c42c551b9366..35d61631d691 100644
--- a/sci-biology/t-coffee/ChangeLog
+++ b/sci-biology/t-coffee/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/t-coffee
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.49 2012/12/11 14:39:22 jlec Exp $
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.50 2013/01/14 10:49:03 jlec Exp $
+
+*t-coffee-9.03.1318-r1 (14 Jan 2013)
+
+  14 Jan 2013; Justin Lecher <jlec@gentoo.org> -t-coffee-9.03.1318.ebuild,
+  +t-coffee-9.03.1318-r1.ebuild, metadata.xml:
+  Don't build TMalign, but depend on sci-chemistry/tm-align; fixes #451802 and
+  #451804
 
 *t-coffee-9.03.1318 (11 Dec 2012)
 
diff --git a/sci-biology/t-coffee/metadata.xml b/sci-biology/t-coffee/metadata.xml
index 3ea57edd4222..fbe2c20e6448 100644
--- a/sci-biology/t-coffee/metadata.xml
+++ b/sci-biology/t-coffee/metadata.xml
@@ -1,12 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<maintainer>
-		<email>weaver@gentoo.org</email>
-		<name>Andrey Kislyuk</name>
-	</maintainer>
-	<herd>sci-biology</herd>
-	<longdescription>
+  <maintainer>
+    <email>weaver@gentoo.org</email>
+    <name>Andrey Kislyuk</name>
+  </maintainer>
+  <herd>sci-biology</herd>
+  <longdescription>
 		T-Coffee is a multiple sequence alignment package. Given a set of
 		sequences (Proteins or DNA), T-Coffee generates a multiple sequence
 		alignment. Version 2.00 and higher can mix sequences and structures.
diff --git a/sci-biology/t-coffee/t-coffee-9.03.1318.ebuild b/sci-biology/t-coffee/t-coffee-9.03.1318-r1.ebuild
index d4325f1ffae8..403b9411b895 100644
--- a/sci-biology/t-coffee/t-coffee-9.03.1318.ebuild
+++ b/sci-biology/t-coffee/t-coffee-9.03.1318-r1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/t-coffee-9.03.1318.ebuild,v 1.1 2012/12/11 14:39:22 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/t-coffee-9.03.1318-r1.ebuild,v 1.1 2013/01/14 10:49:03 jlec Exp $
 
 EAPI=5
 
@@ -15,10 +15,12 @@ SRC_URI="http://www.tcoffee.org/Packages/Stable/Version_${MY_PV}/${MY_P}.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="examples"
 
-RDEPEND="sci-biology/clustalw"
+RDEPEND="
+	sci-biology/clustalw
+	sci-chemistry/tm-align"
 DEPEND=""
 
 S="${WORKDIR}/${MY_P}"
@@ -42,11 +44,11 @@ src_compile() {
 	emake \
 		CC="$(tc-getCC)" \
 		CFLAGS="${CFLAGS}" \
-		-C t_coffee_source all
+		-C t_coffee_source t_coffee
 }
 
 src_install() {
-	dobin t_coffee_source/{t_coffee,TMalign}
+	dobin t_coffee_source/t_coffee
 
 	if use examples; then
 		insinto /usr/share/${PN}