3 files changed, 44 insertions, 20 deletions
diff --git a/sci-biology/clustalw-mpi/ChangeLog b/sci-biology/clustalw-mpi/ChangeLog
index 75b85ce08aea..0737af626ec5 100644
--- a/sci-biology/clustalw-mpi/ChangeLog
+++ b/sci-biology/clustalw-mpi/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/clustalw-mpi
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw-mpi/ChangeLog,v 1.6 2009/03/24 21:12:02 ribosome Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw-mpi/ChangeLog,v 1.7 2011/06/19 10:00:09 jlec Exp $
+
+*clustalw-mpi-0.13-r1 (19 Jun 2011)
+
+  19 Jun 2011; Justin Lecher <jlec@gentoo.org> +files/0.13-gentoo.patch,
+  -clustalw-mpi-0.13.ebuild, +clustalw-mpi-0.13-r1.ebuild:
+  Respect LDFLAGS, #335232
 
   24 Mar 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml:
   Giving up maintainership of this package.
diff --git a/sci-biology/clustalw-mpi/clustalw-mpi-0.13.ebuild b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild
index 73fa8a59e2a0..0a24f2937278 100644
--- a/sci-biology/clustalw-mpi/clustalw-mpi-0.13.ebuild
+++ b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild
@@ -1,26 +1,25 @@
-# Copyright 1999-2006 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw-mpi/clustalw-mpi-0.13.ebuild,v 1.3 2006/11/02 02:59:50 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild,v 1.1 2011/06/19 10:00:09 jlec Exp $
 
-inherit toolchain-funcs
+EAPI=4
+
+inherit eutils toolchain-funcs
 
 DESCRIPTION="A parallel (MPI) implemention of the Clustal-W general purpose multiple alignment algorithm"
-LICENSE="public-domain"
-HOMEPAGE="http://www.bii.a-star.edu.sg/achievements/applications/clustalw/index.asp"
+HOMEPAGE="http://www.bii.a-star.edu.sg/achievements/applications/clustalw/index.php"
 SRC_URI="http://web.bii.a-star.edu.sg/~kuobin/${PN}/${P}.tar.gz"
 
 SLOT="0"
+KEYWORDS="~amd64 ~x86"
+LICENSE="public-domain"
 IUSE="mpi_njtree static_pairalign"
-KEYWORDS="~x86"
 
 DEPEND="virtual/mpi"
+RDEPEND="${DEPEND}"
 
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	sed -e "s/CFLAGS  = -c -O3/CFLAGS = -c ${CFLAGS}/" \
-		-e "s/LFLAGS	= -lm/LFLAGS = -lm ${CFLAGS}/" -i Makefile || \
-			die "Failed to apply CFLAGS."
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-gentoo.patch
 	if use mpi_njtree; then
 		sed -e "s/TREES_FLAG/#TREES_FLAG/" -i Makefile || \
 			die "Failed to configure MPI code for NJ trees."
@@ -31,11 +30,7 @@ src_unpack() {
 	fi
 }
 
-src_compile() {
-	emake || die
-}
-
 src_install() {
-	dobin clustalw-mpi || die
-	newdoc README.${PN} README || die
+	dobin ${PN}
+	newdoc README.${PN} README
 }
diff --git a/sci-biology/clustalw-mpi/files/0.13-gentoo.patch b/sci-biology/clustalw-mpi/files/0.13-gentoo.patch
new file mode 100644
index 000000000000..6e36061cbb39
--- /dev/null
+++ b/sci-biology/clustalw-mpi/files/0.13-gentoo.patch
@@ -0,0 +1,23 @@
+ Makefile |    6 +++---
+ 1 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index f2107ce..835232b 100644
+--- a/Makefile
++++ b/Makefile
+@@ -25,12 +25,12 @@ TREES_FLAG = -DSERIAL_NJTREE
+ PAIRALIGN_FLAG = -DDYNAMIC_SCHEDULING_PAIRALIGN 
+ #PAIRALIGN_FLAG = -DSTATIC_SCHEDULING_PAIRALIGN
+ 
+-CFLAGS  = -c -O3
++CFLAGS  += -c
+ #CFLAGS  = -c -O3 -funroll-all-loops
+-LFLAGS	= -lm 
++LIBS	= -lm 
+ 
+ clustalw-mpi: $(OBJECTS) 
+-	$(CC) -o $@ $(OBJECTS) $(LFLAGS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJECTS) $(LIBS)
+ 
+ interface.o : interface.c $(HEADERS) param.h
+ 	$(CC) $(CFLAGS) $*.c