Version BUmp, 312897

Package-Manager: portage-2.2.0_alpha41/cvs/Linux x86_64

5 files changed, 88 insertions, 7 deletions

diff --git a/sci-biology/raxml/ChangeLog b/sci-biology/raxml/ChangeLog
index 12abc66afb9a..18a21292326a 100644
--- a/sci-biology/raxml/ChangeLog
+++ b/sci-biology/raxml/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/raxml
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/raxml/ChangeLog,v 1.6 2011/06/21 06:38:10 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/raxml/ChangeLog,v 1.7 2011/06/27 05:59:01 jlec Exp $
+
+*raxml-7.2.6 (27 Jun 2011)
+
+  27 Jun 2011; Justin Lecher <jlec@gentoo.org> +raxml-7.2.6.ebuild,
+  +files/raxml-7.2.6-makefile.patch, metadata.xml:
+  Version BUmp, 312897
 
 *raxml-7.2.5-r1 (21 Jun 2011)
 
diff --git a/sci-biology/raxml/Manifest b/sci-biology/raxml/Manifest
index 4b2f9db674d7..cfd9bb706bc6 100644
--- a/sci-biology/raxml/Manifest
+++ b/sci-biology/raxml/Manifest
@@ -2,17 +2,20 @@
 Hash: SHA1
 
 AUX raxml-7.2.5-makefile.patch 1420 RMD160 55bfdf943c50d133986bd2f8a9da059b9cbf1f00 SHA1 666faa75663e6c520412f4ed3bf65fe9bde187a7 SHA256 f3c9d9eaacf7a7e0d1594e3d689f938ff82c2dbdb4c4c4f2ed81a861ebd7adb5
+AUX raxml-7.2.6-makefile.patch 777 RMD160 c561a8e5117295fdf094b165795098e1ac626569 SHA1 be59886d3ef00737507863d087a537266e40aa48 SHA256 0e87b5cd6375669e660ef6e3c37e51e751ea8846de6c52060f484380c28610d5
 DIST RAxML-7.2.2.tar.bz2 184132 RMD160 b2bec2d590c0899e245989d2f6e0ffba506d66cc SHA1 5c5bb777f150d6b7ee5051b82f8b3f398efd4ccf SHA256 294816da5e7c3ca6b766f6e95aa5f032447e22460518b6916853eb80b3491ba9
 DIST RAxML-7.2.5.tar.bz2 198933 RMD160 d87541fcc73b4b6f662b1752ae2a7ec5376a05ca SHA1 9d75e0d4b0a136a82731feda7af9e0e2238ede6b SHA256 35ec543ad0e7879c86f1671d5f352dfe529c6684c6ea9d7fcc600423e37c3156
+DIST RAxML-7.2.6.tar.bz2 202803 RMD160 8d31ca70e653917b198a482a2ed2e5acd9072486 SHA1 0e33022682ebabd353c38a1c766b68da266395df SHA256 d45bcbe45e3ed5f8d6ba3c99b9da9b202c72a9fb196a9d32d2961ee4cb791868
 EBUILD raxml-7.2.2.ebuild 1304 RMD160 1e059aa2ef7a3f7665575d674a2d90ee9c8f21fa SHA1 2af59b45059e78064a9abc281148524f778975e2 SHA256 f41d0caa2e83661627fc21c312cb728074c76c6e5bbdbab1e6c07ac05046e22d
 EBUILD raxml-7.2.5-r1.ebuild 1025 RMD160 23271fbcccfb2dbbd4d728ebce3cc57aee139f1c SHA1 c721f72719eacd662b234c935363ef62627cbcda SHA256 31cd2cbd9ff528177b003fe0775bd0c9589fb6e96c641b372a5a095d103a2654
 EBUILD raxml-7.2.5.ebuild 1304 RMD160 dbcceec05e567fd3af969309de45d03c44d9f6fb SHA1 eb599184d32592ee745a6fc4523d6f790c434040 SHA256 24653c9c70408aacc2728e5237f8303dc2e20bbc13d076d7a61bde2bbfd3c6cc
-MISC ChangeLog 1074 RMD160 8df1680810c63cf427e220c7a0cc994715caddf5 SHA1 3e7d8bc5c1f9973655cd0ab5c301db09fdbab640 SHA256 f6872eed4b92b727117d445b4c1ca11dd8c9172bed26ea653d46de4bc3e93604
-MISC metadata.xml 339 RMD160 e204f70642579ae8d095983675851b681330c31a SHA1 21bb6e7ec4b97b6cbff33f0d34faf73dd018b5d5 SHA256 aac1952d3b2936edae355e265b85bda835bc53e8782778c495e214a05e1fb0e5
+EBUILD raxml-7.2.6.ebuild 1022 RMD160 0bf1dcc2151a5a792c81c7434ddcacb90ef4691c SHA1 23bd6ead37ef405537df567690fed61cebfe8644 SHA256 19d92360d3e0042bed4f659caad3de986b750d290112d3d21e805a7b633562cc
+MISC ChangeLog 1245 RMD160 f4735fe883d52a1a56634b4329591ad985a20ecc SHA1 151fea6f58333e6b0e814c645cfe255acab10d7b SHA256 9c0aa287c55c3ee6f272926b6cf1481aadbe646c7a5820f4afca7b262a02734e
+MISC metadata.xml 344 RMD160 8ea584bc5a4b2cbefc385d178dc68d52ffb578e7 SHA1 7abc92a015607b3570d2aa8234345aec1b7396b8 SHA256 ed3d77b6cdfecc5005ad4e3eaefbb831660e05a85908f3e23f29f3cd2051ec16
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.17 (GNU/Linux)
 
-iEYEARECAAYFAk4APFcACgkQgAnW8HDreRZR5QCghDOF85lOX8gN1fpZAJPLuBeT
-ozQAnAkHgNEgZsGWftWuBU1aFfVT4MBv
-=EDL5
+iEYEARECAAYFAk4IHCoACgkQgAnW8HDreRYvNwCfTA6aJ1SyZgdKjaowWc1wRM+P
+R7AAnA9y0YG79eIh9KM2qIcUTn8cMdZz
+=mK2y
 -----END PGP SIGNATURE-----
diff --git a/sci-biology/raxml/files/raxml-7.2.6-makefile.patch b/sci-biology/raxml/files/raxml-7.2.6-makefile.patch
new file mode 100644
index 000000000000..ae83e2eef4e7
--- /dev/null
+++ b/sci-biology/raxml/files/raxml-7.2.6-makefile.patch
@@ -0,0 +1,29 @@
+ Makefile.gcc |    6 +++---
+ 1 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/Makefile.gcc b/Makefile.gcc
+index 716b6c6..f0c1de2 100644
+--- a/Makefile.gcc
++++ b/Makefile.gcc
+@@ -1,10 +1,10 @@
+ # Makefile August 2006 by Alexandros Stamatakis
+ # Makefile cleanup October 2006, Courtesy of Peter Cordes <peter@cordes.ca>
+ 
+-CC = gcc 
++CC ?= gcc 
+ 
+ 
+-CFLAGS = -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse
++CFLAGS += -D_GNU_SOURCE
+ 
+ 
+ 
+@@ -19,7 +19,7 @@ all : raxmlHPC
+ GLOBAL_DEPS = axml.h globalVariables.h
+ 
+ raxmlHPC : $(objs)
+-	$(CC) -o raxmlHPC $(objs) $(LIBRARIES) 
++	$(CC) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES) 
+ 
+ classify.o : classify.c $(GLOBAL_DEPS)
+ evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
diff --git a/sci-biology/raxml/metadata.xml b/sci-biology/raxml/metadata.xml
index 3f2ec4ab4025..9fbd5c20ef5f 100644
--- a/sci-biology/raxml/metadata.xml
+++ b/sci-biology/raxml/metadata.xml
@@ -6,5 +6,7 @@
 		<name>Andrey Kislyuk</name>
 	</maintainer>
 	<herd>sci-biology</herd>
-	<use><flag name='sse3'>Enable optimization for SSE3 capable chips</flag></use>
+	<use>
+		<flag name="sse3">Enable optimization for SSE3 capable chips</flag>
+	</use>
 </pkgmetadata>
diff --git a/sci-biology/raxml/raxml-7.2.6.ebuild b/sci-biology/raxml/raxml-7.2.6.ebuild
new file mode 100644
index 000000000000..5d573e87651d
--- /dev/null
+++ b/sci-biology/raxml/raxml-7.2.6.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/raxml/raxml-7.2.6.ebuild,v 1.1 2011/06/27 05:59:01 jlec Exp $
+
+EAPI=4
+
+inherit eutils flag-o-matic toolchain-funcs
+
+DESCRIPTION="A Program for Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees"
+HOMEPAGE="http://wwwkramer.in.tum.de/exelixis/software.html"
+SRC_URI="http://wwwkramer.in.tum.de/exelixis/software/RAxML-${PV}.tar.bz2"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86"
+IUSE="sse3 +threads"
+
+# mpi is not supported in version 7.2.2. mpi is enabled by adding -DPARALLEL to CFLAGS
+DEPEND="" # mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/RAxML-${PV}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-makefile.patch
+
+	use sse3 && append-cflags -D__SIM_SSE3
+	use threads && \
+		append-cflags -D_USE_PTHREADS && \
+		append-ldflags -pthread
+
+	tc-export CC
+}
+
+src_compile() {
+	emake -f Makefile.gcc
+}
+
+src_install() {
+	dobin raxmlHPC
+}