Version bump

Package-Manager: portage-2.2_rc30/cvs/Linux x86_64

4 files changed, 53 insertions, 54 deletions

diff --git a/sci-biology/raxml/ChangeLog b/sci-biology/raxml/ChangeLog
index 297144aff04b..3efdd7ff0089 100644
--- a/sci-biology/raxml/ChangeLog
+++ b/sci-biology/raxml/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/raxml
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/raxml/ChangeLog,v 1.4 2009/10/31 17:56:05 maekke Exp $
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/raxml/ChangeLog,v 1.5 2010/01/27 15:58:33 weaver Exp $
+
+*raxml-7.2.5 (27 Jan 2010)
+
+  27 Jan 2010; Andrey Kislyuk <weaver@gentoo.org> -raxml-7.0.4.ebuild,
+  +raxml-7.2.5.ebuild:
+  Version bump
 
   31 Oct 2009; Markus Meier <maekke@gentoo.org> raxml-7.2.2.ebuild:
   amd64/x86 stable, bug #290929
diff --git a/sci-biology/raxml/Manifest b/sci-biology/raxml/Manifest
index 303a670e4250..f19f2a019425 100644
--- a/sci-biology/raxml/Manifest
+++ b/sci-biology/raxml/Manifest
@@ -1,16 +1,6 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
-DIST RAxML-7.0.4.tar.bz2 435099 RMD160 c3cc2fa38bf3cdbfcd4251400f572dccbb671288 SHA1 ee8bb3a07f89ff00d59872f970ac2159186255ff SHA256 d6affcfc214fcebbb5e017e38422b40468710575f072e484591c1ada19217a5c
 DIST RAxML-7.2.2.tar.bz2 184132 RMD160 b2bec2d590c0899e245989d2f6e0ffba506d66cc SHA1 5c5bb777f150d6b7ee5051b82f8b3f398efd4ccf SHA256 294816da5e7c3ca6b766f6e95aa5f032447e22460518b6916853eb80b3491ba9
-EBUILD raxml-7.0.4.ebuild 1156 RMD160 0f91a92b761421ed72d01a3e99a59833710a5ef8 SHA1 1e3b7db6ff5c26de591d720c5617d8c68fc2e84c SHA256 073e97cd8f9351893e2ea7c8f912e1284e859b0ccf8f6b1ac60444fcf466b6f6
+DIST RAxML-7.2.5.tar.bz2 198933 RMD160 d87541fcc73b4b6f662b1752ae2a7ec5376a05ca SHA1 9d75e0d4b0a136a82731feda7af9e0e2238ede6b SHA256 35ec543ad0e7879c86f1671d5f352dfe529c6684c6ea9d7fcc600423e37c3156
 EBUILD raxml-7.2.2.ebuild 1302 RMD160 d9faf5d1467d92a4713c5fe65614684d1b110f0a SHA1 44ca81922015263df5860b2755ae204dbd8aa073 SHA256 5306afbdd44a3dfa1ac901eff54d82c3c975daddce7d35fec6e4905f416fff8a
-MISC ChangeLog 699 RMD160 b71dfc97f71ce2ed421c576bc843eb98c2eefa5d SHA1 6042e4c594bad23009a964c85a644e14492a74d6 SHA256 d103240454c22ddd63089b0339b900c642454f185f5529a670227aad10113c72
+EBUILD raxml-7.2.5.ebuild 1304 RMD160 daac22281ba7c7d4a83d3565e48da277c24704ec SHA1 7a1ae21922c60c267f7029dc6dbec5a51000fe0e SHA256 469b8e57a10bdd20c688448b04a35c445b9d464a0f642546c463c5c9c206b548
+MISC ChangeLog 837 RMD160 b052546f781e8ad73e52fa9f2e44e7453f339ae1 SHA1 96b98bc7f575f61cd019a4cc6b40f0c743eaf66a SHA256 9a2499b65c0e7cc4ccc372e2b265d14d7a4e6dd0cc687b9dd0c0969a0caad1db
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.11 (GNU/Linux)
-
-iEYEARECAAYFAkrsekkACgkQkKaRLQcq0GJIPwCgpy+NQxES55rCkLLIk6knTwQ9
-PzsAn1xFarj3Riysj1iI77GCh+Fz5wn9
-=WPNx
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diff --git a/sci-biology/raxml/raxml-7.0.4.ebuild b/sci-biology/raxml/raxml-7.0.4.ebuild
deleted file mode 100644
index 54780b8e9a4f..000000000000
--- a/sci-biology/raxml/raxml-7.0.4.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/raxml/raxml-7.0.4.ebuild,v 1.1 2009/09/04 03:04:43 weaver Exp $
-
-EAPI="2"
-
-inherit toolchain-funcs
-
-DESCRIPTION="A Program for Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees"
-HOMEPAGE="http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm"
-SRC_URI="http://icwww.epfl.ch/~stamatak/index-Dateien/software/RAxML-${PV}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE="+mpi +threads"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="mpi? ( virtual/mpi )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/RAxML-${PV}"
-
-src_prepare() {
-	sed -i -e 's/CFLAGS =/CFLAGS := ${CFLAGS}/' \
-		-e 's/CC = gcc/CC = '$(tc-getCC)'/' \
-		Makefile.* || die
-}
-
-src_compile() {
-	emake -f Makefile.gcc || die
-	if use mpi; then emake -f Makefile.MPI clean && emake -f Makefile.MPI || die; fi
-	if use threads; then emake -f Makefile.PTHREADS clean && emake -f Makefile.PTHREADS || die; fi
-}
-
-src_install() {
-	dobin raxmlHPC || die
-	if use mpi; then dobin raxmlHPC-MPI || die; fi
-	if use threads; then dobin raxmlHPC-PTHREADS || die; fi
-}
diff --git a/sci-biology/raxml/raxml-7.2.5.ebuild b/sci-biology/raxml/raxml-7.2.5.ebuild
new file mode 100644
index 000000000000..6f3a6a52161b
--- /dev/null
+++ b/sci-biology/raxml/raxml-7.2.5.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/raxml/raxml-7.2.5.ebuild,v 1.1 2010/01/27 15:58:33 weaver Exp $
+
+EAPI="2"
+
+inherit 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-${PV}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="+threads"
+KEYWORDS="~amd64 ~x86"
+
+# mpi is not supported in version 7.2.2. mpi is enabled by adding -DPARALLEL to CFLAGS
+DEPEND="" # mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/RAxML-${PV}"
+
+src_prepare() {
+	sed -i -e 's/CFLAGS =/CFLAGS := ${CFLAGS}/' \
+		-e 's/CC = gcc/CC = '$(tc-getCC)'/' \
+		Makefile.* || die
+}
+
+src_compile() {
+	emake -f Makefile.gcc || die
+	emake -f Makefile.SSE3.gcc clean && emake -f Makefile.SSE3.gcc || die
+	if use threads; then
+		emake -f Makefile.PTHREADS.gcc clean && emake -f Makefile.PTHREADS.gcc || die
+		emake -f Makefile.SSE3.PTHREADS.gcc clean && emake -f Makefile.SSE3.PTHREADS.gcc || die
+	fi
+}
+
+src_install() {
+	dobin raxmlHPC raxmlHPC-SSE3 || die
+	if use threads; then dobin raxmlHPC-PTHREADS raxmlHPC-PTHREADS-SSE3 || die; fi
+}