sci-biology/mafft: version Bump

Package-Manager: portage-2.2.0_alpha179/cvs/Linux x86_64
Manifest-Sign-Key: 0x8009D6F070EB7916

3 files changed, 73 insertions, 5 deletions

diff --git a/sci-biology/mafft/ChangeLog b/sci-biology/mafft/ChangeLog
index f392d0624a36..424e38021ece 100644
--- a/sci-biology/mafft/ChangeLog
+++ b/sci-biology/mafft/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/mafft
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/ChangeLog,v 1.16 2013/06/06 08:09:28 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/ChangeLog,v 1.17 2013/06/12 13:42:20 jlec Exp $
+
+*mafft-7.046 (12 Jun 2013)
+
+  12 Jun 2013; Justin Lecher <jlec@gentoo.org> +mafft-7.046.ebuild:
+  version Bump
 
   06 Jun 2013; Justin Lecher <jlec@gentoo.org> Manifest:
   Update to new upstream tarball
diff --git a/sci-biology/mafft/Manifest b/sci-biology/mafft/Manifest
index 2db710518980..33ae7a819bd3 100644
--- a/sci-biology/mafft/Manifest
+++ b/sci-biology/mafft/Manifest
@@ -11,6 +11,7 @@ DIST mafft-7.037-without-extensions-src.tgz 371344 SHA256 9c4688e55d8f47202ea8fd
 DIST mafft-7.040-without-extensions-src.tgz 373505 SHA256 3c2014c49d31c9f435bb14ce06381f915cd36ec4407c3975e0469ed2fdcee0f8 SHA512 4a1579d1030c2ede68111cc6e39749dfbb6e392278c41d4ea8219d9821ccc1fa458940feca0e8c40761a97116df6b5da97a4690666a6a61bf6cc470caa49edf5 WHIRLPOOL f022e9439043a268ceb83e073ac035623ed0918cf486a3a38dcc27da6ac55dfe97b6683fb55be71d5e41eeb9bcda6433cd822eeba692ed961328b432c51e7ca6
 DIST mafft-7.043-without-extensions-src.tgz 379777 SHA256 cb0dcf9988732ddd4510eb310e63c0b481bb09e90c91d4624e566edc23dca0ad SHA512 ab7527a1decdb528d7b61f454d5d5564b0a1fbf0f54f03f9d59c264c9bcabb689ba51fbf1c82e9578eae5b5463edb901999f89e5eabf6926689b320c20bdcdfa WHIRLPOOL c2e12afd8d3c89585fcb7abe3537558856e3fb25cf03a3c231c446cc5110a1da9cc192fb9d15918f0ed380ba49fef67c8e9e358a2e892c7975da6b510d318455
 DIST mafft-7.045-without-extensions-src.tgz 380217 SHA256 afcd4c13ebd4cde3e6890c5fc5098922e3312e21096d5a62df32bfcdf48b4cdb SHA512 6d0466c2a0d7813503c5c05e33cc59cb8fde3f9efc5b58b8bcf92bf82c964a5cbb6f140134c9080ed684b64643f410735073d37a19b812806268837d280b8f0c WHIRLPOOL 2f02668901c829b1731ceb67ab4365bed204025f6ffa7f0f60a7e57d7a90ce31dc835856e947f7b2b3d0ed6067add69964c081092fed638c1a6f6518597e6b17
+DIST mafft-7.046-without-extensions-src.tgz 380226 SHA256 01eba5cfd8bb37dc6830b4cd3b7bb74c2892d3d06f8b2da23886ef5c27404b3e SHA512 305f7ae0d110364e8197be2c8fa87094df062cbdf9726d32ce96ded2122a51ffe3ac6359bbf45cfc57bd13f55c0a02a06eac757eed860317ff27358c393cf77e WHIRLPOOL de67470bd0e0c295459364e858b7b80b6d1532b57cb8d4913296ac6c75580f01b247d936aa198a8346aaa9859fb3122d29c486fa89e8f707c7599ba3d7ec82f2
 EBUILD mafft-6.240-r1.ebuild 1004 SHA256 70cb92f9d6a0a9e6dab1e5bae147191ffbe54c4517df9d2efd859cceb6df41e6 SHA512 40ddd365b68b82446ba3931525ad1d1d91a1e442af2d0e8efa20448b69b3d79b0fb8c24adffadd5cbd2e1e10ff32643af7eb6058a53a9b28bfbaa17f97f1ca2f WHIRLPOOL d2d0a212d863f125bd866de9003c05ad3f5a92434550cd75567ce572cc50c25d12bbb18019040be2f6a686d28ce609e27537038198f678eb60186a80a06a7fe1
 EBUILD mafft-6.707.ebuild 998 SHA256 ca548edebc7b720371b27b456d63c806141c2d6337d1436cd973b6c5261581bc SHA512 b8067e0e56d0bec8a2f2af3d11d03cd92db1432f1c1b6bfe680ee7d9958a537b3f6f60219c813b74c753d7d7f353495164c947fe953f9113997aedd03a2ca8f6 WHIRLPOOL a0781c7b82d4fb07837ff00526cc748c4102492166449b6b0274381a42f364236efbce58c46561fdf120a81c0d4bd0a7b94a761034c6c2ec6128a1ae1858070d
 EBUILD mafft-6.811.ebuild 1166 SHA256 a83f99b61abe2933ec68b7f0bc65708c36670b658dc225e470a693817e73fdfa SHA512 ab298b855b637f183f7f5869fe528cca32e9dfda5fe978fe7d6e189141aed5a1cfcbf0cd803cda98b747c35d8366376d03ec548ef8db0f41780b550a774bc86f WHIRLPOOL f1bbe9eceb8d495b1cfad1069c7531b3c528934d456b225583c36ef357dcbfe5b8b941315c20a98d1675cf46b1b1916ec1eb9c3fb56d0b53e406f861f823b20b
@@ -18,12 +19,13 @@ EBUILD mafft-7.037.ebuild 1188 SHA256 9db220c35a72637ffe20a1d0f26d15877036ee25be
 EBUILD mafft-7.040.ebuild 1840 SHA256 e32d74d2f1d05672daac4e8b5eb05dd27086d85cd3c1dcdbe960ea04d5c34c7a SHA512 14038c3c70103aa69393344c6e486d288b9750c83dcac16789253557d9ed2cd5aea1c56bb80960bf0c4a5a43641f9f3b937c7a0a8fd713892ebc5d04e57337cd WHIRLPOOL acb0279404cd71a3caa8458881b9fe9de1c828ebf17819cdf6d1ff47603440b5fc4dbbdb4664ba2511498fa35c99dd1d2b9d0321a454a65d39d8903d1252a7e4
 EBUILD mafft-7.043.ebuild 1843 SHA256 50105f72dea8b0ea4d21e88a2e24f30d192ccaed5723e2c5d0455bc1034a379f SHA512 2e1544da85dfa08ec63c02e1a8efd842388a92e4aad0dc07dae0b86e9560d893bb7aa6f3355b08c13ed3070bbd22aa8dcc85b48a646dafef8aae84901867b5fd WHIRLPOOL cdbe60eee4f932d8252bbd4e324e159d248f24694cd6af84d98b4f8b6b9e1e3b1741c635a63c4b78490e24303806fa980dc455031da76588f4b950b00785d023
 EBUILD mafft-7.045.ebuild 1881 SHA256 547f1942e788f73bd77e06186e9e346c23e83a60c331d107e4bb388f04918dee SHA512 fed739530adc0e6702bbe6897c2ebb1f031d92e964e17adbb2417ee00f2d9bfe19322bc44d947eecfdeb939e787716619df4f1fa5f0e36474eed4bb47be2731a WHIRLPOOL 53c0245cd106eaa88e0b2c046b01e0588f08b422323bf40fc38ee661231a47118e389acc74c3848b557af7a9f9cfba4b5ef03ce8e0ba5653bdfe902fc4376af5
-MISC ChangeLog 2886 SHA256 7b2040aa0ae9be385c91b8209bad13e2590172fc7986f4c7fd114bae937ce7b3 SHA512 f9c2b020feb589d1486ae02c93ce863fbcb0fcc2838af46a24f7e66e73d93db1dc3708c4a2ec4684eba30f1dd6ebe9f6dad0cd4cdc68ddea3a2a0b45f5f61723 WHIRLPOOL 32eb647d81edd01aaf591c27b46cbb85fc59b35304cf1fa880c3545331314317d2e526a15446dd5f17d39f0120c55a4f85c818c5dd8d557e6fae2ce1f36a3804
+EBUILD mafft-7.046.ebuild 1881 SHA256 975f6ef7ab7ce88af52fda3e12f74772a70cfc77d485a3c002a2fc92cb958bdf SHA512 fd5638a81afa72f94b03c3686d5e09b902c15d593eaa7da9f3f6395bf3a51057724d45c2688bbadfbd59a6666a22b12dbdc99f07ddda15344a9eda7999e9d68b WHIRLPOOL 77dfa0f72d0debf2818f03f731bbf6edcda69393f870238defba98c00d0ca0f6d7e6d0a2367bae78432ea71176321f4cbdb6fab8b36c2d389a7aeb86636edc3c
+MISC ChangeLog 2998 SHA256 b27f7fcbbf719dd3618ff75324362ea17075c52ee8a7e9e639503615614ff7a4 SHA512 a5c31f147a508c238d3964e3450299b3b9b86065ec848032fc7829416849e0faaeb07ed61f985937315a38c24684f0013432d6efa5da537eb917ecc5dc22297f WHIRLPOOL 9584a7bfc1baf849fd3133694003f7d1e4bf7e5875067f3997c7c8b0ad3b23896b43a86d634d6765d501e2b0b6ae6c6d47f5169b1cc781df3647184bc4a02ec0
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.20 (GNU/Linux)
 
-iEYEAREKAAYFAlGwQ7kACgkQgAnW8HDreRbRXwCeMwDJkW0ZXq+iobur4rZM+REf
-FgMAn2a2zW67HIooeC8VurNHwzTv+tSl
-=4nok
+iEYEAREKAAYFAlG4er0ACgkQgAnW8HDreRZ9eQCfTWmiALN6edbmCLAn7STbyouy
+z9kAn2p6eOB7g8GLYA0+TcGbxmK85tYC
+=Vgae
 -----END PGP SIGNATURE-----
diff --git a/sci-biology/mafft/mafft-7.046.ebuild b/sci-biology/mafft/mafft-7.046.ebuild
new file mode 100644
index 000000000000..121e8324c8c5
--- /dev/null
+++ b/sci-biology/mafft/mafft-7.046.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/mafft-7.046.ebuild,v 1.1 2013/06/12 13:42:20 jlec Exp $
+
+EAPI=5
+
+inherit eutils flag-o-matic multilib toolchain-funcs
+
+EXTENSIONS="-without-extensions"
+
+DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
+HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html"
+SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~x64-macos ~x86-macos"
+IUSE="threads"
+
+S="${WORKDIR}"/${P}${EXTENSIONS}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PN}-7.037-respect.patch
+	use threads && append-cppflags -Denablemultithread
+	sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile || die
+	sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed"
+}
+
+src_compile() {
+	pushd core > /dev/null || die
+	emake \
+		$(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \
+		PREFIX="${EPREFIX}"/usr \
+		CC="$(tc-getCC)" \
+		CFLAGS="${CFLAGS}"
+	popd > /dev/null || die
+}
+
+src_test() {
+	export MAFFT_BINARIES="${S}"/core
+	cd test || die
+	bash ../core/mafft sample > test.fftns2 || die
+	bash ../core/mafft --maxiterate 100  sample > test.fftnsi || die
+	bash ../core/mafft --globalpair sample > test.gins1 || die
+	bash ../core/mafft --globalpair --maxiterate 100  sample > test.ginsi || die
+	bash ../core/mafft --localpair sample > test.lins1 || die
+	bash ../core/mafft --localpair --maxiterate 100  sample > test.linsi || die
+
+	diff test.fftns2 sample.fftns2 || die
+	diff test.fftnsi sample.fftnsi || die
+	diff test.gins1 sample.gins1 || die
+	diff test.ginsi sample.ginsi || die
+	diff test.lins1 sample.lins1 || die
+}
+
+src_install() {
+	pushd core
+	emake PREFIX="${ED}usr" install
+	popd
+	dodoc readme
+}