sci-biology/vaal: Version BUmp

Package-Manager: portage-2.2.0_alpha163/cvs/Linux x86_64
Manifest-Sign-Key: 0x70EB7916

4 files changed, 73 insertions, 24 deletions

diff --git a/sci-biology/vaal/ChangeLog b/sci-biology/vaal/ChangeLog
index b7764f8287da..c435e0fe4092 100644
--- a/sci-biology/vaal/ChangeLog
+++ b/sci-biology/vaal/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/vaal
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/ChangeLog,v 1.10 2012/06/25 19:09:19 jlec Exp $
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/ChangeLog,v 1.11 2013/02/20 16:23:04 jlec Exp $
+
+*vaal-45166 (20 Feb 2013)
+
+  20 Feb 2013; Justin Lecher <jlec@gentoo.org> +vaal-45166.ebuild,
+  metadata.xml:
+  Version BUmp
 
 *vaal-42179 (25 Jun 2012)
 
diff --git a/sci-biology/vaal/Manifest b/sci-biology/vaal/Manifest
index cb25bfac7a51..33538a3b16b9 100644
--- a/sci-biology/vaal/Manifest
+++ b/sci-biology/vaal/Manifest
@@ -1,23 +1,24 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA512
+Hash: SHA256
 
-AUX vaal-1.2-as-needed.patch 905 RMD160 5daf6a4603fb729bac33ad54cbf5a79be65860bd SHA1 ffae4e00b6cb0497e87cd09857c62ebe19449c79 SHA256 6d097b3b72d394753e194974acf98a347e7e7046aaf865949aa551f0ee08a1f2
-AUX vaal-1.2-gcc-x86-no-autocast.patch 1877 RMD160 dbcac734c896600c89c7c2ab73abeb03374a0bad SHA1 607371fad2443a65151b15ad6f08d4462056415b SHA256 a365d038dffdf6ea1ece2a0e55426c436f457b3cb0e640345decb00f2849a285
-AUX vaal-1.2-respect-flags.patch 1838 RMD160 fe1464f977dfd1abe34c736e19990eab5f413655 SHA1 a4b83b2896e3c92bba6182e173f204f374dcd433 SHA256 42a1435657533c39ef9011be722ee217d0823c0f5802aaf2365136fddae49866
-AUX vaal-1.6-gcc47.patch 5516 RMD160 bb7da5ee61c3752531e1a6fc4c89756a45b41ba8 SHA1 327ef829288558cb2d8fb219d9fda0e56b79e51b SHA256 cbd9e5c1904a1392c1195258ebabb60a75ee6645bf3e25a45b4ebe2d4c42a6d9
-AUX vaal-1.6-respect-flags.patch 767 RMD160 de83d5978ae3931c72ecb952e165e6d965be7180 SHA1 ab7f29dfa3134432cf3a57c66a09d1c49071c97a SHA256 f23b40e845727cdc5241cc909ebcd89c2b6d612cebe4f21ac7211c53246c6131
-DIST VAAL.1.6.tgz 1096114 RMD160 d12115fe558831533e48570e7dd4c583e8ea4924 SHA1 ae490f7488374c468df1724b1a3eac64879c3e0c SHA256 4bfcd0825b14438ad72b9dbacc1e324d960bd25fc56b0d492bad59c9ff4205e6
-DIST VAAL_manual.doc 48128 RMD160 08d809c847f1842483ed653df9bb6ed5ee1d10a8 SHA1 836f8be0f0200358131c23174eeca5d2d7454a68 SHA256 08b662105e8db41b33ea5d6626b58d5a5d793b1dd40fdc663a7068d9abacdc83
-DIST vaal-42179.tar.gz 1126379 RMD160 b47e1e7517f889025858b303272c5c8a5efbc5db SHA1 7dc1340a0a6380a7967cd9f187b46afbb2205628 SHA256 1580cb3cd7706e681b43d10cfe497908e2d6c2228abcc2fc525b7c0df6d0c243
-EBUILD vaal-1.6.ebuild 1118 RMD160 bc17a1f95a9bc6dd10dfb8ff7d811d1d0447514a SHA1 df15a17339aaeadd3855d3b1204104591b310e30 SHA256 03ab4ec79facae3d73b25d2e29e961343dff6f28db80843685cac47455a5ee09
-EBUILD vaal-42179.ebuild 1046 RMD160 5b193e87e736f00211882382c875aa053f772fe6 SHA1 a5ac16ae167abe27f143b555114f35809e025bc3 SHA256 65dfd8ddee707fe0b8bdd6a51b924bff0dfe0bee380a307720024d5630a3a68d
-MISC ChangeLog 1796 RMD160 5127d46c3f765fc147896aa8bb6dcfb41c7f60d5 SHA1 28c95e51ec0d62ec43390a92d038100e025b9eb7 SHA256 942ab28b241008e15df09dc2caf9ac3b4eec6c7d025a733c2b263fd98e082b75
-MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
+AUX vaal-1.2-as-needed.patch 905 SHA256 6d097b3b72d394753e194974acf98a347e7e7046aaf865949aa551f0ee08a1f2 SHA512 efbe4aade5e415b689aa6cdddcf2ec23a64c46be6c4876c5ebacd3a820c95f46f12a2d4f5d3a210c55cefc0521f7070c0a37d975be882e022d06fe2276d93003 WHIRLPOOL 9ab2cced694387b835889c16a02eecfb3a3def995aa86f3d5c699299399c0a64ea9256bc1042a85ab1c5bcdc6df6e9701bee6ea69aadc316ba84299a6948c550
+AUX vaal-1.2-gcc-x86-no-autocast.patch 1877 SHA256 a365d038dffdf6ea1ece2a0e55426c436f457b3cb0e640345decb00f2849a285 SHA512 03ee1e8c4f891ef881d6d636383a62a95db22c8f3248b7dad152584332552a1f55a8754893060665c0710b687a1d07d9da6366a9350205fe2bbf8ba36fe9025e WHIRLPOOL 6a520a96877a919ea71b8c587b68c0290228a3ca80dd16fa1ed4cb7d105f979a2b02e8106fb66d7055e17b0f97b3795cab58c812e0241c9f6008b772061d804b
+AUX vaal-1.2-respect-flags.patch 1838 SHA256 42a1435657533c39ef9011be722ee217d0823c0f5802aaf2365136fddae49866 SHA512 d261b6e28b0fab6831bc3e24251f0672d9a8a7ccc1b5fafa83094c713965d0a4ea68a6854335f0d305b3eae91e0cdfef0cb8eff298ca72a2551180881307f1cd WHIRLPOOL 813dc25001bb82bd15b024e37c1e63be3a0baa7ad990918c41ef2a439e2393971f6ea98d682a9454fb9d1d80701a2ab38df931a6c80c7409bd7428e1bc741281
+AUX vaal-1.6-gcc47.patch 5516 SHA256 cbd9e5c1904a1392c1195258ebabb60a75ee6645bf3e25a45b4ebe2d4c42a6d9 SHA512 e05bd7906c197620ecf5300bcfc849b7bf9d25c8b3f4d0134f5a9e71f0f30f318a24769f81a835895752d1b0f2f98e96eef2cc4c6406a71720ac707748492c86 WHIRLPOOL 302fde231f5a38a94a543667cbd1abf8fb59f0624f2d5878a2aa2431a660cf9eb9de6b4e92751b545750f0c1fe52e614f06c7c6cfe0104ba6bca137ca73db6d0
+AUX vaal-1.6-respect-flags.patch 767 SHA256 f23b40e845727cdc5241cc909ebcd89c2b6d612cebe4f21ac7211c53246c6131 SHA512 f0638e8f8eac229c2ff9dbbbbf69dfa677841e306da978e2baca4bc3503f9b0e3e15e4b2187bc41c3be6b584fbd6ed4126786c2fb4f5924d849c3331196c909f WHIRLPOOL bd06f76c4a530aac4a1334572401d845be31ee3ba29dcfcd9b5521bd219d45234f380cc4f5e4df39a701fa5ae8c7e0d1fa133882a52abba9091632e1b1371090
+DIST VAAL.1.6.tgz 1096114 SHA256 4bfcd0825b14438ad72b9dbacc1e324d960bd25fc56b0d492bad59c9ff4205e6
+DIST VAAL_manual.doc 48128 SHA256 08b662105e8db41b33ea5d6626b58d5a5d793b1dd40fdc663a7068d9abacdc83 SHA512 4da21b6559659764e108c118773bd8ed365b67e3a22de52c7c13429979bb765e7f5d05955ce746a7a55e8d3a6baa752ad575289e71dfd7fb5b8b7207f5cff171 WHIRLPOOL 3a7432974921946e28cd037e47b79fd31631f7a7915a96589a8485b84a3296e1e7d8768e84f4f9086b2648e270f9f84f1e73261bb0b492b3fa7a6cc6fe36f175
+DIST vaal-42179.tar.gz 1126379 SHA256 1580cb3cd7706e681b43d10cfe497908e2d6c2228abcc2fc525b7c0df6d0c243 SHA512 2ddfd2a1394509badb917e808460f32492b0c56afe3a66dcf5b8ed588c17b9ef58fe4df8af14fc30286499092a71ae8887e2fcda25665a2dbb3373dcb12fed26 WHIRLPOOL 4654d0347a20fb03bf5cfcc976c22808031a6ce086490018519b3dc679d552e61af38544d6931e91be0fa2835ae3b9009b673885bc2ddcea7d49d009c8a1d839
+DIST vaal-45166.tar.gz 1142160 SHA256 a6aec3e5bd338d33c300b92c5d2b776dfc26ade91c6f10f14e6bb0047aa19429 SHA512 360a7a2000e832fcb2308bfee54d74f57c710ab2f10fb5544a48d09d59383be3da1b9e9dd4425236a3597d7fa2e6591fa30674cb5e2970fd722c406124829d07 WHIRLPOOL cfdde08342c227ca01fae5d687e51bd71e91b05bd808abd42a8640b90d61efb94ea972336e9a3aa1356439f0bfe14274d00f82ce2d6ee266efac43fcf9cc4b78
+EBUILD vaal-1.6.ebuild 1118 SHA256 03ab4ec79facae3d73b25d2e29e961343dff6f28db80843685cac47455a5ee09 SHA512 4073649404ed533b5130bf40272542701526e68ce93dc75a928e9bdda717e5d8d1a36824b3f4e34b5fc6d5692ac42923a4d8afbb5be92f1885c377dc4b5fa805 WHIRLPOOL de32e3278c3d4b803727cabfa1a7e1994ce2223e5101ac766e68a2d449b147d5f5457c68acdd2b64aab95a46288dd0c5f7647eb2a10123c36515e534dbd473a2
+EBUILD vaal-42179.ebuild 1046 SHA256 65dfd8ddee707fe0b8bdd6a51b924bff0dfe0bee380a307720024d5630a3a68d SHA512 b3723802f61404cc7b6f52c7e144ca35d11a57c32b21517680da6b99b252accf9700fa9ecda81b68521f12083d3c984963441bf40d03c8e9f57e1442158e606b WHIRLPOOL 3451a212d9b667d2541dd0e32bd7e9cc87000fe0e014ca8050f631133c645ef4ca8f6b1f8a3bf5c5bd587718f26ba99e48dd85c0148252314ea8451b900ff190
+EBUILD vaal-45166.ebuild 1045 SHA256 daac146813f7f7ba2664c661e1364f035a67583a3d8b314deb7fd17335678d60 SHA512 60fa5f959cec4b032ff4ee3373ac61ce76d7638a983d42d19e931b5ae0a375e76afdf114b72cd96c3555d7bee775c78392832a9ea8466ab3e50062c825a871bd WHIRLPOOL 9a5e22deaafe2252b2ea1872b12b4345b1fe3566a64203716d121ec3992a00c6786e0ed5713d2456d6055a109f31906e8e28d04702a87a3e5ef183f56f34700c
+MISC ChangeLog 1922 SHA256 e04f754fa6127c8061d0b966c23ea9e4fa4aa37c925aa1279da9bdee4e1fdcd2 SHA512 5328b5de9265cd1a2ae8b7c49f8922180ee6837ff7893cb2c317cbef9e827546af861da74531f92f0a8aef7b80092d1e0d9cf13a068b609192bdb25307a94962 WHIRLPOOL c8fde37292bbeef970ef6d53953b755bdc46737c9e3a36e54bb04a0eb2a738af422fafb5413f5333aff8eafe5332567a1b56fbf9a3c50b058c9cc114829c4fc1
+MISC metadata.xml 266 SHA256 98c7d1da8a728a1f1d796a79d51f25e4164e24048ec1aacbbf0ae2ffb171ff35 SHA512 879cdcca092d4c82b8c63672c91e08e7b01e81419d2c7c7b766de96ba2a32dd1e21c18968ed7172eec8604f52c92b19a31773f428bce9461d9b8190384680194 WHIRLPOOL 0f46288ab7090ad3da5b31816792427e4ad1a950e39a503bb406ebe8789cffedd9c85b46bfbf040fffb8aad443f512c28716a0a6436d0c06309155277060cdcd
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diff --git a/sci-biology/vaal/metadata.xml b/sci-biology/vaal/metadata.xml
index 3302123e5718..fc7c76942a10 100644
--- a/sci-biology/vaal/metadata.xml
+++ b/sci-biology/vaal/metadata.xml
@@ -1,9 +1,9 @@
 <?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>
+  <maintainer>
+    <email>weaver@gentoo.org</email>
+    <name>Andrey Kislyuk</name>
+  </maintainer>
+  <herd>sci-biology</herd>
 </pkgmetadata>
diff --git a/sci-biology/vaal/vaal-45166.ebuild b/sci-biology/vaal/vaal-45166.ebuild
new file mode 100644
index 000000000000..8bef5eb8e9c8
--- /dev/null
+++ b/sci-biology/vaal/vaal-45166.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/vaal-45166.ebuild,v 1.1 2013/02/20 16:23:04 jlec Exp $
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=yes
+
+inherit autotools-utils
+
+DESCRIPTION="A variant ascertainment algorithm that can be used to detect SNPs, indels, and other polymorphisms"
+HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd/"
+SRC_URI="
+	ftp://ftp.broad.mit.edu/pub/crd/VAAL/latest_source_code/${P}.tar.gz
+	ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL_manual.doc"
+
+LICENSE="Whitehead-MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="openmp"
+
+DEPEND=">=dev-libs/boost-1.41.0-r3"
+RDEPEND="${DEPEND}"
+
+DOCS=( "${DISTDIR}/VAAL_manual.doc" )
+
+src_prepare() {
+	sed \
+		-e '/COPYING/d' \
+		-i src/Makefile.am || die
+
+	sed \
+		-e 's:-ggdb::g' \
+		-e '/AC_OPENMP_CEHCK/d' \
+		-i configure.ac || die
+	autotools-utils_src_prepare
+}
+
+src_configure(){
+	local myeconfargs=( $(use_enable openmp) )
+	autotools-utils_src_configure
+}