sci-biology/vaal: Version BUmp

Package-Manager: portage-2.2.0_alpha177/cvs/Linux x86_64
Manifest-Sign-Key: 0x8009D6F070EB7916

3 files changed, 56 insertions, 7 deletions

diff --git a/sci-biology/vaal/ChangeLog b/sci-biology/vaal/ChangeLog
index db7966fe00f9..651a8ce3bb13 100644
--- a/sci-biology/vaal/ChangeLog
+++ b/sci-biology/vaal/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/vaal
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/ChangeLog,v 1.12 2013/03/12 12:12:45 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/ChangeLog,v 1.13 2013/06/02 11:57:40 jlec Exp $
+
+*vaal-46233 (02 Jun 2013)
+
+  02 Jun 2013; Justin Lecher <jlec@gentoo.org> +vaal-46233.ebuild:
+  Version BUmp
 
   12 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
diff --git a/sci-biology/vaal/Manifest b/sci-biology/vaal/Manifest
index 20aaf859ab64..747afd061e83 100644
--- a/sci-biology/vaal/Manifest
+++ b/sci-biology/vaal/Manifest
@@ -1,5 +1,5 @@
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-Hash: SHA256
+Hash: SHA512
 
 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
@@ -10,15 +10,17 @@ DIST VAAL.1.6.tgz 1096114 SHA256 4bfcd0825b14438ad72b9dbacc1e324d960bd25fc56b0d4
 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
+DIST vaal-46233.tar.gz 1148052 SHA256 a1c27ae25583c1333c5169bb33a37cf461bc93b1c18c7e49f585c1cdc9e5a131 SHA512 7a6927d06e1788411063d38e446b7e3c93192e4322a33ea652855f72e550f35debcdb970b895f1fb8504411a54d9096f3dcf506faebd33d50eb033937e15a321 WHIRLPOOL e848bcd6b2dd0c0c52142a3d55acef6a98b816e37355d22386bf3a2fac21e1318a821a394ebd5851cd530aa9afb0d178debc3f74638ee0d0820209a0f432f59f
 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
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+EBUILD vaal-46233.ebuild 1045 SHA256 4e80f9a244e69c770b065a7e95b68f7a8bf2fec636365817f9f286ef7308f9a3 SHA512 0a4abd319528334fd1ea93e84a467d5f5d71244b2b21506ac072da9fd2a60093f2e9c4747e38f4a1683eff57ace9b7c76886411be279d1f5317cce5bbb4bf180 WHIRLPOOL ebb2b6666b4639fee8d6667e70e0843e9e458c3de1609d07005592f1a07b5e9c3676bd01b4bee6ef6badedc884f594ba3f99013ec041b1c988b249e7a4fc6584
+MISC ChangeLog 2172 SHA256 4800928662ffe7abc3fabdba8c8cc98c7490f23ffad02566f7844f1874e51204 SHA512 782226ee80f415ec646e05251ad86953affdd2a3fef343d1deafe221c19d7eb547caa8064947e1212d406440c5578506bac307e024afd79a965ba2ee64c70c50 WHIRLPOOL 4f16bd20c7c98f2421f1fe11f3c99d6cabd6cbf65594bb1dc08853cf675e15913582975b0063465eaca107c91446a8472e931c440feb8e84fd381b203f68a2e7
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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diff --git a/sci-biology/vaal/vaal-46233.ebuild b/sci-biology/vaal/vaal-46233.ebuild
new file mode 100644
index 000000000000..ae327c59596c
--- /dev/null
+++ b/sci-biology/vaal/vaal-46233.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-46233.ebuild,v 1.1 2013/06/02 11:57:40 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
+}