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-rw-r--r--sci-biology/vaal/ChangeLog8
-rw-r--r--sci-biology/vaal/Manifest5
-rw-r--r--sci-biology/vaal/files/vaal-1.6-respect-flags.patch12
-rw-r--r--sci-biology/vaal/vaal-1.6.ebuild37
4 files changed, 60 insertions, 2 deletions
diff --git a/sci-biology/vaal/ChangeLog b/sci-biology/vaal/ChangeLog
index d16a99ff8074..2e40d33271f1 100644
--- a/sci-biology/vaal/ChangeLog
+++ b/sci-biology/vaal/ChangeLog
@@ -1,6 +1,12 @@
# ChangeLog for sci-biology/vaal
# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/ChangeLog,v 1.4 2010/02/14 19:50:10 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/ChangeLog,v 1.5 2010/09/20 04:50:54 weaver Exp $
+
+*vaal-1.6 (20 Sep 2010)
+
+ 20 Sep 2010; Andrey Kislyuk <weaver@gentoo.org> +vaal-1.6.ebuild,
+ +files/vaal-1.6-respect-flags.patch:
+ Version bump. Addresses boost problems and compilation issues
*vaal-1.2-r1 (14 Feb 2010)
diff --git a/sci-biology/vaal/Manifest b/sci-biology/vaal/Manifest
index b60c59372524..29abbeb21b71 100644
--- a/sci-biology/vaal/Manifest
+++ b/sci-biology/vaal/Manifest
@@ -1,8 +1,11 @@
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-respect-flags.patch 789 RMD160 e0143e9bf68eb5022d42c97ee52d12ae2a722f61 SHA1 0fea63571d064cac3c8430486ad0daf37aa42171 SHA256 1756741a5e9aa46cf7bb05ebfa40c5fb81f5d36f14ca491d6e096aad3a12244b
DIST VAAL.1.2.tgz 978333 RMD160 f81c1a33348e7c2ef2a6b07c1ceeeda564b9b521 SHA1 f51a4000149cbd9ae674ee0d7781c27aee6e31a9 SHA256 cfb9d73fd4ac5720f65b54e7f763e28a503d65c61269939d5f43dbf88dd17375
+DIST VAAL.1.6.tgz 1096114 RMD160 d12115fe558831533e48570e7dd4c583e8ea4924 SHA1 ae490f7488374c468df1724b1a3eac64879c3e0c SHA256 4bfcd0825b14438ad72b9dbacc1e324d960bd25fc56b0d492bad59c9ff4205e6
DIST VAAL_manual.doc 48128 RMD160 08d809c847f1842483ed653df9bb6ed5ee1d10a8 SHA1 836f8be0f0200358131c23174eeca5d2d7454a68 SHA256 08b662105e8db41b33ea5d6626b58d5a5d793b1dd40fdc663a7068d9abacdc83
EBUILD vaal-1.2-r1.ebuild 1097 RMD160 67eef005074040c7c9e0192147cbbeff02c865c4 SHA1 67e80bb076583cd173b87c0c5028fad4cad47e59 SHA256 ca425d9f49cc25f8837a058cc760ecf27a892fe7cb702ba53171ec333c69e75a
-MISC ChangeLog 851 RMD160 d94de44d7f7791483a15a9f78c53d857d2be0a6e SHA1 2dc2bf07bf013750e8e36f435080bffcb8058fc0 SHA256 4c6b2dc97cf9f2e3183de2a1c4d7de56e9b80c9d666e51fc83581456d20cf299
+EBUILD vaal-1.6.ebuild 909 RMD160 44aa17fa766bc1e34a103884226b79a3523136de SHA1 0a07b68aadbc25d6d75c39da519d0e7d04fa6cee SHA256 a60c7ea07c8e076337ba3e7522bbecd8335c06adb225ee66533aa054353ab08b
+MISC ChangeLog 1048 RMD160 dd645b401620d6597bb2116916dce5f7392dd447 SHA1 8108f114ddc8a918e08978a79967bc9c43c13cff SHA256 708813c8f2c595fe5851edeec6fd0f50a04e3ef2b846e80cfefc584c77440444
MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
diff --git a/sci-biology/vaal/files/vaal-1.6-respect-flags.patch b/sci-biology/vaal/files/vaal-1.6-respect-flags.patch
new file mode 100644
index 000000000000..c17910c2ce6a
--- /dev/null
+++ b/sci-biology/vaal/files/vaal-1.6-respect-flags.patch
@@ -0,0 +1,12 @@
+diff -dur vaal-33805.orig/configure.ac vaal-33805/configure.ac
+--- vaal-33805.orig/configure.ac 2010-09-20 04:37:49.858059826 +0000
++++ vaal-33805/configure.ac 2010-09-20 04:39:41.178059477 +0000
+@@ -14,7 +14,7 @@
+ AC_OPENMP
+ AC_OPENMP_CEHCK
+
+-CXXFLAGS=" -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote ."
++CXXFLAGS=" ${CXXFLAGS} -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote ."
+
+ OS_RELEASE="`uname -r`"
+ AC_SUBST(CXXFLAGS)
diff --git a/sci-biology/vaal/vaal-1.6.ebuild b/sci-biology/vaal/vaal-1.6.ebuild
new file mode 100644
index 000000000000..9d6c01769235
--- /dev/null
+++ b/sci-biology/vaal/vaal-1.6.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/vaal-1.6.ebuild,v 1.1 2010/09/20 04:50:54 weaver Exp $
+
+EAPI="2"
+
+inherit base autotools
+
+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/VAAL.${PV}.tgz
+ ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL_manual.doc"
+
+LICENSE="Whitehead-MIT"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=">=dev-libs/boost-1.41.0-r3"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-respect-flags.patch
+)
+
+S="${WORKDIR}/vaal-33805"
+
+src_prepare() {
+ base_src_prepare
+ eautoreconf
+}
+
+src_install() {
+ einstall || die
+ insinto /usr/share/doc/${PF}
+ doins "${DISTDIR}/VAAL_manual.doc"
+}