sci-biology/seqan: Version BUmp

(Portage version: 2.2.14_rc1/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

4 files changed, 101 insertions, 2 deletions

diff --git a/sci-biology/seqan/ChangeLog b/sci-biology/seqan/ChangeLog
index 02a4845e6eca..eaf19ac1f317 100644
--- a/sci-biology/seqan/ChangeLog
+++ b/sci-biology/seqan/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/seqan
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/seqan/ChangeLog,v 1.4 2013/07/17 07:09:45 jlec Exp $
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/seqan/ChangeLog,v 1.5 2014/10/17 13:51:56 jlec Exp $
+
+*seqan-1.4.2 (17 Oct 2014)
+
+  17 Oct 2014; Justin Lecher <jlec@gentoo.org> +seqan-1.4.2.ebuild,
+  +files/seqan-1.4.2-include.patch, +files/seqan-1.4.2-shared.patch:
+  Version BUmp
 
   17 Jul 2013; Justin Lecher <jlec@gentoo.org> seqan-1.3.1-r1.ebuild:
   Add missing dep
diff --git a/sci-biology/seqan/files/seqan-1.4.2-include.patch b/sci-biology/seqan/files/seqan-1.4.2-include.patch
new file mode 100644
index 000000000000..5baee4d8ebc0
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-1.4.2-include.patch
@@ -0,0 +1,16 @@
+ core/include/seqan/index/index_qgram_openaddressing.h | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/core/include/seqan/index/index_qgram_openaddressing.h b/core/include/seqan/index/index_qgram_openaddressing.h
+index 4a6c2e6..8cc9a42 100644
+--- a/core/include/seqan/index/index_qgram_openaddressing.h
++++ b/core/include/seqan/index/index_qgram_openaddressing.h
+@@ -35,6 +35,8 @@
+ #ifndef SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H
+ #define SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H
+ 
++#include <smmintrin.h>
++
+ namespace SEQAN_NAMESPACE_MAIN
+ {
+ 
diff --git a/sci-biology/seqan/files/seqan-1.4.2-shared.patch b/sci-biology/seqan/files/seqan-1.4.2-shared.patch
new file mode 100644
index 000000000000..0f438ff07bce
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-1.4.2-shared.patch
@@ -0,0 +1,22 @@
+ util/cmake/SeqAnBuildSystem.cmake | 8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/util/cmake/SeqAnBuildSystem.cmake b/util/cmake/SeqAnBuildSystem.cmake
+index bcba2c0..d53cd01 100644
+--- a/util/cmake/SeqAnBuildSystem.cmake
++++ b/util/cmake/SeqAnBuildSystem.cmake
+@@ -144,10 +144,10 @@ macro (seqan_register_apps)
+     set (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -DSEQAN_ENABLE_DEBUG=1")
+ 
+     # enable static linkage for seqan apps
+-    if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW)
+-      set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
+-      set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
+-    endif ()
++#    if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW)
++#      set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
++#      set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
++#    endif ()
+ 
+     # Get all direct entries of the current source directory into ENTRIES.
+     file (GLOB ENTRIES
diff --git a/sci-biology/seqan/seqan-1.4.2.ebuild b/sci-biology/seqan/seqan-1.4.2.ebuild
new file mode 100644
index 000000000000..f1e36479061b
--- /dev/null
+++ b/sci-biology/seqan/seqan-1.4.2.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/seqan/seqan-1.4.2.ebuild,v 1.1 2014/10/17 13:51:56 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit cmake-utils flag-o-matic python-single-r1
+
+DESCRIPTION="C++ Sequence Analysis Library"
+HOMEPAGE="http://www.seqan.de/"
+SRC_URI="http://packages.${PN}.de/${PN}-src/${PN}-src-${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="${PYTHON_DEPS}
+	sci-biology/samtools"
+DEPEND="${RDEPEND}"
+
+#S="${WORKDIR}"/${P}/cmake
+
+PATCHES=(
+	"${FILESDIR}"/${P}-shared.patch
+	"${FILESDIR}"/${P}-include.patch
+)
+
+src_prepare() {
+	rm -f \
+		util/cmake/FindZLIB.cmake \
+		|| die
+	touch extras/apps/seqan_flexbar/README || die
+	sed \
+		-e "s:share/doc:share/doc/${PF}:g" \
+		-i docs/CMakeLists.txt util/cmake/SeqAnBuildSystem.cmake || die
+	cmake-utils_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DZLIB_INCLUDE_DIRS="${EPREFIX}"/usr/include
+	)
+	cmake-utils_src_configure
+}
+
+src_install() {
+	mkdir -p "${BUILD_DIR}"/docs/html || die
+	cmake-utils_src_install
+	chmod 755 "${ED}"/usr/bin/*sh || die
+}