gentoo resync : 11.02.2018

6 files changed, 206 insertions, 5 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index e15ec4201e57..9a5f4f97aa06 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest
index 098e20d47def..8163dbb4a085 100644
--- a/sci-biology/seqan/Manifest
+++ b/sci-biology/seqan/Manifest
@@ -1,9 +1,13 @@
 AUX seqan-1.4.2-buildsystem.patch 870 BLAKE2B 2b3e32e4bea47caf6165e1c0ab89cdadf1e4d4756bb3ddd77b943b89a9366fb28d49dfdc22d69d5c431f78a83fc73b20c486085804a153c987020b3e28120b20 SHA512 d769eb4137c8c0ddb7137ecfdb0673ba8648ae720673848cbb473a0c80d479b6e5c564c12f1a9dd01953d955605eb2f273e04808ae50058c565e997381c3f748
 AUX seqan-1.4.2-include.patch 552 BLAKE2B f8d67014e59751616227471995254684b3edfacacfb455099f99c719f5602c88f0d106df01354921557d3324f77e03934606f698801516bc8432837c6211b67e SHA512 b02ab4fe49a511494134e44855d865f0ff210392810970834deb304499b5017764ed1c04d8f8dbfb513c333ac302946e5c72c9160cd38a5ef5ad095a865cb6d0
 AUX seqan-1.4.2-shared.patch 974 BLAKE2B e46b6b61c4927ca36c53e68e39c77eb5d983221dd074040a8911a7d7dfb04d2fb4c4ded0f3c9b6d90082a26f704654daa1d2b70e547b9ad657cc48bb96fc435b SHA512 a509c243244b6b40b26700a73be267558ceb17c4e0079f3eca606835ecfe8d1417b88fd37719ca9cf226e6d2d33ee3e22790b20e39a86a300f722eb186cabaad
+AUX seqan-2.4.0-fix-pthread.patch 541 BLAKE2B 16d42c72d6ea0654ba6727ce1007b89d3fc76141320f5a71cfd0fe102b8e511ccb36d48e021baf0928ac8857e97f6addde3f15f4f0577c531285027f23f5eea8 SHA512 f8a3df0892a81a65562dbd85f0945e5722df524e07b9949f860df4e0f07c285df3a48a112c8e1e5dca28a97c219dc9feed677e803ec5d3964216f7052b6f431b
 AUX seqan.pc.in 263 BLAKE2B ffd2a2c1ac74af7bc6b33c5959792551447ee61fe87fbb8bc6966ad44c33ae5bd512e836bc67175a3bf1895554364e48fcfea207f94f18ef72b7eae74fbe82d5 SHA512 bde1c89624284a37dac1a8717049a3b14340a2543003d9cf8406bddf4033541b65b617b802b18c80b2c7733d55ad9d7484bd85fdc927582363885da6d0210af7
 DIST seqan-src-1.4.2.tar.gz 120601994 BLAKE2B 62de2f961ba3c7c564090d746877d2b0b94ec7967c56f28786a286160770e66f0a8f08aacbe76d828cf429f92f0aa640ab29f5220297686979df9b7e9f9a0408 SHA512 dbb56167c507b70111619a414054d9e70f1db42507bbfdf9e40c5dcbbe9489ad4187d882e638a675e96551c860c08f8203c929c4c9a558b19ea7d6059f50492a
 DIST seqan-src-2.2.0.tar.gz 110936119 BLAKE2B be41f266e140ec5992f7e9e507659dc7902aad0e0dd17e6a8c6c9ef0b11f690454a771ba10a5998ccf70e2e50ef9b24904ebf537d982b2cbc68963c004097614 SHA512 1097372976ec9c86baa3787ac38aa4fde3a3e153d81c22435e6a12df87d8063165f27406de33851bffadd904b0ac4ea579a28625cff6257fe8c14d906f408421
+DIST seqan-v2.4.0.tar.gz 109626901 BLAKE2B a10b5ee9a95667f560a8c2aec3808131f5f838f3c07d56584f4b29e9622912bf3d00b958b02db7c9d62dd52d9d08a171abcccef7f50cddf0407538168cf2c592 SHA512 f92cfc97304581920850c5d49fe4336f7c3855e99c3bcb035b6172fa7307e08e6f06fb06d1cd8f5b447c3220fc7f669684fbfe25641b43e9f6953999cf9ddd4b
 EBUILD seqan-1.4.2-r1.ebuild 1961 BLAKE2B 8bd6fbfbc385169de7b230a7f895132968f70f96e1869e760379618d84ac1c8c0028eba27750d9dd64ccf0ac7e97f0a2f2ddf76f1851a6b6e0d112f52acfed4c SHA512 abbfc75ee90a12ffb200a02fb713dcd8098e040b79c2a204155a4e5c167966f829b17e6f5bc86752978f1ec2e0f84a474fbc77db49e4e44a6e5bd7bdbcfe6761
 EBUILD seqan-2.2.0-r1.ebuild 2667 BLAKE2B d261655308170cc44243c759a280ec39bb203f35dadf14518ac12cb940a78197d356bd3dd8fcdaa0e7d7887bc01108b81d62e468b606065c7fb93d13264c0503 SHA512 6221563c1e5b4332d66f1524b856ef87da90aa730907c3e2427a7ab18493f381eeffc7ea506690131cfecc3f3f692eb447d008dede764cbd5b11475a738f0289
-MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
+EBUILD seqan-2.4.0.ebuild 1917 BLAKE2B c53b1c51fd7b8a1c1498f5b2072f26a7829545f626fef177e0e64bc488784f7b9273c2f101db4c045203b3198aa6f37fa6f3226c633575815fbb95174ed5d30a SHA512 6f17b5d2d3be7a19fadcad798f0328fe467bc811d0a931c7b43df87fe23d17ebf2fb48aa197b838c9756bf9f3af7eaa04d346b0b5a05b03b28d03e4e80400c71
+EBUILD seqan-9999.ebuild 1860 BLAKE2B 745e69b7a80868f3faf45a6dfc9727835c8482737b3902a9e0f809a456ce5b3335d821d1106579da01fa495bc3df1caf222f425e41e172479b7de4e4a6e6a2b4 SHA512 3da317388c84933b817705825385c20c3673208c9a3fa1867078f7aea6a9959c6db3b8463cc3713d728180e30093cb1e30220072866305ac58f7b3de6b412f83
+MISC metadata.xml 372 BLAKE2B d620401f1aab9be80ddb6dc7abe737fd3e6322c560136e2c3b33d9246beca2986b4d91225b506e8c3035550994c3f714a11c0d8b17efd30c29278002d4eb7a12 SHA512 ae6c49e7e45c0ce4dd4fe27d21c5376c6fb8d7bfd2f98b7775f4689811680fa92c0b71ac0db70f6969660c4aee344f710ef752a467d6d46dd83aa47386d2ec17
diff --git a/sci-biology/seqan/files/seqan-2.4.0-fix-pthread.patch b/sci-biology/seqan/files/seqan-2.4.0-fix-pthread.patch
new file mode 100644
index 000000000000..b5e4b3642d42
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-2.4.0-fix-pthread.patch
@@ -0,0 +1,12 @@
+--- a/util/cmake/seqan-config.cmake
++++ b/util/cmake/seqan-config.cmake
+@@ -307,7 +307,8 @@
+ 
+ # some OSes don't link pthread fully when building statically so we explicitly include whole archive
+ if (UNIX AND NOT APPLE)
+-    set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,--whole-archive -lpthread -Wl,--no-whole-archive")
++    find_package (Threads)
++    set (SEQAN_LIBRARIES ${SEQAN_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT})
+ endif ()
+ 
+ if ((${CMAKE_SYSTEM_NAME} STREQUAL "FreeBSD") OR (${CMAKE_SYSTEM_NAME} STREQUAL "OpenBSD"))
diff --git a/sci-biology/seqan/metadata.xml b/sci-biology/seqan/metadata.xml
index 959160fe46b1..077f6458a927 100644
--- a/sci-biology/seqan/metadata.xml
+++ b/sci-biology/seqan/metadata.xml
@@ -1,8 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<use>
+		<flag name="tools">Build and install SeqAn commandline tools, such as the Yara aligner</flag>
+	</use>
 </pkgmetadata>
diff --git a/sci-biology/seqan/seqan-2.4.0.ebuild b/sci-biology/seqan/seqan-2.4.0.ebuild
new file mode 100644
index 000000000000..8b337e77e6be
--- /dev/null
+++ b/sci-biology/seqan/seqan-2.4.0.ebuild
@@ -0,0 +1,92 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+: ${CMAKE_MAKEFILE_GENERATOR:=ninja}
+PYTHON_COMPAT=( python2_7 )
+
+inherit cmake-utils multibuild python-any-r1 toolchain-funcs
+
+DESCRIPTION="C++ Sequence Analysis Library"
+HOMEPAGE="http://www.seqan.de/"
+
+if [[ ${PV} == *9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/seqan/seqan.git"
+	EGIT_BRANCH="develop"
+else
+	SRC_URI="https://github.com/seqan/seqan/archive/seqan-v${PV}.tar.gz"
+	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+	S=${WORKDIR}/seqan-seqan-v${PV}
+fi
+
+LICENSE="BSD GPL-3"
+SLOT="0"
+IUSE="cpu_flags_x86_sse4_1 doc tools"
+REQUIRED_USE="cpu_flags_x86_sse4_1"
+
+RDEPEND="
+	app-arch/bzip2:=
+	sys-libs/zlib:=
+	!!sci-biology/seqan:2.0
+	!!sci-biology/seqan:2.1
+	!!sci-biology/seqan:2.2"
+DEPEND="
+	${RDEPEND}
+	doc? (
+		$(python_gen_any_dep 'dev-python/sphinx[${PYTHON_USEDEP}]')
+		${PYTHON_DEPS}
+	)"
+
+PATCHES=( "${FILESDIR}"/${PN}-2.4.0-fix-pthread.patch )
+
+python_check_deps() {
+	use doc && has_version "dev-python/sphinx[${PYTHON_USEDEP}]"
+}
+
+pkg_setup() {
+	if [[ ${MERGE_TYPE} != binary ]]; then
+		use doc && python-any-r1_pkg_setup
+		use tools && tc-check-openmp
+
+		MULTIBUILD_VARIANTS=(
+			$(usev tools)
+			library
+		)
+	fi
+}
+
+src_configure() {
+	my_configure() {
+		local mycmakeargs=( -DCMAKE_INSTALL_DOCDIR="share/doc/${PF}" )
+		case "${MULTIBUILD_ID}" in
+			tools)
+				mycmakeargs+=(
+					-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_APPS
+					-DSEQAN_NO_DOX=ON
+				)
+				;;
+			library)
+				mycmakeargs+=(
+					-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY
+					-DSEQAN_NO_DOX=$(usex !doc)
+				)
+				;;
+			*)
+				die "${MULTIBUILD_ID} is not recognized"
+				;;
+		esac
+		cmake-utils_src_configure
+	}
+	multibuild_foreach_variant my_configure
+}
+
+src_compile() {
+	multibuild_foreach_variant cmake-utils_src_compile
+}
+
+src_install() {
+	multibuild_foreach_variant cmake-utils_src_install
+}
diff --git a/sci-biology/seqan/seqan-9999.ebuild b/sci-biology/seqan/seqan-9999.ebuild
new file mode 100644
index 000000000000..0005819ff4d3
--- /dev/null
+++ b/sci-biology/seqan/seqan-9999.ebuild
@@ -0,0 +1,90 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+: ${CMAKE_MAKEFILE_GENERATOR:=ninja}
+PYTHON_COMPAT=( python2_7 )
+
+inherit cmake-utils multibuild python-any-r1 toolchain-funcs
+
+DESCRIPTION="C++ Sequence Analysis Library"
+HOMEPAGE="http://www.seqan.de/"
+
+if [[ ${PV} == *9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/seqan/seqan.git"
+	EGIT_BRANCH="develop"
+else
+	SRC_URI="https://github.com/seqan/seqan/archive/seqan-v${PV}.tar.gz"
+	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+	S=${WORKDIR}/seqan-seqan-v${PV}
+fi
+
+LICENSE="BSD GPL-3"
+SLOT="0"
+IUSE="cpu_flags_x86_sse4_1 doc tools"
+REQUIRED_USE="cpu_flags_x86_sse4_1"
+
+RDEPEND="
+	app-arch/bzip2:=
+	sys-libs/zlib:=
+	!!sci-biology/seqan:2.0
+	!!sci-biology/seqan:2.1
+	!!sci-biology/seqan:2.2"
+DEPEND="
+	${RDEPEND}
+	doc? (
+		$(python_gen_any_dep 'dev-python/sphinx[${PYTHON_USEDEP}]')
+		${PYTHON_DEPS}
+	)"
+
+python_check_deps() {
+	use doc && has_version "dev-python/sphinx[${PYTHON_USEDEP}]"
+}
+
+pkg_setup() {
+	if [[ ${MERGE_TYPE} != binary ]]; then
+		use doc && python-any-r1_pkg_setup
+		use tools && tc-check-openmp
+
+		MULTIBUILD_VARIANTS=(
+			$(usev tools)
+			library
+		)
+	fi
+}
+
+src_configure() {
+	my_configure() {
+		local mycmakeargs=( -DCMAKE_INSTALL_DOCDIR="share/doc/${PF}" )
+		case "${MULTIBUILD_ID}" in
+			tools)
+				mycmakeargs+=(
+					-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_APPS
+					-DSEQAN_NO_DOX=ON
+				)
+				;;
+			library)
+				mycmakeargs+=(
+					-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY
+					-DSEQAN_NO_DOX=$(usex !doc)
+				)
+				;;
+			*)
+				die "${MULTIBUILD_ID} is not recognized"
+				;;
+		esac
+		cmake-utils_src_configure
+	}
+	multibuild_foreach_variant my_configure
+}
+
+src_compile() {
+	multibuild_foreach_variant cmake-utils_src_compile
+}
+
+src_install() {
+	multibuild_foreach_variant cmake-utils_src_install
+}