sci-biology/seqan: Version bump to 2.4.0

* Add USE=tools option to install command-line tools

Closes: https://bugs.gentoo.org/618278
Package-Manager: Portage-2.3.24, Repoman-2.3.6

4 files changed, 112 insertions, 4 deletions

diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest
index 634425a08433..d26b1ac375fb 100644
--- a/sci-biology/seqan/Manifest
+++ b/sci-biology/seqan/Manifest
@@ -1,2 +1,3 @@
 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
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
+}