commit: 3155495650f555369e58b58f54fc6766e9691f20 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Feb 11 12:20:48 2018 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Feb 11 12:20:48 2018 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=31554956
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 sci-biology/seqan/Manifest | 1 + .../seqan/files/seqan-2.4.0-fix-pthread.patch | 12 +++ sci-biology/seqan/metadata.xml | 11 ++- sci-biology/seqan/seqan-2.4.0.ebuild | 92 ++++++++++++++++++++++ 4 files changed, 112 insertions(+), 4 deletions(-) diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest index 634425a0843..d26b1ac375f 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 00000000000..b5e4b3642d4 --- /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 959160fe46b..077f6458a92 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>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> + <maintainer type="project"> + <email>[email protected]</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 00000000000..8b337e77e6b --- /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 +}
