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commit: 3155495650f555369e58b58f54fc6766e9691f20 |
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Author: David Seifert <soap <AT> gentoo <DOT> org> |
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AuthorDate: Sun Feb 11 12:20:48 2018 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Sun Feb 11 12:20:48 2018 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=31554956 |
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|
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sci-biology/seqan: Version bump to 2.4.0 |
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|
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* Add USE=tools option to install command-line tools |
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|
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Closes: https://bugs.gentoo.org/618278 |
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Package-Manager: Portage-2.3.24, Repoman-2.3.6 |
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|
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sci-biology/seqan/Manifest | 1 + |
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.../seqan/files/seqan-2.4.0-fix-pthread.patch | 12 +++ |
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sci-biology/seqan/metadata.xml | 11 ++- |
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sci-biology/seqan/seqan-2.4.0.ebuild | 92 ++++++++++++++++++++++ |
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4 files changed, 112 insertions(+), 4 deletions(-) |
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|
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diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest |
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index 634425a0843..d26b1ac375f 100644 |
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--- a/sci-biology/seqan/Manifest |
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+++ b/sci-biology/seqan/Manifest |
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@@ -1,2 +1,3 @@ |
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DIST seqan-src-1.4.2.tar.gz 120601994 BLAKE2B 62de2f961ba3c7c564090d746877d2b0b94ec7967c56f28786a286160770e66f0a8f08aacbe76d828cf429f92f0aa640ab29f5220297686979df9b7e9f9a0408 SHA512 dbb56167c507b70111619a414054d9e70f1db42507bbfdf9e40c5dcbbe9489ad4187d882e638a675e96551c860c08f8203c929c4c9a558b19ea7d6059f50492a |
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DIST seqan-src-2.2.0.tar.gz 110936119 BLAKE2B be41f266e140ec5992f7e9e507659dc7902aad0e0dd17e6a8c6c9ef0b11f690454a771ba10a5998ccf70e2e50ef9b24904ebf537d982b2cbc68963c004097614 SHA512 1097372976ec9c86baa3787ac38aa4fde3a3e153d81c22435e6a12df87d8063165f27406de33851bffadd904b0ac4ea579a28625cff6257fe8c14d906f408421 |
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+DIST seqan-v2.4.0.tar.gz 109626901 BLAKE2B a10b5ee9a95667f560a8c2aec3808131f5f838f3c07d56584f4b29e9622912bf3d00b958b02db7c9d62dd52d9d08a171abcccef7f50cddf0407538168cf2c592 SHA512 f92cfc97304581920850c5d49fe4336f7c3855e99c3bcb035b6172fa7307e08e6f06fb06d1cd8f5b447c3220fc7f669684fbfe25641b43e9f6953999cf9ddd4b |
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|
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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 |
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new file mode 100644 |
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index 00000000000..b5e4b3642d4 |
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--- /dev/null |
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+++ b/sci-biology/seqan/files/seqan-2.4.0-fix-pthread.patch |
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@@ -0,0 +1,12 @@ |
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+--- a/util/cmake/seqan-config.cmake |
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++++ b/util/cmake/seqan-config.cmake |
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+@@ -307,7 +307,8 @@ |
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+ |
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+ # some OSes don't link pthread fully when building statically so we explicitly include whole archive |
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+ if (UNIX AND NOT APPLE) |
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+- set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,--whole-archive -lpthread -Wl,--no-whole-archive") |
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++ find_package (Threads) |
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++ set (SEQAN_LIBRARIES ${SEQAN_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT}) |
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+ endif () |
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+ |
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+ if ((${CMAKE_SYSTEM_NAME} STREQUAL "FreeBSD") OR (${CMAKE_SYSTEM_NAME} STREQUAL "OpenBSD")) |
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|
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diff --git a/sci-biology/seqan/metadata.xml b/sci-biology/seqan/metadata.xml |
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index 959160fe46b..077f6458a92 100644 |
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--- a/sci-biology/seqan/metadata.xml |
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+++ b/sci-biology/seqan/metadata.xml |
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@@ -1,8 +1,11 @@ |
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<?xml version="1.0" encoding="UTF-8"?> |
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<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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<pkgmetadata> |
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- <maintainer type="project"> |
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- <email>sci-biology@g.o</email> |
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- <name>Gentoo Biology Project</name> |
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- </maintainer> |
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+ <maintainer type="project"> |
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+ <email>sci-biology@g.o</email> |
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+ <name>Gentoo Biology Project</name> |
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+ </maintainer> |
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+ <use> |
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+ <flag name="tools">Build and install SeqAn commandline tools, such as the Yara aligner</flag> |
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+ </use> |
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</pkgmetadata> |
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|
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diff --git a/sci-biology/seqan/seqan-2.4.0.ebuild b/sci-biology/seqan/seqan-2.4.0.ebuild |
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new file mode 100644 |
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index 00000000000..8b337e77e6b |
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--- /dev/null |
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+++ b/sci-biology/seqan/seqan-2.4.0.ebuild |
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@@ -0,0 +1,92 @@ |
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+# Copyright 1999-2018 Gentoo Foundation |
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+# Distributed under the terms of the GNU General Public License v2 |
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+ |
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+EAPI=6 |
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+ |
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+: ${CMAKE_MAKEFILE_GENERATOR:=ninja} |
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+PYTHON_COMPAT=( python2_7 ) |
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+ |
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+inherit cmake-utils multibuild python-any-r1 toolchain-funcs |
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+ |
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+DESCRIPTION="C++ Sequence Analysis Library" |
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+HOMEPAGE="http://www.seqan.de/" |
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+ |
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+if [[ ${PV} == *9999 ]]; then |
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+ inherit git-r3 |
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+ EGIT_REPO_URI="https://github.com/seqan/seqan.git" |
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+ EGIT_BRANCH="develop" |
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+else |
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+ SRC_URI="https://github.com/seqan/seqan/archive/seqan-v${PV}.tar.gz" |
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+ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
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+ |
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+ S=${WORKDIR}/seqan-seqan-v${PV} |
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+fi |
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+ |
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+LICENSE="BSD GPL-3" |
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+SLOT="0" |
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+IUSE="cpu_flags_x86_sse4_1 doc tools" |
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+REQUIRED_USE="cpu_flags_x86_sse4_1" |
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+ |
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+RDEPEND=" |
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+ app-arch/bzip2:= |
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+ sys-libs/zlib:= |
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+ !!sci-biology/seqan:2.0 |
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+ !!sci-biology/seqan:2.1 |
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+ !!sci-biology/seqan:2.2" |
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+DEPEND=" |
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+ ${RDEPEND} |
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+ doc? ( |
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+ $(python_gen_any_dep 'dev-python/sphinx[${PYTHON_USEDEP}]') |
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+ ${PYTHON_DEPS} |
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+ )" |
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+ |
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+PATCHES=( "${FILESDIR}"/${PN}-2.4.0-fix-pthread.patch ) |
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+ |
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+python_check_deps() { |
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+ use doc && has_version "dev-python/sphinx[${PYTHON_USEDEP}]" |
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+} |
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+ |
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+pkg_setup() { |
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+ if [[ ${MERGE_TYPE} != binary ]]; then |
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+ use doc && python-any-r1_pkg_setup |
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+ use tools && tc-check-openmp |
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+ |
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+ MULTIBUILD_VARIANTS=( |
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+ $(usev tools) |
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+ library |
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+ ) |
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+ fi |
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+} |
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+ |
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+src_configure() { |
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+ my_configure() { |
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+ local mycmakeargs=( -DCMAKE_INSTALL_DOCDIR="share/doc/${PF}" ) |
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+ case "${MULTIBUILD_ID}" in |
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+ tools) |
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+ mycmakeargs+=( |
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+ -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_APPS |
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+ -DSEQAN_NO_DOX=ON |
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+ ) |
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+ ;; |
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+ library) |
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+ mycmakeargs+=( |
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+ -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY |
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+ -DSEQAN_NO_DOX=$(usex !doc) |
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+ ) |
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+ ;; |
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+ *) |
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+ die "${MULTIBUILD_ID} is not recognized" |
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+ ;; |
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+ esac |
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+ cmake-utils_src_configure |
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+ } |
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+ multibuild_foreach_variant my_configure |
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+} |
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+ |
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+src_compile() { |
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+ multibuild_foreach_variant cmake-utils_src_compile |
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+} |
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+ |
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+src_install() { |
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+ multibuild_foreach_variant cmake-utils_src_install |
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+} |