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-rw-r--r--sci-biology/seqan/files/seqan-2.4.0-cmake-add_library-static.patch38
-rw-r--r--sci-biology/seqan/files/seqan-2.4.0-installpaths.patch24
-rw-r--r--sci-biology/seqan/seqan-2.4.0-r1.ebuild79
-rw-r--r--sci-biology/seqan/seqan-2.4.0.ebuild27
4 files changed, 151 insertions, 17 deletions
diff --git a/sci-biology/seqan/files/seqan-2.4.0-cmake-add_library-static.patch b/sci-biology/seqan/files/seqan-2.4.0-cmake-add_library-static.patch
new file mode 100644
index 000000000000..7617d9f9a665
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-2.4.0-cmake-add_library-static.patch
@@ -0,0 +1,38 @@
+From 1877d143ad9f42d80692073538e3f32b37e15967 Mon Sep 17 00:00:00 2001
+From: Andreas Sturmlechner <asturm@gentoo.org>
+Date: Sun, 7 Mar 2021 19:35:44 +0100
+Subject: [PATCH] Fix linking with BUILD_SHARED_LIBS=ON default in EAPI-7
+
+Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
+---
+ apps/mason2/CMakeLists.txt | 2 +-
+ apps/pair_align/lib/CMakeLists.txt | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/apps/mason2/CMakeLists.txt b/apps/mason2/CMakeLists.txt
+index 2218187..c042ea7 100644
+--- a/apps/mason2/CMakeLists.txt
++++ b/apps/mason2/CMakeLists.txt
+@@ -52,7 +52,7 @@ add_definitions (-DSEQAN_REVISION="${SEQAN_REVISION}")
+ add_definitions (-DSEQAN_DATE="${SEQAN_DATE}")
+
+ # We define a library for the reusable parts of Mason.
+-add_library (mason_sim
++add_library (mason_sim STATIC
+ external_split_merge.h
+ external_split_merge.cpp
+ fragment_generation.h
+diff --git a/apps/pair_align/lib/CMakeLists.txt b/apps/pair_align/lib/CMakeLists.txt
+index 75faef7..3b9576e 100644
+--- a/apps/pair_align/lib/CMakeLists.txt
++++ b/apps/pair_align/lib/CMakeLists.txt
+@@ -53,5 +53,5 @@ endforeach(GAPS_T)
+
+ # This part can be used instead for cmake version greater or equal to 2.8.8.
+ # This requires to update the script above as well.
+-add_library(pair_align_lib pair_align_lib.cpp pair_align_lib.h ${LIB_TARGETS})
++add_library(pair_align_lib STATIC pair_align_lib.cpp pair_align_lib.h ${LIB_TARGETS})
+ target_link_libraries(pair_align_lib ${SEQAN_LIBRARIES})
+--
+2.30.1
+
diff --git a/sci-biology/seqan/files/seqan-2.4.0-installpaths.patch b/sci-biology/seqan/files/seqan-2.4.0-installpaths.patch
new file mode 100644
index 000000000000..35f0718f9d8d
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-2.4.0-installpaths.patch
@@ -0,0 +1,24 @@
+--- a/util/cmake/SeqAnBuildSystem.cmake 2018-01-11 12:32:45.591134000 +0100
++++ b/util/cmake/SeqAnBuildSystem.cmake 2018-01-11 12:51:55.193282581 +0100
+@@ -399,10 +399,10 @@
+ # Install pkg-config file, except on Windows.
+ if (NOT CMAKE_SYSTEM_NAME MATCHES Windows)
+ configure_file("util/pkgconfig/seqan.pc.in" "${CMAKE_BINARY_DIR}/util/pkgconfig/seqan-${SEQAN_VERSION_MAJOR}.pc" @ONLY)
+- install(FILES "${CMAKE_BINARY_DIR}/util/pkgconfig/seqan-${SEQAN_VERSION_MAJOR}.pc" DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/pkgconfig)
++ install(FILES "${CMAKE_BINARY_DIR}/util/pkgconfig/seqan-${SEQAN_VERSION_MAJOR}.pc" DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+ endif (NOT CMAKE_SYSTEM_NAME MATCHES Windows)
+ # Install FindSeqAn TODO(h-2) rename seqan-config.cmake to seqan-config${SEQAN_VERSION_MAJOR}.cmake after 2.x cycle
+- install(FILES "${CMAKE_CURRENT_SOURCE_DIR}/util/cmake/seqan-config.cmake" DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/cmake/seqan/)
++ install(FILES "${CMAKE_CURRENT_SOURCE_DIR}/util/cmake/seqan-config.cmake" DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/seqan2/)
+
+ # Install headers
+ file (GLOB HEADERS
+@@ -473,7 +473,7 @@
+ set (CMAKE_INSTALL_DOCDIR "${CMAKE_INSTALL_DATAROOTDIR}/doc" CACHE STRING "Documentation root (DATAROOTDIR/doc)" FORCE)
+ endif ()
+ set (SEQAN_PREFIX_SHARE "${CMAKE_INSTALL_DATADIR}/${APP_NAME}")
+- set (SEQAN_PREFIX_SHARE_DOC "${CMAKE_INSTALL_DOCDIR}/${APP_NAME}")
++ set (SEQAN_PREFIX_SHARE_DOC "${CMAKE_INSTALL_DOCDIR}/examples/")
+ endif ()
+ endmacro (seqan_setup_install_vars)
+
diff --git a/sci-biology/seqan/seqan-2.4.0-r1.ebuild b/sci-biology/seqan/seqan-2.4.0-r1.ebuild
new file mode 100644
index 000000000000..76a73d759bef
--- /dev/null
+++ b/sci-biology/seqan/seqan-2.4.0-r1.ebuild
@@ -0,0 +1,79 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake multibuild toolchain-funcs
+
+DESCRIPTION="C++ Sequence Analysis Library"
+HOMEPAGE="https://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 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="${RDEPEND}"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-fix-pthread.patch
+ "${FILESDIR}"/${P}-installpaths.patch
+ "${FILESDIR}"/${P}-cmake-add_library-static.patch
+)
+
+pkg_setup() {
+ if [[ ${MERGE_TYPE} != binary ]]; then
+ use tools && tc-check-openmp
+
+ MULTIBUILD_VARIANTS=( $(usev tools) library )
+ fi
+}
+
+src_configure() {
+ my_configure() {
+ local mycmakeargs=(
+ -DSEQAN_NO_DOX=ON
+ )
+ case "${MULTIBUILD_ID}" in
+ tools)
+ mycmakeargs+=(
+ -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_APPS
+ )
+ ;;
+ library)
+ mycmakeargs+=(
+ -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY
+ )
+ ;;
+ *)
+ die "${MULTIBUILD_ID} is not recognized"
+ ;;
+ esac
+ cmake_src_configure
+ }
+ multibuild_foreach_variant my_configure
+}
+
+src_compile() {
+ multibuild_foreach_variant cmake_src_compile
+}
+
+src_install() {
+ multibuild_foreach_variant cmake_src_install
+}
diff --git a/sci-biology/seqan/seqan-2.4.0.ebuild b/sci-biology/seqan/seqan-2.4.0.ebuild
index 5653a1ec94e4..cf73c6984d0e 100644
--- a/sci-biology/seqan/seqan-2.4.0.ebuild
+++ b/sci-biology/seqan/seqan-2.4.0.ebuild
@@ -1,14 +1,12 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
-: ${CMAKE_MAKEFILE_GENERATOR:=ninja}
-
-inherit cmake-utils multibuild toolchain-funcs
+inherit cmake multibuild toolchain-funcs
DESCRIPTION="C++ Sequence Analysis Library"
-HOMEPAGE="http://www.seqan.de/"
+HOMEPAGE="https://www.seqan.de/"
if [[ ${PV} == *9999 ]]; then
inherit git-r3
@@ -17,8 +15,7 @@ if [[ ${PV} == *9999 ]]; then
else
SRC_URI="https://github.com/seqan/seqan/archive/seqan-v${PV}.tar.gz"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
- S=${WORKDIR}/seqan-seqan-v${PV}
+ S="${WORKDIR}"/seqan-seqan-v${PV}
fi
LICENSE="BSD GPL-3"
@@ -32,8 +29,7 @@ RDEPEND="
!!sci-biology/seqan:2.0
!!sci-biology/seqan:2.1
!!sci-biology/seqan:2.2"
-DEPEND="
- ${RDEPEND}"
+DEPEND="${RDEPEND}"
PATCHES=( "${FILESDIR}"/${PN}-2.4.0-fix-pthread.patch )
@@ -41,10 +37,7 @@ pkg_setup() {
if [[ ${MERGE_TYPE} != binary ]]; then
use tools && tc-check-openmp
- MULTIBUILD_VARIANTS=(
- $(usev tools)
- library
- )
+ MULTIBUILD_VARIANTS=( $(usev tools) library )
fi
}
@@ -69,15 +62,15 @@ src_configure() {
die "${MULTIBUILD_ID} is not recognized"
;;
esac
- cmake-utils_src_configure
+ cmake_src_configure
}
multibuild_foreach_variant my_configure
}
src_compile() {
- multibuild_foreach_variant cmake-utils_src_compile
+ multibuild_foreach_variant cmake_src_compile
}
src_install() {
- multibuild_foreach_variant cmake-utils_src_install
+ multibuild_foreach_variant cmake_src_install
}