diff options
Diffstat (limited to 'sci-chemistry/relion')
| -rw-r--r-- | sci-chemistry/relion/Manifest | 3 | ||||
| -rw-r--r-- | sci-chemistry/relion/files/relion-4.0.0-build.patch | 39 | ||||
| -rw-r--r-- | sci-chemistry/relion/metadata.xml | 3 | ||||
| -rw-r--r-- | sci-chemistry/relion/relion-3.1.1.ebuild | 44 | ||||
| -rw-r--r-- | sci-chemistry/relion/relion-4.0.0.ebuild | 71 | ||||
| -rw-r--r-- | sci-chemistry/relion/relion-9999.ebuild | 69 |
6 files changed, 184 insertions, 45 deletions
diff --git a/sci-chemistry/relion/Manifest b/sci-chemistry/relion/Manifest index 6aa383614..75b932e28 100644 --- a/sci-chemistry/relion/Manifest +++ b/sci-chemistry/relion/Manifest @@ -1 +1,2 @@ -DIST relion-3.1.1.tar.gz 2340685 BLAKE2B 0e98db3af7ceb312111260d8af51225d9a6b82314f1f066fe52464b533e59f44f5487ba66110708d661506074be4d52eeb7e04d88344a939bbd33139a33f6dec SHA512 fddf6f8a3d63e4f73aa1f529e4fa8fa7da98d9226b6539530c83496b94793ceef27d013a2d902a794993ab994f8d6467569ea4b681b4dd948654acf482529b22 +DIST class_ranker_0.1.3_torch_1.0.1.pt.tar.gz 2190018 BLAKE2B 157d380693cb97f2f94aea5ee8b1c9b64c50cead45c65d8d95584b12a4901622df025e4bdfccfc9c87286a3d442ffc26ed2a89953b9361f59d7ae2852fcc3a6b SHA512 0e9d4046a9ba211c07abcc44d0b51c7d69805eb946ed96abdd1663760906188050d476268214b4e7a84f529f51226c39f40c3b418373437fae2f4bb24990f338 +DIST relion-4.0.0.tar.gz 3342593 BLAKE2B d2293531cdf3c5779a8f6beb5bc753931388f1c577faa89a927c6ccd72436db0d9a84fbe08b836601b466bc23e9df6500f9e87da1630adecd2b0cf0e245d63e6 SHA512 1e873868bc54a13a7cca74c4a623f5f2aeeec7bd2df04f74d0421127a9c9a3b40a56ebc5b04a9f4138cca1208417b05a30c38ae78106d53b92deeadbeeaf4209 diff --git a/sci-chemistry/relion/files/relion-4.0.0-build.patch b/sci-chemistry/relion/files/relion-4.0.0-build.patch new file mode 100644 index 000000000..d7cb7bf2e --- /dev/null +++ b/sci-chemistry/relion/files/relion-4.0.0-build.patch @@ -0,0 +1,39 @@ +From 138b9c71b41a3c8782c991053a28bfe074bffdd9 Mon Sep 17 00:00:00 2001 +From: Takanori Nakane <nakane.t@gmail.com> +Date: Fri, 28 Oct 2022 19:51:29 +0900 +Subject: [PATCH] Repaired the build failure reported in #826 (by + @prehensilecode and @acaprez) + +--- + src/apps/CMakeLists.txt | 16 ++++++++-------- + 1 file changed, 8 insertions(+), 8 deletions(-) + +diff --git a/src/apps/CMakeLists.txt b/src/apps/CMakeLists.txt +index 9870b735..30985aa7 100644 +--- a/src/apps/CMakeLists.txt ++++ b/src/apps/CMakeLists.txt +@@ -273,16 +273,16 @@ if (CUDA_FOUND) + + + +- file(GLOB REL_JAZ_CUDA_SRC "${CMAKE_SOURCE_DIR}/src/jaz/cuda/*.cu" "${CMAKE_SOURCE_DIR}/src/jaz/cuda/kernels/*.cu" ) ++ file(GLOB REL_JAZ_CUDA_SRC "${CMAKE_SOURCE_DIR}/src/jaz/cuda/*.cu") + cuda_add_library(relion_jaz_gpu_util ${REL_JAZ_CUDA_SRC}) + +- #list(APPEND EXTRA_LIBS "${CUDA_CUFFT_LIBRARIES}") +- #if(BUILD_SHARED_LIBS) +- # install (TARGETS relion_jaz_gpu_util LIBRARY DESTINATION lib) +- #else() +- # target_link_libraries(relion_jaz_gpu_util relion_lib) +- # target_link_libraries(relion_jaz_gpu_util ${CUDA_CUFFT_LIBRARIES}) +- #endif() ++ list(APPEND EXTRA_LIBS "${CUDA_CUFFT_LIBRARIES}") ++ if(BUILD_SHARED_LIBS) ++ install (TARGETS relion_jaz_gpu_util LIBRARY DESTINATION lib) ++ else() ++ target_link_libraries(relion_jaz_gpu_util relion_lib) ++ target_link_libraries(relion_jaz_gpu_util ${CUDA_CUFFT_LIBRARIES}) ++ endif() + + target_link_libraries(relion_lib relion_jaz_gpu_util ${CUDA_CUFFT_LIBRARIES}) + target_link_libraries(relion_lib relion_jaz_gpu_util ${CUDA_CUFFT_LIBRARIES} ${CUDA_curand_LIBRARY}) diff --git a/sci-chemistry/relion/metadata.xml b/sci-chemistry/relion/metadata.xml index 8fe354309..101a056b9 100644 --- a/sci-chemistry/relion/metadata.xml +++ b/sci-chemistry/relion/metadata.xml @@ -13,4 +13,7 @@ <flag name="gui">Enable relion gui</flag> <flag name="cuda">Enable CUDA support</flag> </use> + <upstream> + <remote-id type="github">3dem/relion</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/relion/relion-3.1.1.ebuild b/sci-chemistry/relion/relion-3.1.1.ebuild deleted file mode 100644 index db5753988..000000000 --- a/sci-chemistry/relion/relion-3.1.1.ebuild +++ /dev/null @@ -1,44 +0,0 @@ -# Copyright 2019-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit cmake - -DESCRIPTION="Image-processing software for cryo-electron microscopy" -HOMEPAGE="https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page" -SRC_URI="https://github.com/3dem/relion/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64" -IUSE="+gui cuda" - -DEPEND=" - gui? ( x11-libs/fltk ) - dev-cpp/tbb - sci-libs/fftw:3.0 - media-libs/tiff - virtual/mpi - cuda? ( dev-util/nvidia-cuda-toolkit ) - " -RDEPEND=" - ${DEPEND} - sci-chemistry/ctffind - cuda? ( sci-chemistry/MotionCor2 ) -" -BDEPEND="${DEPEND}" - -src_configure() { - CMAKE_BUILD_TYPE=Release - mycmakeargs=( - -DBUILD_SHARED_LIBS=ON - -DALTCPU=$(usex !cuda) - -DFORCE_OWN_FFTW=OFF - -DFORCE_OWN_FLTK=OFF - -DFORCE_OWN_TBB=OFF - -DCUDA=$(usex cuda) - -DGUI=$(usex gui) - ) - cmake_src_configure -} diff --git a/sci-chemistry/relion/relion-4.0.0.ebuild b/sci-chemistry/relion/relion-4.0.0.ebuild new file mode 100644 index 000000000..c6d7d90db --- /dev/null +++ b/sci-chemistry/relion/relion-4.0.0.ebuild @@ -0,0 +1,71 @@ +# Copyright 2019-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake + +DESCRIPTION="Image-processing software for cryo-electron microscopy" +HOMEPAGE="https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page" + +if [[ ${PV} = *9999* ]]; then + EGIT_REPO_URI="https://github.com/3dem/relion.git" + [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="ver${PV:0:4}" + inherit git-r3 + SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz" +else + SRC_URI=" + https://github.com/3dem/relion/archive/${PV}.tar.gz -> ${P}.tar.gz + ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz + " + KEYWORDS="~amd64" +fi + +LICENSE="GPL-2" +SLOT="0" +IUSE="+gui cuda" + +DEPEND=" + gui? ( x11-libs/fltk ) + cuda? ( dev-util/nvidia-cuda-toolkit ) + dev-cpp/tbb + sci-libs/fftw:3.0 + media-libs/tiff + virtual/mpi +" +RDEPEND=" + ${DEPEND} + sci-chemistry/ctffind +" +BDEPEND="${DEPEND}" + +PATCHES=( "${FILESDIR}/${PN}-4.0.0-build.patch" ) + +src_unpack() { + git-r3_src_unpack + default +} + +src_prepare() { + cmake_src_prepare + mkdir -p "${S}/external/torch_models/" + cp "${DISTDIR}/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz" "${S}/external/torch_models/" + mkdir -p "${S}/external/torch_models/class_ranker/" + cp "${WORKDIR}/class_ranker_0.1.3_torch_1.0.1.pt" "${S}/external/torch_models/class_ranker/" + sed -e "s:{CMAKE_INSTALL_PREFIX}/lib:{CMAKE_INSTALL_PREFIX}/$(get_libdir):g" -i CMakeLists.txt || die + sed -e "s:LIBRARY DESTINATION lib:LIBRARY DESTINATION $(get_libdir):g" -i src/apps/CMakeLists.txt || die +} + +src_configure() { + CMAKE_BUILD_TYPE=Release + mycmakeargs=( + -DBUILD_SHARED_LIBS=ON + -DALTCPU=$(usex !cuda) + -DFORCE_OWN_FFTW=OFF + -DFORCE_OWN_FLTK=OFF + -DFORCE_OWN_TBB=OFF + -DCUDA=$(usex cuda) + -DGUI=$(usex gui) + ) + cmake_src_configure +} diff --git a/sci-chemistry/relion/relion-9999.ebuild b/sci-chemistry/relion/relion-9999.ebuild new file mode 100644 index 000000000..12e09d2fe --- /dev/null +++ b/sci-chemistry/relion/relion-9999.ebuild @@ -0,0 +1,69 @@ +# Copyright 2019-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake + +DESCRIPTION="Image-processing software for cryo-electron microscopy" +HOMEPAGE="https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page" + +if [[ ${PV} = *9999* ]]; then + EGIT_REPO_URI="https://github.com/3dem/relion.git" + [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="ver${PV:0:4}" + inherit git-r3 + SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz" +else + SRC_URI=" + https://github.com/3dem/relion/archive/${PV}.tar.gz -> ${P}.tar.gz + ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz + " + KEYWORDS="~amd64" +fi + +LICENSE="GPL-2" +SLOT="0" +IUSE="+gui cuda" + +DEPEND=" + gui? ( x11-libs/fltk ) + cuda? ( dev-util/nvidia-cuda-toolkit ) + dev-cpp/tbb + sci-libs/fftw:3.0 + media-libs/tiff + virtual/mpi +" +RDEPEND=" + ${DEPEND} + sci-chemistry/ctffind +" +BDEPEND="${DEPEND}" + +src_unpack() { + git-r3_src_unpack + default +} + +src_prepare() { + cmake_src_prepare + mkdir -p "${S}/external/torch_models/" + cp "${DISTDIR}/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz" "${S}/external/torch_models/" + mkdir -p "${S}/external/torch_models/class_ranker/" + cp "${WORKDIR}/class_ranker_0.1.3_torch_1.0.1.pt" "${S}/external/torch_models/class_ranker/" + sed -e "s:{CMAKE_INSTALL_PREFIX}/lib:{CMAKE_INSTALL_PREFIX}/$(get_libdir):g" -i CMakeLists.txt || die + sed -e "s:LIBRARY DESTINATION lib:LIBRARY DESTINATION $(get_libdir):g" -i src/apps/CMakeLists.txt || die +} + +src_configure() { + CMAKE_BUILD_TYPE=Release + mycmakeargs=( + -DBUILD_SHARED_LIBS=ON + -DALTCPU=$(usex !cuda) + -DFORCE_OWN_FFTW=OFF + -DFORCE_OWN_FLTK=OFF + -DFORCE_OWN_TBB=OFF + -DCUDA=$(usex cuda) + -DGUI=$(usex gui) + ) + cmake_src_configure +} |