commit: c2861a35cb4f890544347dc141403e8dc32c8ff5
Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 1 12:03:34 2023 +0000
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Wed Feb 1 12:03:34 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c2861a35
sci-chemistry/relion: Update relion ebuilds
Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org>
sci-chemistry/relion/metadata.xml | 1 +
sci-chemistry/relion/relion-4.0.0.ebuild | 30 +++++++++++++-
sci-chemistry/relion/relion-9999.ebuild | 69 ++++++++++++++++++++++++++++++++
3 files changed, 98 insertions(+), 2 deletions(-)
diff --git a/sci-chemistry/relion/metadata.xml
b/sci-chemistry/relion/metadata.xml
index 33e6e7e5d..101a056b9 100644
--- a/sci-chemistry/relion/metadata.xml
+++ b/sci-chemistry/relion/metadata.xml
@@ -11,6 +11,7 @@
</maintainer>
<use>
<flag name="gui">Enable relion gui</flag>
+ <flag name="cuda">Enable CUDA support</flag>
</use>
<upstream>
<remote-id type="github">3dem/relion</remote-id>
diff --git a/sci-chemistry/relion/relion-4.0.0.ebuild
b/sci-chemistry/relion/relion-4.0.0.ebuild
index a40375f64..c6d7d90db 100644
--- a/sci-chemistry/relion/relion-4.0.0.ebuild
+++ b/sci-chemistry/relion/relion-4.0.0.ebuild
@@ -7,11 +7,22 @@ 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"
+
+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 -> ${P}.tar.gz
+
ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz
+ "
+ KEYWORDS="~amd64"
+fi
LICENSE="GPL-2"
SLOT="0"
-KEYWORDS="~amd64"
IUSE="+gui cuda"
DEPEND="
@@ -30,6 +41,21 @@ BDEPEND="${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=(
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
+}
