* [gentoo-commits] proj/sci:master commit in: sci-chemistry/relion/
@ 2019-10-30 8:04 Alexey Shvetsov
0 siblings, 0 replies; 7+ messages in thread
From: Alexey Shvetsov @ 2019-10-30 8:04 UTC (permalink / raw
To: gentoo-commits
commit: 683635a1f893c4e12944e48fd6ff2ad65a401b7e
Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Wed Oct 30 08:04:29 2019 +0000
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Wed Oct 30 08:04:29 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=683635a1
sci-chemistry/relion: Update rdeps
Package-Manager: Portage-2.3.78, Repoman-2.3.17
Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org>
sci-chemistry/relion/relion-3.0.8.ebuild | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/sci-chemistry/relion/relion-3.0.8.ebuild b/sci-chemistry/relion/relion-3.0.8.ebuild
index 34b1277a7..799f8f090 100644
--- a/sci-chemistry/relion/relion-3.0.8.ebuild
+++ b/sci-chemistry/relion/relion-3.0.8.ebuild
@@ -22,7 +22,11 @@ DEPEND="
virtual/mpi
cuda? ( dev-util/nvidia-cuda-toolkit )
"
-RDEPEND="${DEPEND}"
+RDEPEND="
+ ${DEPEND}
+ sci-chemistry/ctffind
+ cuda? ( sci-chemistry/MotionCor2 )
+"
BDEPEND="${DEPEND}"
src_prepare() {
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/relion/
@ 2019-10-30 8:04 Alexey Shvetsov
0 siblings, 0 replies; 7+ messages in thread
From: Alexey Shvetsov @ 2019-10-30 8:04 UTC (permalink / raw
To: gentoo-commits
commit: 669fb165704ebae28b3781a18aa215d6f07c8340
Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Wed Oct 30 08:03:26 2019 +0000
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Wed Oct 30 08:03:26 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=669fb165
sci-chemistry/relion: Add relion
Package-Manager: Portage-2.3.78, Repoman-2.3.17
Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org>
sci-chemistry/relion/metadata.xml | 16 ++++++++++++
sci-chemistry/relion/relion-3.0.8.ebuild | 45 ++++++++++++++++++++++++++++++++
2 files changed, 61 insertions(+)
diff --git a/sci-chemistry/relion/metadata.xml b/sci-chemistry/relion/metadata.xml
new file mode 100644
index 000000000..8fe354309
--- /dev/null
+++ b/sci-chemistry/relion/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci-chemistry@gentoo.org</email>
+ <name>Gentoo Chemistry Project</name>
+ </maintainer>
+ <maintainer type="person">
+ <email>alexxy@gentoo.org</email>
+ <name>Alexey Shvetsov</name>
+ </maintainer>
+ <use>
+ <flag name="gui">Enable relion gui</flag>
+ <flag name="cuda">Enable CUDA support</flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-chemistry/relion/relion-3.0.8.ebuild b/sci-chemistry/relion/relion-3.0.8.ebuild
new file mode 100644
index 000000000..34b1277a7
--- /dev/null
+++ b/sci-chemistry/relion/relion-3.0.8.ebuild
@@ -0,0 +1,45 @@
+# Copyright 2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake-utils
+
+DESCRIPTION="Image-processing software for cryo-electron microscopy"
+HOMEPAGE="http://www2.mrc-lmb.cam.ac.uk/relion"
+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}"
+BDEPEND="${DEPEND}"
+
+src_prepare() {
+ # hack build type =D
+ sed 's:release:gentoo:g' -i CMakeLists.txt
+ cmake-utils_src_prepare
+}
+
+src_configure() {
+ mycmakeargs=(
+ -DBUILD_SHARED_LIBS=ON
+ -DALTCPU=ON
+ -DFORCE_OWN_FFTW=OFF
+ -DFORCE_OWN_FLTK=OFF
+ -DFORCE_OWN_TBB=OFF
+ -DCUDA=$(usex cuda)
+ -DGUI=$(usex gui)
+ )
+ cmake-utils_src_configure
+}
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/relion/
@ 2019-10-30 8:51 Alexey Shvetsov
0 siblings, 0 replies; 7+ messages in thread
From: Alexey Shvetsov @ 2019-10-30 8:51 UTC (permalink / raw
To: gentoo-commits
commit: 21d29b592468986f2ef6584361ef2e799460feb5
Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Wed Oct 30 08:51:16 2019 +0000
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Wed Oct 30 08:51:16 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=21d29b59
sci-chemistry/relion: Fix altcpu with cuda
Package-Manager: Portage-2.3.78, Repoman-2.3.17
Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org>
sci-chemistry/relion/relion-3.0.8.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-chemistry/relion/relion-3.0.8.ebuild b/sci-chemistry/relion/relion-3.0.8.ebuild
index 799f8f090..2f88a8ef9 100644
--- a/sci-chemistry/relion/relion-3.0.8.ebuild
+++ b/sci-chemistry/relion/relion-3.0.8.ebuild
@@ -38,7 +38,7 @@ src_prepare() {
src_configure() {
mycmakeargs=(
-DBUILD_SHARED_LIBS=ON
- -DALTCPU=ON
+ -DALTCPU=$(usex !cuda)
-DFORCE_OWN_FFTW=OFF
-DFORCE_OWN_FLTK=OFF
-DFORCE_OWN_TBB=OFF
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/relion/
@ 2019-10-30 9:19 Alexey Shvetsov
0 siblings, 0 replies; 7+ messages in thread
From: Alexey Shvetsov @ 2019-10-30 9:19 UTC (permalink / raw
To: gentoo-commits
commit: 2d55f94767c7b0747b390b9f681167ba68d8f752
Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Wed Oct 30 09:18:42 2019 +0000
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Wed Oct 30 09:18:42 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2d55f947
sci-chemistry/relion: Set build type to release
Package-Manager: Portage-2.3.78, Repoman-2.3.17
Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org>
sci-chemistry/relion/relion-3.0.8.ebuild | 7 +------
1 file changed, 1 insertion(+), 6 deletions(-)
diff --git a/sci-chemistry/relion/relion-3.0.8.ebuild b/sci-chemistry/relion/relion-3.0.8.ebuild
index 2f88a8ef9..178b8249c 100644
--- a/sci-chemistry/relion/relion-3.0.8.ebuild
+++ b/sci-chemistry/relion/relion-3.0.8.ebuild
@@ -29,13 +29,8 @@ RDEPEND="
"
BDEPEND="${DEPEND}"
-src_prepare() {
- # hack build type =D
- sed 's:release:gentoo:g' -i CMakeLists.txt
- cmake-utils_src_prepare
-}
-
src_configure() {
+ CMAKE_BUILD_TYPE=Release
mycmakeargs=(
-DBUILD_SHARED_LIBS=ON
-DALTCPU=$(usex !cuda)
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/relion/
@ 2021-01-18 11:55 Andrew Ammerlaan
0 siblings, 0 replies; 7+ messages in thread
From: Andrew Ammerlaan @ 2021-01-18 11:55 UTC (permalink / raw
To: gentoo-commits
commit: 6dbf9e007c0841a5604a16252f380e3c7797482c
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 11:55:07 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 11:55:07 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6dbf9e00
sci-chemistry/relion: version bump 3.1.1
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-chemistry/relion/{relion-3.0.8.ebuild => relion-3.1.1.ebuild} | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/sci-chemistry/relion/relion-3.0.8.ebuild b/sci-chemistry/relion/relion-3.1.1.ebuild
similarity index 84%
rename from sci-chemistry/relion/relion-3.0.8.ebuild
rename to sci-chemistry/relion/relion-3.1.1.ebuild
index 178b8249c..db5753988 100644
--- a/sci-chemistry/relion/relion-3.0.8.ebuild
+++ b/sci-chemistry/relion/relion-3.1.1.ebuild
@@ -1,12 +1,12 @@
-# Copyright 2019 Gentoo Authors
+# Copyright 2019-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-inherit cmake-utils
+inherit cmake
DESCRIPTION="Image-processing software for cryo-electron microscopy"
-HOMEPAGE="http://www2.mrc-lmb.cam.ac.uk/relion"
+HOMEPAGE="https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page"
SRC_URI="https://github.com/3dem/relion/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-2"
@@ -40,5 +40,5 @@ src_configure() {
-DCUDA=$(usex cuda)
-DGUI=$(usex gui)
)
- cmake-utils_src_configure
+ cmake_src_configure
}
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/relion/
@ 2021-12-26 14:14 Andrew Ammerlaan
0 siblings, 0 replies; 7+ messages in thread
From: Andrew Ammerlaan @ 2021-12-26 14:14 UTC (permalink / raw
To: gentoo-commits
commit: 24f95ca3827040b3cac0d00bdd1f3ad010693fd8
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Sun Dec 26 14:14:40 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sun Dec 26 14:14:40 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=24f95ca3
sci-chemistry/relion: drop USE cuda
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-chemistry/relion/metadata.xml | 1 -
sci-chemistry/relion/relion-3.1.1.ebuild | 18 ++++++++----------
2 files changed, 8 insertions(+), 11 deletions(-)
diff --git a/sci-chemistry/relion/metadata.xml b/sci-chemistry/relion/metadata.xml
index 8fe354309..cdabe7f2c 100644
--- a/sci-chemistry/relion/metadata.xml
+++ b/sci-chemistry/relion/metadata.xml
@@ -11,6 +11,5 @@
</maintainer>
<use>
<flag name="gui">Enable relion gui</flag>
- <flag name="cuda">Enable CUDA support</flag>
</use>
</pkgmetadata>
diff --git a/sci-chemistry/relion/relion-3.1.1.ebuild b/sci-chemistry/relion/relion-3.1.1.ebuild
index db5753988..39e4ab229 100644
--- a/sci-chemistry/relion/relion-3.1.1.ebuild
+++ b/sci-chemistry/relion/relion-3.1.1.ebuild
@@ -12,20 +12,18 @@ SRC_URI="https://github.com/3dem/relion/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64"
-IUSE="+gui cuda"
+IUSE="+gui"
DEPEND="
- gui? ( x11-libs/fltk )
- dev-cpp/tbb
- sci-libs/fftw:3.0
- media-libs/tiff
- virtual/mpi
- cuda? ( dev-util/nvidia-cuda-toolkit )
- "
+ gui? ( x11-libs/fltk )
+ dev-cpp/tbb
+ sci-libs/fftw:3.0
+ media-libs/tiff
+ virtual/mpi
+"
RDEPEND="
${DEPEND}
sci-chemistry/ctffind
- cuda? ( sci-chemistry/MotionCor2 )
"
BDEPEND="${DEPEND}"
@@ -37,7 +35,7 @@ src_configure() {
-DFORCE_OWN_FFTW=OFF
-DFORCE_OWN_FLTK=OFF
-DFORCE_OWN_TBB=OFF
- -DCUDA=$(usex cuda)
+ -DCUDA=OFF
-DGUI=$(usex gui)
)
cmake_src_configure
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/relion/
@ 2023-02-01 12:03 Alexey Shvetsov
0 siblings, 0 replies; 7+ messages in thread
From: Alexey Shvetsov @ 2023-02-01 12:03 UTC (permalink / raw
To: gentoo-commits
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
+}
^ permalink raw reply related [flat|nested] 7+ messages in thread
end of thread, other threads:[~2023-02-01 12:03 UTC | newest]
Thread overview: 7+ messages (download: mbox.gz follow: Atom feed
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