Warp をテンプレートにして作成
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開始行:
&size(10){過去ページ(windows版)[[Warp20241209]]};
WarpTools です. Warpはwindows向けのDeskTopアプリです
本家様 [[https://github.com/warpem/warp>+https://github.c...
Warp is a set of tools for cryo-EM and cryo-ET data proce...
condaで提供されている [[https://anaconda.org/warpem/warp>...
&size(10){rockylinux8なら「2.0.0dev34」までは大丈夫っぽい...
ここではpyenv-anaconda/miniforge3でconda環境を敷いている.
っで
#code(nonumber){{
git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install miniforge3-25.11.0-1
source /apps/pyenv/versions/miniforge3-25.11.0-1/etc/prof...
conda update -n base -c conda-forge conda
(既に環境があるなら)
source /apps/pyenv/versions/miniforge3-25.11.0-1/etc/prof...
}}
その上で warp を構築します
#code(nonumber){{
[root@rockylinux9 ~]# conda create -n warp warp -c warpem...
(確認)
[root@rockylinux9 ~]# conda activate warp
(warp) [root@rockylinux9 ~]# conda list
:
cuda-tools 11.8.0 0 ...
:
dotnet 8.0.408 ha770c72_1 ...
dotnet-aspnetcore 8.0.15 ha770c72_1 ...
dotnet-runtime 8.0.15 h84d6215_1 ...
dotnet-sdk 8.0.408 h84d6215_1 ...
:
mkl 2024.0.0 ha957f24_496...
mkl-devel 2024.0.0 ha770c72_496...
mkl-include 2024.0.0 ha957f24_496...
:
numpy 2.3.3 py311h2e0452...
:
python 3.11.9 hb806964_0_c...
:
pytorch 2.0.1 py3.11_cuda1...
pytorch-cuda 11.8 h7e8668a_6 ...
pytorch-mutex 1.0 cuda ...
:
setuptools 80.9.0 pyhff2d567_0...
:
warp 2.0.0dev36 py311_0 ...
:
(warp) [root@rockylinux9 ~]#
(warp) [root@rockylinux9 ~]# pip install reliontomotools
(warp) [root@rockylinux9 ~]# conda deactivate
[root@rockylinux9 ~]#
}}
***environment-modules [#i2a88d13]
「/apps/modulefiles/warp」
#code(nonumber){{
#%Module1.0
set root /apps/pyenv/versions/miniforge3-25.11.0-1/envs/w...
prepend-path PATH $root/bin
prepend-path LD_LIBRARY_PATH $root/lib
}}
コマンドとしては「MTools」や「WarpTools」「Noise2Map」「N...
***warp-tm-vis [#l2890f00]
Visualize 3D template matching results from Warp
github [[https://github.com/warpem/warp-tm-vis>+https://g...
pipy [[https://pypi.org/project/warp-tm-vis/>+https://pyp...
warp 仮想環境に uv をインストールします
#code(nonumber){{
[root@rockylinux9 ~]# source /apps/pyenv/versions/minifor...
[root@rockylinux9 ~]# conda activate warp
(warp) [root@rockylinux9 ~]# pip install uv
(warp) [root@rockylinux9 ~]# conda list
:
urllib3 2.5.0 pyhd8ed1ab_0...
uv 0.8.19 pypi_0 ...
warp 2.0.0dev36 py311_0 ...
:
(warp) [root@rockylinux9 ~]# conda deactivate
[root@rockylinux9 ~]#
}}
それで各ユーザで「module load warp」の後で「uvx warp-tm-v...
#code(nonumber){{
[saber@rockylinux9 ~]$ module use /apps/modulefiles
[saber@rockylinux9 ~]$ module load warp
[saber@rockylinux9 ~]$ which uvx
/apps/pyenv/versions/miniforge3-25.11.0-1/envs/warp/bin/uvx
[saber@rockylinux9 ~]$ uvx warp-tm-vis
:
:
Traceback (most recent call last):
File "/home/saber/.cache/uv/archive-v0/BfNHFpjYtsocHmIu...
from warp_tm_vis.cli import cli
File "/home/saber/.cache/uv/archive-v0/BfNHFpjYtsocHmIu...
console = rich.console.Console()
^^^^^^^^^^^^
AttributeError: module 'rich' has no attribute 'console'....
[saber@rockylinux9 ~]$
}}
とエラーが発せします。ここで「cli.py」の中身を修正します
「from rich.console import Console」を追加します
#code(diff,nonumber){{
from enum import Enum
from pathlib import Path
import mrcfile
import napari
import napari.utils.notifications
import rich
+from rich.console import Console
import typer
}}
これで一応は起動する
#code(nonumber){{
[saber@rockylinux9 ~]$ uvx warp-tm-vis
Usage: warp-tm-vis [OPTIONS]
Visualize Warp template matching results and the effects...
lq Options qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq...
x * --reconstruction-directory -rdir ...
x ...
x ...
x * --matching-directory -mdir ...
x * --matching-pattern -mp ...
x * --correlation-volume-pattern -cvp ...
x --load-volumes --no-load-volum...
x ...
x --help ...
mqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq...
[saber@rockylinux9 ~]$
}}
ファイルを正しく指定するとアプリが立ち上がりますが、こち...
***reliontomotools [#s6a07b17]
Complementary tools for Relion tomo
github [[https://github.com/joton/reliontomotools>+https:...
pipy [[https://pypi.org/project/reliontomotools/>+https:/...
こちらも warp 仮想環境に追加するようにしました.
#code(nonumber){{
[root@rockylinux9 ~]# source /apps/pyenv/versions/minifor...
[root@rockylinux9 ~]# conda activate warp
(warp) [root@rockylinux9 ~]# pip install reliontomotools
(確認)
(warp) [root@rockylinux9 ~]# conda list
tzdata 2025b h78e105d_0 ...
↓
tzdata 2025.2 pypi_0 ...
(warp) [root@rockylinux9 ~]# conda deactivate
[root@rockylinux9 ~]#
}}
「pip install reliontomotools」の結果、既に存在しているパ...
あと新規追加でemfile, mrcfile, pandas, reliontomotools ら...
environment-modulesはそのまま.
***warpをソースから作ってみた [#qedff33a]
どうも v2.0.0dev36 からrockylinux8では上手く動かない様子....
っで、2.28でも動くようにするにはソースから構築しかない. ...
#code(nonumber){{
[root@rockylinux8 ~]# cat /etc/redhat-release
Rocky Linux release 8.10 (Green Obsidian)
[root@rockylinux8 ~]# git clone https://github.com/yyuu/p...
[root@rockylinux8 ~]# export PYENV_ROOT=/apps/pyenv
[root@rockylinux8 ~]# export PATH=$PYENV_ROOT/bin:$PATH
[root@rockylinux8 ~]# pyenv install miniforge3-25.3.1-0
[root@rockylinux8 ~]# source /apps/pyenv/versions/minifor...
[root@rockylinux8 ~]# cd /apps/
[root@rockylinux8 apps]# git clone https://github.com/war...
[root@rockylinux8 apps]# cd warp/
[root@rockylinux8 warp]# conda env create -f warp_build.yml
[root@rockylinux8 warp]# conda activate warp_build
(warp_build) [root@rockylinux8 warp]# conda install 'cmak...
(warp_build) [root@rockylinux8 warp]# ./scripts/build-nat...
(warp_build) [root@rockylinux8 warp]# ./scripts/publish-u...
(warp_build) [root@rockylinux8 warp]# conda install uv
(warp_build) [root@rockylinux8 warp]# pip install reliont...
}}
Environment-modules
「/apps/modulefiles/warp」
#code(nonumber){{
#%Module1.0
set root /apps/pyenv/versions/miniforge3-25.3.1-0/envs/wa...
set warp /apps/warp/Release/linux-x64/publish
prepend-path PATH $warp:$root/bin
#prepend-path LD_LIBRARY_PATH $warp/lib:$root/lib
}}
終了行:
&size(10){過去ページ(windows版)[[Warp20241209]]};
WarpTools です. Warpはwindows向けのDeskTopアプリです
本家様 [[https://github.com/warpem/warp>+https://github.c...
Warp is a set of tools for cryo-EM and cryo-ET data proce...
condaで提供されている [[https://anaconda.org/warpem/warp>...
&size(10){rockylinux8なら「2.0.0dev34」までは大丈夫っぽい...
ここではpyenv-anaconda/miniforge3でconda環境を敷いている.
っで
#code(nonumber){{
git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install miniforge3-25.11.0-1
source /apps/pyenv/versions/miniforge3-25.11.0-1/etc/prof...
conda update -n base -c conda-forge conda
(既に環境があるなら)
source /apps/pyenv/versions/miniforge3-25.11.0-1/etc/prof...
}}
その上で warp を構築します
#code(nonumber){{
[root@rockylinux9 ~]# conda create -n warp warp -c warpem...
(確認)
[root@rockylinux9 ~]# conda activate warp
(warp) [root@rockylinux9 ~]# conda list
:
cuda-tools 11.8.0 0 ...
:
dotnet 8.0.408 ha770c72_1 ...
dotnet-aspnetcore 8.0.15 ha770c72_1 ...
dotnet-runtime 8.0.15 h84d6215_1 ...
dotnet-sdk 8.0.408 h84d6215_1 ...
:
mkl 2024.0.0 ha957f24_496...
mkl-devel 2024.0.0 ha770c72_496...
mkl-include 2024.0.0 ha957f24_496...
:
numpy 2.3.3 py311h2e0452...
:
python 3.11.9 hb806964_0_c...
:
pytorch 2.0.1 py3.11_cuda1...
pytorch-cuda 11.8 h7e8668a_6 ...
pytorch-mutex 1.0 cuda ...
:
setuptools 80.9.0 pyhff2d567_0...
:
warp 2.0.0dev36 py311_0 ...
:
(warp) [root@rockylinux9 ~]#
(warp) [root@rockylinux9 ~]# pip install reliontomotools
(warp) [root@rockylinux9 ~]# conda deactivate
[root@rockylinux9 ~]#
}}
***environment-modules [#i2a88d13]
「/apps/modulefiles/warp」
#code(nonumber){{
#%Module1.0
set root /apps/pyenv/versions/miniforge3-25.11.0-1/envs/w...
prepend-path PATH $root/bin
prepend-path LD_LIBRARY_PATH $root/lib
}}
コマンドとしては「MTools」や「WarpTools」「Noise2Map」「N...
***warp-tm-vis [#l2890f00]
Visualize 3D template matching results from Warp
github [[https://github.com/warpem/warp-tm-vis>+https://g...
pipy [[https://pypi.org/project/warp-tm-vis/>+https://pyp...
warp 仮想環境に uv をインストールします
#code(nonumber){{
[root@rockylinux9 ~]# source /apps/pyenv/versions/minifor...
[root@rockylinux9 ~]# conda activate warp
(warp) [root@rockylinux9 ~]# pip install uv
(warp) [root@rockylinux9 ~]# conda list
:
urllib3 2.5.0 pyhd8ed1ab_0...
uv 0.8.19 pypi_0 ...
warp 2.0.0dev36 py311_0 ...
:
(warp) [root@rockylinux9 ~]# conda deactivate
[root@rockylinux9 ~]#
}}
それで各ユーザで「module load warp」の後で「uvx warp-tm-v...
#code(nonumber){{
[saber@rockylinux9 ~]$ module use /apps/modulefiles
[saber@rockylinux9 ~]$ module load warp
[saber@rockylinux9 ~]$ which uvx
/apps/pyenv/versions/miniforge3-25.11.0-1/envs/warp/bin/uvx
[saber@rockylinux9 ~]$ uvx warp-tm-vis
:
:
Traceback (most recent call last):
File "/home/saber/.cache/uv/archive-v0/BfNHFpjYtsocHmIu...
from warp_tm_vis.cli import cli
File "/home/saber/.cache/uv/archive-v0/BfNHFpjYtsocHmIu...
console = rich.console.Console()
^^^^^^^^^^^^
AttributeError: module 'rich' has no attribute 'console'....
[saber@rockylinux9 ~]$
}}
とエラーが発せします。ここで「cli.py」の中身を修正します
「from rich.console import Console」を追加します
#code(diff,nonumber){{
from enum import Enum
from pathlib import Path
import mrcfile
import napari
import napari.utils.notifications
import rich
+from rich.console import Console
import typer
}}
これで一応は起動する
#code(nonumber){{
[saber@rockylinux9 ~]$ uvx warp-tm-vis
Usage: warp-tm-vis [OPTIONS]
Visualize Warp template matching results and the effects...
lq Options qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq...
x * --reconstruction-directory -rdir ...
x ...
x ...
x * --matching-directory -mdir ...
x * --matching-pattern -mp ...
x * --correlation-volume-pattern -cvp ...
x --load-volumes --no-load-volum...
x ...
x --help ...
mqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq...
[saber@rockylinux9 ~]$
}}
ファイルを正しく指定するとアプリが立ち上がりますが、こち...
***reliontomotools [#s6a07b17]
Complementary tools for Relion tomo
github [[https://github.com/joton/reliontomotools>+https:...
pipy [[https://pypi.org/project/reliontomotools/>+https:/...
こちらも warp 仮想環境に追加するようにしました.
#code(nonumber){{
[root@rockylinux9 ~]# source /apps/pyenv/versions/minifor...
[root@rockylinux9 ~]# conda activate warp
(warp) [root@rockylinux9 ~]# pip install reliontomotools
(確認)
(warp) [root@rockylinux9 ~]# conda list
tzdata 2025b h78e105d_0 ...
↓
tzdata 2025.2 pypi_0 ...
(warp) [root@rockylinux9 ~]# conda deactivate
[root@rockylinux9 ~]#
}}
「pip install reliontomotools」の結果、既に存在しているパ...
あと新規追加でemfile, mrcfile, pandas, reliontomotools ら...
environment-modulesはそのまま.
***warpをソースから作ってみた [#qedff33a]
どうも v2.0.0dev36 からrockylinux8では上手く動かない様子....
っで、2.28でも動くようにするにはソースから構築しかない. ...
#code(nonumber){{
[root@rockylinux8 ~]# cat /etc/redhat-release
Rocky Linux release 8.10 (Green Obsidian)
[root@rockylinux8 ~]# git clone https://github.com/yyuu/p...
[root@rockylinux8 ~]# export PYENV_ROOT=/apps/pyenv
[root@rockylinux8 ~]# export PATH=$PYENV_ROOT/bin:$PATH
[root@rockylinux8 ~]# pyenv install miniforge3-25.3.1-0
[root@rockylinux8 ~]# source /apps/pyenv/versions/minifor...
[root@rockylinux8 ~]# cd /apps/
[root@rockylinux8 apps]# git clone https://github.com/war...
[root@rockylinux8 apps]# cd warp/
[root@rockylinux8 warp]# conda env create -f warp_build.yml
[root@rockylinux8 warp]# conda activate warp_build
(warp_build) [root@rockylinux8 warp]# conda install 'cmak...
(warp_build) [root@rockylinux8 warp]# ./scripts/build-nat...
(warp_build) [root@rockylinux8 warp]# ./scripts/publish-u...
(warp_build) [root@rockylinux8 warp]# conda install uv
(warp_build) [root@rockylinux8 warp]# pip install reliont...
}}
Environment-modules
「/apps/modulefiles/warp」
#code(nonumber){{
#%Module1.0
set root /apps/pyenv/versions/miniforge3-25.3.1-0/envs/wa...
set warp /apps/warp/Release/linux-x64/publish
prepend-path PATH $warp:$root/bin
#prepend-path LD_LIBRARY_PATH $warp/lib:$root/lib
}}
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