![[PukiWiki]](image/picc.png "[PukiWiki]")
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
Warp is a set of tools for cryo-EM and cryo-ET data processing including, among other tools: Warp, M, WarpTools, MTools, MCore, and Noise2Map.
condaで提供されている https://anaconda.org/warpem/warp
rockylinux8なら「2.0.0dev34」までは大丈夫っぽい。だが、それより最新版は動かないっぽい...
ここではpyenv-anaconda/miniforge3でconda環境を敷いている.
っで
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/profile.d/conda.sh
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/profile.d/conda.shその上で warp を構築します
[root@rockylinux9 ~]# conda create -n warp warp -c warpem -c nvidia/label/cuda-11.8.0 -c pytorch -c conda-forge
(確認)
[root@rockylinux9 ~]# conda activate warp
(warp) [root@rockylinux9 ~]# conda list
:
cuda-tools 11.8.0 0 nvidia/label/cuda-11.8.0
:
dotnet 8.0.408 ha770c72_1 conda-forge
dotnet-aspnetcore 8.0.15 ha770c72_1 conda-forge
dotnet-runtime 8.0.15 h84d6215_1 conda-forge
dotnet-sdk 8.0.408 h84d6215_1 conda-forge
:
mkl 2024.0.0 ha957f24_49657 conda-forge
mkl-devel 2024.0.0 ha770c72_49657 conda-forge
mkl-include 2024.0.0 ha957f24_49657 conda-forge
:
numpy 2.3.3 py311h2e04523_0 conda-f
:
python 3.11.9 hb806964_0_cpython conda-forge
:
pytorch 2.0.1 py3.11_cuda11.8_cudnn8.7.0_0 pytorch
pytorch-cuda 11.8 h7e8668a_6 pytorch
pytorch-mutex 1.0 cuda pytorch
:
setuptools 80.9.0 pyhff2d567_0 conda-forge
:
warp 2.0.0dev36 py311_0 warpem
:
(warp) [root@rockylinux9 ~]#
(warp) [root@rockylinux9 ~]# pip install reliontomotools
(warp) [root@rockylinux9 ~]# conda deactivate
[root@rockylinux9 ~]#「/apps/modulefiles/warp」
#%Module1.0
set root /apps/pyenv/versions/miniforge3-25.11.0-1/envs/warp
prepend-path PATH $root/bin
prepend-path LD_LIBRARY_PATH $root/libコマンドとしては「MTools」や「WarpTools」「Noise2Map」「Noise2Tomo」でしょうか
Visualize 3D template matching results from Warp
github https://github.com/warpem/warp-tm-vis
pipy https://pypi.org/project/warp-tm-vis/
warp 仮想環境に uv をインストールします
[root@rockylinux9 ~]# source /apps/pyenv/versions/miniforge3-25.11.0-1/etc/profile.d/conda.sh
[root@rockylinux9 ~]# conda activate warp
(warp) [root@rockylinux9 ~]# pip install uv
(warp) [root@rockylinux9 ~]# conda list
:
urllib3 2.5.0 pyhd8ed1ab_0 conda-forge
uv 0.8.19 pypi_0 pypi <-- uv のみが追加インストールされる
warp 2.0.0dev36 py311_0 warpem
:
(warp) [root@rockylinux9 ~]# conda deactivate
[root@rockylinux9 ~]#それで各ユーザで「module load warp」の後で「uvx warp-tm-vis」と実行します
[saber@rockylinux9 ~]$ 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/BfNHFpjYtsocHmIu8TDlv/bin/warp-tm-vis", line 6, in <module>
from warp_tm_vis.cli import cli
File "/home/saber/.cache/uv/archive-v0/BfNHFpjYtsocHmIu8TDlv/lib/python3.11/site-packages/warp_tm_vis/cli.py", line 18, in <module>
console = rich.console.Console()
^^^^^^^^^^^^
AttributeError: module 'rich' has no attribute 'console'. Did you mean: '_console'?
[saber@rockylinux9 ~]$とエラーが発せします。ここで「cli.py」の中身を修正します
「from rich.console import Console」を追加します
|
これで一応は起動する
[saber@rockylinux9 ~]$ uvx warp-tm-vis
Usage: warp-tm-vis [OPTIONS]
Visualize Warp template matching results and the effects of thresholding
lq Options qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqk
x * --reconstruction-directory -rdir PATH directory containing tomograms e.g. x
x warp_tiltseries/reconstruction/deconv x
x [required] x
x * --matching-directory -mdir PATH matching directory e.g. warp_tiltseries/matching [required] x
x * --matching-pattern -mp TEXT matching pattern e.g. "*_flipx.star" [required] x
x * --correlation-volume-pattern -cvp TEXT correlation volume pattern e.g. "*_flipx_corr.mrc" [required] x
x --load-volumes --no-load-volumes whether or not to load reconstructions and correlation volumes x
x [default: load-volumes] x
x --help Show this message and exit. x
mqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqj
[saber@rockylinux9 ~]$ファイルを正しく指定するとアプリが立ち上がりますが、こちらはnapariで、ssh越しのリモートでは遅いです。コンソールとかで操作した方がよさげ.
Complementary tools for Relion tomo
github https://github.com/joton/reliontomotools
pipy https://pypi.org/project/reliontomotools/
こちらも warp 仮想環境に追加するようにしました.
[root@rockylinux9 ~]# source /apps/pyenv/versions/miniforge3-25.3.1-0/etc/profile.d/conda.sh
[root@rockylinux9 ~]# conda activate warp
(warp) [root@rockylinux9 ~]# pip install reliontomotools
(確認)
(warp) [root@rockylinux9 ~]# conda list
tzdata 2025b h78e105d_0 conda-forge
↓
tzdata 2025.2 pypi_0 pypi
(warp) [root@rockylinux9 ~]# conda deactivate
[root@rockylinux9 ~]#「pip install reliontomotools」の結果、既に存在しているパッケージの変更としては tzdataが 2025b -> 2025.2 へ変更されました.
あと新規追加でemfile, mrcfile, pandas, reliontomotools らが追加された. この変更で warp の挙動とかに影響があれば、別のconda仮想環境を作る感じかな.
environment-modulesはそのまま.
どうも v2.0.0dev36 からrockylinux8では上手く動かない様子. 原因はGLIBC. condaパッケージ品は GLIBC_2.29 を要求するのですが、rockylinux8は 2.28 までなのでエラー。
っで、2.28でも動くようにするにはソースから構築しかない. っで作ってみる
[root@rockylinux8 ~]# cat /etc/redhat-release
Rocky Linux release 8.10 (Green Obsidian)
[root@rockylinux8 ~]# git clone https://github.com/yyuu/pyenv.git /apps/pyenv
[root@rockylinux8 ~]# export PYENV_ROOT=/apps/pyenv
[root@rockylinux8 ~]# export PATH=$PYENV_ROOT/bin:$PATH
[root@rockylinux8 ~]# pyenv install miniforge3-25.3.1-0
[root@rockylinux8 ~]# source /apps/pyenv/versions/miniforge3-25.3.1-0/etc/profile.d/conda.sh
[root@rockylinux8 ~]# cd /apps/
[root@rockylinux8 apps]# git clone https://github.com/warpem/warp
[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 'cmake<4'
(warp_build) [root@rockylinux8 warp]# ./scripts/build-native-unix.sh
(warp_build) [root@rockylinux8 warp]# ./scripts/publish-unix.sh
(warp_build) [root@rockylinux8 warp]# conda install uv
(warp_build) [root@rockylinux8 warp]# pip install reliontomotoolsEnvironment-modules
「/apps/modulefiles/warp」
#%Module1.0
set root /apps/pyenv/versions/miniforge3-25.3.1-0/envs/warp_build
set warp /apps/warp/Release/linux-x64/publish
prepend-path PATH $warp:$root/bin
#prepend-path LD_LIBRARY_PATH $warp/lib:$root/lib
