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#author("2023-06-20T14:10:52+00:00","default:sysosa","sysosa") #author("2023-06-20T14:15:59+00:00","default:sysosa","sysosa") 本家様[[https://github.com/keitaroyam/servalcat>+https://github.com/keitaroyam/servalcat]] Servalcat(''S''tructur''e'' ''r''efinement and ''val''idation for ''c''rystallography and single p''a''r''t''icle analysis) deepL先生訳「結晶構造解析と単粒子解析のための構造の精密化と検証」 gitのサイトに書かれているように #code(nonumber){{ pip install servalcat }} でインストール可能の様子. ここではpyenv/minicondaでservalcat向けの環境を作ってそこにservalcat を用意してみた #code(nonumber){{ [root@centos7 ~]# cat /etc/redhat-release CentOS Linux release 7.9.2009 (Core) [root@centos7 ~]# git clone https://github.com/yyuu/pyenv.git /apps/pyenv [root@centos7 ~]# export PYENV_ROOT=/apps/pyenv [root@centos7 ~]# export PATH=$PYENV_ROOT/bin:$PATH [root@centos7 ~]# pyenv install miniconda3-4.7.12 [root@centos7 ~]# pyenv global miniconda3-4.7.12 [root@centos7 ~]# pyenv versions system * miniconda3-4.7.12 (set by /apps/pyenv/version) [root@centos7 ~]# export PATH=$PYENV_ROOT/versions/miniconda3-4.7.12/bin/:$PATH [root@centos7 ~]# conda config --add channels conda-forge [root@centos7 ~]# conda config --remove channels defaults [root@centos7 ~]# conda info active environment : None user config file : /root/.condarc populated config files : /root/.condarc conda version : 4.7.12 conda-build version : not installed python version : 3.7.4.final.0 virtual packages : __cuda=12.0 base environment : /apps/pyenv/versions/miniconda3-4.7.12 (writable) channel URLs : https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch package cache : /apps/pyenv/versions/miniconda3-4.7.12/pkgs /root/.conda/pkgs envs directories : /apps/pyenv/versions/miniconda3-4.7.12/envs /root/.conda/envs platform : linux-64 user-agent : conda/4.7.12 requests/2.22.0 CPython/3.7.4 Linux/3.10.0-1160.el7.x86_64 centos/7.9.2009 glibc/2.17 UID:GID : 0:0 netrc file : None offline mode : False [root@centos7 ~]# [root@centos7 ~]# conda update conda -y (以上でpyenv/miniconda環境の構築が終わって、次にservalcat環境を作る) [root@centos7 ~]# conda create -n servalcat pip [root@centos7 ~]# source activate servalcat (servalcat) [root@centos7 ~]# pip install servalcat (servalcat) [root@centos7 ~]# conda deactivate [root@centos7 ~]# }} ***EnvironmentModules [#q8d14bad] #code(nonumber){{ [root@centos7 ~]# vi /apps/modulefiles/servalcat #%Module1.0 set root /apps/pyenv/versions/miniconda3-4.7.12/envs/servalcat prepend-path PATH $root/bin [root@centos7 ~]# }} ***使ってみる [#df8b2f13] REFMAC5との連携があるので、ccp4のロードも行う #code(nonumber){{ [saber@centos7 ~]$ module use --append /apps/modulefiles/ <-- この部分は$HOME/.bashrcらに記載すれば宜しいかと [saber@centos7 ~]$ module load ccp4 [saber@centos7 ~]$ module load servalcat [saber@centos7 ~]$ servalcat usage: servalcat [-h] [--skip_test] [-v] {sfcalc,shiftback,refine_spa,refine_cx,fsc,fofc,trim,translate,localcc,sigmaa,util,refmac5} ... A tool for model refinement and map calculation for cryo-EM SPA. positional arguments: {sfcalc,shiftback,refine_spa,refine_cx,fsc,fofc,trim,translate,localcc,sigmaa,util,refmac5} options: -h, --help show this help message and exit --skip_test Skip installation test -v, --version show program's version number and exit # Finished on 2022-12-21 23:50:18.340847 [saber@centos7 ~]$ }} ***offline環境へ持っていく [#pc378a67] #code(nonumber){{ [root@centos7 ~]# conda activate servalcat (servalcat) [root@centos7 ~]# pip freeze > requirements.txt (servalcat) [root@centos7 ~]# cat requirements.txt gemmi==0.5.7 numpy==1.24.0 pandas==1.5.2 python-dateutil==2.8.2 pytz==2022.7 scipy==1.9.3 servalcat==0.2.122 six==1.16.0 (servalcat) [root@centos7 ~]# mkdir servalcat-packages (servalcat) [root@centos7 ~]# pip download -d ./servalcat-packages -r ./requirements.txt Collecting gemmi==0.5.7 Using cached gemmi-0.5.7-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB) Collecting numpy==1.24.0 Using cached numpy-1.24.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.3 MB) Collecting pandas==1.5.2 Using cached pandas-1.5.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.0 MB) Collecting python-dateutil==2.8.2 Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB) Collecting pytz==2022.7 Using cached pytz-2022.7-py2.py3-none-any.whl (499 kB) Collecting scipy==1.9.3 Using cached scipy-1.9.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (33.4 MB) Collecting servalcat==0.2.122 Using cached servalcat-0.2.122-py3-none-any.whl (114 kB) Collecting six==1.16.0 Using cached six-1.16.0-py2.py3-none-any.whl (11 kB) Saved ./servalcat-packages/gemmi-0.5.7-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl Saved ./servalcat-packages/numpy-1.24.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl Saved ./servalcat-packages/pandas-1.5.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl Saved ./servalcat-packages/python_dateutil-2.8.2-py2.py3-none-any.whl Saved ./servalcat-packages/pytz-2022.7-py2.py3-none-any.whl Saved ./servalcat-packages/scipy-1.9.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl Saved ./servalcat-packages/servalcat-0.2.122-py3-none-any.whl Saved ./servalcat-packages/six-1.16.0-py2.py3-none-any.whl Successfully downloaded gemmi numpy pandas python-dateutil pytz scipy servalcat six (servalcat) [root@centos7 ~]# ls -l servalcat-packages/ total 65136 -rw-r--r--. 1 root root 3097735 Dec 22 00:20 gemmi-0.5.7-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl -rw-r--r--. 1 root root 17266259 Dec 22 00:20 numpy-1.24.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl -rw-r--r--. 1 root root 12013615 Dec 22 00:20 pandas-1.5.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl -rw-r--r--. 1 root root 247702 Dec 22 00:20 python_dateutil-2.8.2-py2.py3-none-any.whl -rw-r--r--. 1 root root 499364 Dec 22 00:20 pytz-2022.7-py2.py3-none-any.whl -rw-r--r--. 1 root root 33430216 Dec 22 00:20 scipy-1.9.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl -rw-r--r--. 1 root root 114766 Dec 22 00:20 servalcat-0.2.122-py3-none-any.whl -rw-r--r--. 1 root root 11053 Dec 22 00:20 six-1.16.0-py2.py3-none-any.whl (servalcat) [root@centos7 ~]# }} ***Singularity [#n657f026] Singularityならファイルとして実行環境を扱えるので、ある意味便利 #code(nonumber){{ [root@centos7 ~]# cat /etc/redhat-release CentOS Linux release 7.9.2009 (Core) [root@centos7 ~]# yum install epel-release [root@centos7 ~]# yum install singularity apptainer-suid [root@centos7 ~]# singularity build --sandbox servalcat docker://python:3.8.12-bullseye [root@centos7 ~]# singularity shell --writable servalcat Apptainer> Apptainer> pip install servalcat Apptainer> Apptainer> exit exit [root@centos7 ~]# [root@centos7 ~]# singularity build servalcat.sif servalcat [root@centos7 ~]# ls -lh servalcat.sif -rwxr-xr-x. 1 root root 375M Dec 22 00:30 servalcat.sif [root@centos7 ~]# }} 使ってみる #code(nonumber){{ [illya@centos7 ~]$ singularity shell /apps/servalcat.sif Apptainer> servalcat usage: servalcat [-h] [--skip_test] [-v] {sfcalc,shiftback,refine_spa,refine_cx,fsc,fofc,trim,translate,localcc,sigmaa,util,refmac5} ... A tool for model refinement and map calculation for cryo-EM SPA. positional arguments: {sfcalc,shiftback,refine_spa,refine_cx,fsc,fofc,trim,translate,localcc,sigmaa,util,refmac5} optional arguments: -h, --help show this help message and exit --skip_test Skip installation test -v, --version show program's version number and exit # Finished on 2022-12-22 00:37:47.175981 Apptainer> servalcat --version Servalcat 0.2.122 with Python 3.8.12 (gemmi 0.5.7, scipy 1.9.3, numpy 1.24.0, pandas 1.5.2) # Finished on 2022-12-22 00:37:51.354880 Apptainer> exit exit [illya@centos7 ~]$ }} ぁrefmac5を忘れた... ぇっとsingularity のbind機能を活かします #code(nonumber){{ [illya@centos7 ~]$ singularity shell -B /apps:/apps /apps/servalcat.sif Apptainer> Apptainer> source /apps/ccp4-8.0/bin/ccp4.setup-sh Apptainer> Apptainer> which refmac5 /apps/ccp4-8.0/bin/refmac5 Apptainer> Apptainer> servalcat --version Servalcat 0.2.122 with Python 3.8.12 (gemmi 0.5.7, scipy 1.9.3, numpy 1.24.0, pandas 1.5.2) # Finished on 2022-12-22 01:05:39.793055 Apptainer> exit [illya@centos7 ~]$ }} これで行けるかな ***pip未掲載の最新版を使いたい [#m153539e] [[https://github.com/keitaroyam/servalcat/actions>+https://github.com/keitaroyam/servalcat/actions]]にてcommitされた時点で自動で作られたバイナリが用意されている 参照先: [[https://keitaroyam.github.io/posts/2023/05/01/servalcat_installation/>+https://keitaroyam.github.io/posts/2023/05/01/servalcat_installation/]] っでこれを使ってみる 最新(表の上位)をクリックします &ref(2023y06m20d_230534412.png,nolink,80%); 「wheels2.zip」がダウンロードされます. これを計算機に運び込んで、展開します #code(nonumber){{ [root@rockylinux9 ~]# cd /apps/src/ [root@rockylinux9 src]# mkdir servalcat [root@rockylinux9 src]# cd servalcat/ [root@rockylinux9 servalcat]# (「wheels2.zip」をコピー) [root@rockylinux9 servalcat]# ls -lh total 15M -rw-r--r--. 1 root root 15M Jun 20 22:30 wheels2.zip [root@rockylinux9 servalcat]# (展開) [root@rockylinux9 servalcat]# unzip wheels2.zip [root@rockylinux9 servalcat]# ls -l total 28884 -rw-r--r--. 1 root root 1071455 Jun 19 11:03 servalcat-0.4.27-cp310-cp310-macosx_10_9_x86_64.whl -rw-r--r--. 1 root root 951255 Jun 19 11:03 servalcat-0.4.27-cp310-cp310-macosx_11_0_arm64.whl -rw-r--r--. 1 root root 1129826 Jun 19 10:49 servalcat-0.4.27-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl -rw-r--r--. 1 root root 1071368 Jun 19 11:03 servalcat-0.4.27-cp311-cp311-macosx_10_9_x86_64.whl -rw-r--r--. 1 root root 951175 Jun 19 11:03 servalcat-0.4.27-cp311-cp311-macosx_11_0_arm64.whl -rw-r--r--. 1 root root 1130328 Jun 19 10:49 servalcat-0.4.27-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl -rw-r--r--. 1 root root 1048899 Jun 19 11:03 servalcat-0.4.27-cp37-cp37m-macosx_10_9_x86_64.whl -rw-r--r--. 1 root root 1149270 Jun 19 10:49 servalcat-0.4.27-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl -rw-r--r--. 1 root root 1071352 Jun 19 11:03 servalcat-0.4.27-cp38-cp38-macosx_10_9_x86_64.whl -rw-r--r--. 1 root root 951200 Jun 19 11:03 servalcat-0.4.27-cp38-cp38-macosx_11_0_arm64.whl -rw-r--r--. 1 root root 1129859 Jun 19 10:49 servalcat-0.4.27-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl -rw-r--r--. 1 root root 1071427 Jun 19 11:03 servalcat-0.4.27-cp39-cp39-macosx_10_9_x86_64.whl -rw-r--r--. 1 root root 951457 Jun 19 11:03 servalcat-0.4.27-cp39-cp39-macosx_11_0_arm64.whl -rw-r--r--. 1 root root 1130342 Jun 19 10:49 servalcat-0.4.27-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl -rw-r--r--. 1 root root 14739449 Jun 20 22:30 wheels2.zip [root@rockylinux9 servalcat]# }} このwhlを入れます. っがその前にcondaの環境を作ります #code(nonumber){{ [root@rockylinux9 ~]# export PYENV_ROOT=/apps/pyenv [root@rockylinux9 ~]# export PATH=$PYENV_ROOT/bin:$PATH [root@rockylinux9 ~]# export PATH=$PYENV_ROOT/versions/anaconda3-2023.03/bin/:$PATH [root@rockylinux9 ~]# conda create -n servalcat python=3.11 [root@rockylinux9 ~]# source activate servalcat (servalcat) [root@rockylinux9 ~]# (servalcat) [root@rockylinux9 ~]# python -mpip install -U --find-link=/apps/src/servalcat/ servalcat Looking in links: /apps/src/servalcat/ Processing /apps/src/servalcat/servalcat-0.4.27-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl Collecting packaging (from servalcat) Using cached packaging-23.1-py3-none-any.whl (48 kB) Collecting numpy>=1.15 (from servalcat) Using cached numpy-1.25.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.6 MB) Collecting scipy (from servalcat) Using cached scipy-1.10.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.1 MB) Collecting pandas>=0.24.2 (from servalcat) Using cached pandas-2.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.2 MB) Collecting gemmi==0.6.2 (from servalcat) Using cached gemmi-0.6.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.4 MB) Collecting python-dateutil>=2.8.2 (from pandas>=0.24.2->servalcat) Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB) Collecting pytz>=2020.1 (from pandas>=0.24.2->servalcat) Using cached pytz-2023.3-py2.py3-none-any.whl (502 kB) Collecting tzdata>=2022.1 (from pandas>=0.24.2->servalcat) Using cached tzdata-2023.3-py2.py3-none-any.whl (341 kB) Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas>=0.24.2->servalcat) Using cached six-1.16.0-py2.py3-none-any.whl (11 kB) Installing collected packages: pytz, gemmi, tzdata, six, packaging, numpy, scipy, python-dateutil, pandas, servalcat Successfully installed gemmi-0.6.2 numpy-1.25.0 packaging-23.1 pandas-2.0.2 python-dateutil-2.8.2 pytz-2023.3 scipy-1.10.1 servalcat-0.4.27 six-1.16.0 tzdata-2023.3 WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv (servalcat) [root@rockylinux9 ~]# (servalcat) [root@rockylinux9 ~]# conda deactivate [root@rockylinux9 ~]# }} そして #code(nonumber){{ [root@rockylinux9 ~]# vi /apps/modulefiles/servalcat #%Module1.0 set root /apps/pyenv/versions/anaconda3-2023.03/envs/servalcat prepend-path PATH $root/bin [root@rockylinux9 ~]# }} とEnvironment-moduleを整備して #code(nonumber){{ [saber@rockylinux9 ~]$ module use /apps/modulefiles/ [saber@rockylinux9 ~]$ module load servalcat [saber@rockylinux9 ~]$ servalcat --version Servalcat 0.4.27 with Python 3.11.3 (gemmi 0.6.2, scipy 1.10.1, numpy 1.25.0, pandas 2.0.2) # Finished on 2023-06-20 23:15:45.960244 [saber@rockylinux9 ~]$ }} となる
