本家様https://github.com/keitaroyam/servalcat
Servalcat(Structure refinement and validation for crystallography and single particle 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
pip install git+https://github.com/project-gemmi/gemmi.git
pip install git+https://github.com/keitaroyam/servalcat.git
でインストール可能の様子.
CentOS7.9でインストールを試みた
[root@centos7 ~]# yum groupinstall "Development Tools" <-- 開発環境のインストール
[root@centos7 ~]# yum install epel-release
[root@centos7 ~]# yum install python3 python3-pip python3-devel
[root@centos7 ~]# yum install --enablerepo=epel python36-numpy <-- epelリポジトリにある python36向けのnumpy
[root@centos7 ~]# which pip3
/usr/bin/pip3
[root@centos7 ~]#
っで
[root@centos7 ~]# pip3 install git+https://github.com/project-gemmi/gemmi.git
WARNING: Running pip install with root privileges is generally not a good idea. Try `pip3 install --user` instead.
Collecting git+https://github.com/project-gemmi/gemmi.git
Cloning https://github.com/project-gemmi/gemmi.git to /tmp/pip-_nczkzfu-build
Installing collected packages: gemmi
Running setup.py install for gemmi ... done
Successfully installed gemmi-0.4.6
[root@centos7 ~]# pip3 install git+https://github.com/keitaroyam/servalcat.git
WARNING: Running pip install with root privileges is generally not a good idea. Try `pip3 install --user` instead.
Collecting git+https://github.com/keitaroyam/servalcat.git
Cloning https://github.com/keitaroyam/servalcat.git to /tmp/pip-i1r_1n__-build
Collecting numpy>=1.15 (from servalcat==0.0.1)
Downloading https://files.pythonhosted.org/packages/45/b2/6c7545bb7a38754d63048c7696804a0d947328125d81bf12beaa692c3ae3/numpy-1.19.5-cp36-cp36m-manylinux1_x86_64.whl (13.4MB)
100% |????????????????????????????????| 13.4MB 150kB/s
Collecting scipy (from servalcat==0.0.1)
Downloading https://files.pythonhosted.org/packages/c8/89/63171228d5ced148f5ced50305c89e8576ffc695a90b58fe5bb602b910c2/scipy-1.5.4-cp36-cp36m-manylinux1_x86_64.whl (25.9MB)
100% |????????????????????????????????| 25.9MB 83kB/s
Collecting pandas (from servalcat==0.0.1)
Downloading https://files.pythonhosted.org/packages/c3/e2/00cacecafbab071c787019f00ad84ca3185952f6bb9bca9550ed83870d4d/pandas-1.1.5-cp36-cp36m-manylinux1_x86_64.whl (9.5MB)
100% |????????????????????????????????| 9.5MB 198kB/s
Requirement already satisfied: gemmi in /usr/local/lib64/python3.6/site-packages (from servalcat==0.0.1)
Collecting pytz>=2017.2 (from pandas->servalcat==0.0.1)
Downloading https://files.pythonhosted.org/packages/70/94/784178ca5dd892a98f113cdd923372024dc04b8d40abe77ca76b5fb90ca6/pytz-2021.1-py2.py3-none-any.whl (510kB)
100% |????????????????????????????????| 512kB 412kB/s
Collecting python-dateutil>=2.7.3 (from pandas->servalcat==0.0.1)
Downloading https://files.pythonhosted.org/packages/d4/70/d60450c3dd48ef87586924207ae8907090de0b306af2bce5d134d78615cb/python_dateutil-2.8.1-py2.py3-none-any.whl (227kB)
100% |????????????????????????????????| 235kB 861kB/s
Collecting six>=1.5 (from python-dateutil>=2.7.3->pandas->servalcat==0.0.1)
Downloading https://files.pythonhosted.org/packages/d9/5a/e7c31adbe875f2abbb91bd84cf2dc52d792b5a01506781dbcf25c91daf11/six-1.16.0-py2.py3-none-any.whl
Installing collected packages: numpy, scipy, pytz, six, python-dateutil, pandas, servalcat
Running setup.py install for servalcat ... done
Successfully installed numpy-1.19.5 pandas-1.1.5 python-dateutil-2.8.1 pytz-2021.1 scipy-1.5.4 servalcat-0.0.1 six-1.16.0
[root@centos7 ~]#
っと以上でインストールは完了
目的の「servalcat」は「/usr/local/bin」に格納される.
大抵は /usr/local/bin にPATHを持っているのでそのまま「servalcat」で利用できるでしょう
[illya@centos7 ~]$ servalcat
usage: servalcat [-h] {sfcalc,shiftback,refine_spa,fsc,fofc,trim,util} ...
positional arguments:
{sfcalc,shiftback,refine_spa,fsc,fofc,trim,util}
optional arguments:
-h, --help show this help message and exit
[illya@centos7 ~]$
memo †
今回はごくごく簡単に済ますためにOS側の領域で pip3 を実行した.
pythonアプリはモジュールの組み合わせでアプリが動く. あるアプリは numpyモジュールのversion〇〇以上、でもあるpythonアプリは同じnumpyでも△△でないとだめとか普通にある. そう言った場合 pyenv/anaconda や venv を使ってアプリごとに環境を整備したほうが安全である. 安全とは他のアプリの実行環境を乱さないこと. pip/pip3はをpyenv/anaconda,venvなしで使うときは要注意かと思っている.
condaで †
conda create -n servalcat python=3.6
source activate servalcat
conda install numpy
pip install git+https://github.com/keitaroyam/servalcat.git
vi /apps/modulefiles/servalcat
#%Module1.0
set root /apps/pyenv/versions/anaconda3-5.3.1/envs/servalcat
prepend-path PATH $root/bin
![[PukiWiki]](image/picc.png "[PukiWiki]")
