MiRPv2

本家様https://github.com/moores-lab/MiRPv2

[root@centos7 ~]# mkdir /apps
[root@centos7 ~]# cd /apps
[root@centos7 apps]# git clone https://github.com/moores-lab/MiRPv2
 
 
[root@centos7 apps]# cd MiRPv2/
[root@centos7 MiRPv2]# ls -lCF
data/  install.py  license.txt  manual.pdf  mirp/
 
[root@centos7 MiRPv2]# ls -l mirp/
total 68
-rw-r--r--. 1 root root  2576 May 21 23:25 generate_seam_references.py
-rw-r--r--. 1 root root  4443 May 21 23:25 generate_segment_averages.py
-rw-r--r--. 1 root root  2318 May 21 23:25 helper_fns.py
-rw-r--r--. 1 root root 27818 May 21 23:25 microtubules.py
-rw-r--r--. 1 root root  1481 May 21 23:25 mirp_initial_seam
-rw-r--r--. 1 root root  1345 May 21 23:25 mirp_pf_sorting
-rw-r--r--. 1 root root  1295 May 21 23:25 mirp_seam_check
-rw-r--r--. 1 root root  2283 May 21 23:25 plot_eulerxy.py
-rw-r--r--. 1 root root  7723 May 21 23:25 starfileIO.py
[root@centos7 MiRPv2]#

• generate_seam_references.py
  EMAN2のpythonモジュールが必要(python2)
  generate_seam_references.pyのメモ書き

  MiRP - a microtubule RELION-based pipeline for cryo-EM image processing.
  This script is dependent on EMAN2 (tested with v2.13) and generates seam
  references for 3D seam classification from a single 3D reference

• generate_segment_averages.py
  EMAN2のpythonモジュールが必要(python2)
  メモ書き

  MiRP - a microtubule RELION-based pipeline for cryo-EM image processing.
  This script is dependent on EMAN2 (tested with v2.13) and generates microtubule
  particles averaged over a 7-particle window

• helper_fns.py、microtubules.py、mirp_initial_seam、mirp_pf_sorting、mirp_seam_check、plot_eulerxy.py
  python3
  メモ書き

  MiRP - a microtubule RELION-based pipeline for cryo-EM image processing.
  MiRP v2 is designed to function with RELION v3.1, and is not compatible with earlier versions of RELION.

• starfileIO.py
  python3
  メモ書き

  MiRP - a microtubule RELION-based pipeline for cryo-EM image processing.
  MiRP v2 is designed to function with RELION v3.1, and is not compatible with earlier versions of RELION.
  starfileIO.py provides functions for reading, editing, and writing starfiles. It supports starfiles with multiple datablocks,
  and is therefore compatible with any version of RELION.

構築方針 †

EMAN2 pythonライブラリ(python2)が必要なアプリがあったり、 python3 で動くアプリもある.

なので EMAN2.31 の実行環境を間借りして EMAN2 pythonライブラリ要求アプリに対応させ、
それ以外は可能ならOS由来のpython3環境側を利用して残りを動かすようにしてみる.

調査して python3 が必要なアプリは下記操作でいけた.
pyenv/anacondaを使わなくても良かった. ただpip3を使ったのでyumとの齟齬に留意が必要かな

[root@centos7 ~]# yum install python3-tkinter
[root@centos7 ~]# pip3 install matplotlib scipy

次にpython2 アプリはEMAN2の eman2.31 が入っていればokでEnvironmentModulesとかで用意されたEMAN2実行環境をロードすれば使えます

module load eman2/2.31