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#author("2025-04-17T00:30:31+00:00","default:sysosa","sysosa") #author("2025-04-17T17:30:04+00:00;2025-04-17T00:30:31+00:00","default:sysosa","sysosa") &color(red){みかんせい}; 本家様 [[https://github.com/anmartinezs/pyseg_system>+https://github.com/anmartinezs/pyseg_system]] De novo analysis for cryo-electron tomography. ***dockerで構築(失敗しました) [#a0e1e053] 一見するとdockerで作るもの？って感じ. 試しにdokcerで作ってみたが、構築に失敗した. #code(nonumber){{ [root@rockylinux9 ~]# cat /etc/redhat-release Rocky Linux release 9.5 (Blue Onyx) (dockerのインストールと起動) [root@rockylinux9 ~]# dnf config-manager --add-repo https://download.docker.com/linux/centos/docker-ce.repo [root@rockylinux9 ~]# dnf install docker-ce -y [root@rockylinux9 ~]# systemctl start docker.service [root@rockylinux9 ~]# docker info Client: Docker Engine - Community Version: 28.0.4 Context: defaul : [root@rockylinux9 ~]# (pyseg_system の取得とdokcer image作成) [root@rockylinux9 ~]# cd /apps/src/ [root@rockylinux9 src]# git clone https://github.com/anmartinezs/pyseg_system [root@rockylinux9 src]# cd pyseg_system [root@rockylinux9 pyseg_system]# git log -1 commit 6baf5f9aaa11ad41b99796e548e51fafa9b4330b (HEAD -> master, origin/master, origin/HEAD) Author: anmartinezs <an.martinez.s.sw@gmail.com> Date: Fri Nov 8 13:10:41 2024 +0100 Update README.md DOI correction [root@rockylinux9 pyseg_system]# docker build . -t pyseg:latest : 251.7 + /usr/local/pyseg_system/sys/soft/miniconda3/bin/conda install --yes --solver=libmamba --channel conda-forge --channel anaconda python=3.7 opencv=4.2.0 graph-tool=2.29 future=0.18.2=py37_0 pip=23.3 252.9 Channels: 252.9 - conda-forge 252.9 - anaconda 252.9 - defaults 252.9 Platform: linux-64 252.9 Collecting package metadata (repodata.json): ...working... done 265.8 Solving environment: ...working... failed 508.0 508.0 LibMambaUnsatisfiableError: Encountered problems while solving: 508.0 - nothing provides openssl >=1.1.1,<1.1.2.0a0 needed by python-3.7.1-h0371630_3 508.0 - nothing provides libopencv 4.2.0 py36_5 needed by opencv-4.2.0-py36_5 : Dockerfile:22 -------------------- 21 | 22 | >>> RUN cd sys && chmod u+x *.sh && ./install_ubuntu_apt_pkgs_docker.sh && ./install_third_parties.sh \ 23 | >>> && ./install_miniconda.sh && ./install_conda_pkgs.sh 24 | RUN cd sys && ./set_bashrc_env.sh -------------------- ERROR: failed to solve: process "/bin/sh -c cd sys && chmod u+x *.sh && ./install_ubuntu_apt_pkgs_docker.sh && ./install_third_parties.sh && ./install_miniconda.sh && ./install_conda_pkgs.sh" did not complete successfully: exit code: 1 [root@rockylinux9 pyseg_system]# }} とエラーになる. 開発元が提供する Dockerfile の問題かと思われる. なのでDockerによる構築は諦めて、地べたで作ってみる. ***構築 [#ze81d0b9] &color(red){みかんせい}; 付属のドキュメント docs/manual/manual.pdf を見ると ubuntu20.04を前提にした作り方が載っている. その個々を読むと一応 RHEL系でも行けるかなと. っでRHEL9系の Rokcylinux9 で作ってみた. #code(nonumber){{ [root@rockylinux9 ~]# cat /etc/redhat-release Rocky Linux release 9.5 (Blue Onyx) [root@rockylinux9 ~]# }} #code(nonumber){{ [root@rockylinux9 ~]# cd /apps [root@rockylinux9 apps]# git clone https://github.com/anmartinezs/pyseg_system [root@rockylinux9 apps]# cd pyseg_system/ [root@rockylinux9 pyseg_system]# }} #code(nonumber){{ /apps/pyseg_system/sys/soft /disperse/latest/build <-- $buildFold /infrstr <-- $infrFold ./sys/install/disperse/latest/sources/cfitsio_3.380.tar.gz /cfitsio ./sys/install/cgal/4.7/sources/CGAL-4.7.tar.gz cp /apps/pyseg_system/sys/install/disperse/latest/sources/cfitsio_3.380.tar.gz /apps/src cd /apps/src tar xf cfitsio_3.380.tar.gz cd cfitsio/ ./configure --enable-shared --enable-static --prefix=/apps/pyseg_system/sys/soft/disperse/latest/infrstr make; make install dnf install CGAL-devel CGAL-qt5-devel dnf --enablerepo=devel install SDL_image-devel mathgl-2.4.4.tar.gz mathgl1が必要 mathgl-2.4.4.tar.gz mathgl-1が必要みたい tar xf mathgl-2.4.4.tar.gz cd mathgl-2.4.4 mkdir build ; cd build cmake -DCMAKE_INSTALL_PREFIX=/apps/local .. vi CMakeCache.txt enable-qt5:BOOL=ON make; make install cd /apps/src git clone https://github.com/thierry-sousbie/DisPerSE cd DisPerSE mkdir build; cd build cmake . -DCMAKE_INSTALL_PREFIX=$buildFold -DCFITSIO_DIR=$infrFold cmake .. -DCMAKE_INSTALL_PREFIX=/apps/pyseg_system/sys/soft/disperse/latest/build -DCFITSIO_DIR=/apps/pyseg_system/sys/soft/disperse/latest/infrstr make; make install ls /apps/src/pyseg_system/sys/soft/disperse/latest/build/bin/ fieldconv mse netconv skelconv conda create -n pyseg python=3.7 opencv=4.2 graph-tool=2.29 future=0.18 "setuptools<58" vtk=8 -c conda-forge conda activate pyseg conda install beautifulsoup4=4.9 lxml=4.6 pillow=6.2 pywavelets=1.1 scikit-image=0.14 scikit-learn=0.20 scikit-fmm=2021.2 scipy=1.2 astropy=4.1 imageio=2.9 -c conda-forge pip install pyfits==3.5 PATH=/apps/pyenv/versions/anaconda3-2024.10-1/envs/pyseg/bin:/apps/src/pyseg_system/sys/soft/disperse/latest/build/bin/ PYTHONPATH=/apps/src/pyseg_system/code }}
