pyseg_system をテンプレートにして作成
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開始行:
&color(red){みかんせい};
本家様 [[https://github.com/anmartinezs/pyseg_system>+htt...
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...
#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...
[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/anma...
[root@rockylinux9 src]# cd pyseg_system
[root@rockylinux9 pyseg_system]# git log -1
commit 6baf5f9aaa11ad41b99796e548e51fafa9b4330b (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:...
:
251.7 + /usr/local/pyseg_system/sys/soft/miniconda3/bin/c...
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): ...wor...
265.8 Solving environment: ...working... failed
508.0
508.0 LibMambaUnsatisfiableError: Encountered problems wh...
508.0 - nothing provides openssl >=1.1.1,<1.1.2.0a0 nee...
508.0 - nothing provides libopencv 4.2.0 py36_5 needed ...
:
Dockerfile:22
--------------------
21 |
22 | >>> RUN cd sys && chmod u+x *.sh && ./install_ubun...
23 | >>> && ./install_miniconda.sh && ./install_con...
24 | RUN cd sys && ./set_bashrc_env.sh
--------------------
ERROR: failed to solve: process "/bin/sh -c cd sys && chm...
[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...
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/anm...
[root@rockylinux9 apps]# cd pyseg_system/
[root@rockylinux9 pyseg_system]#
}}
#code(nonumber){{
/apps/pyseg_system/sys/soft /disperse/latest/build ...
/infrstr ...
./sys/install/disperse/latest/sources/cf...
/cfitsio
./sys/install/cgal/4.7/sources/CGAL-4.7....
cp /apps/pyseg_system/sys/install/disperse/latest/sources...
cd /apps/src
tar xf cfitsio_3.380.tar.gz
cd cfitsio/
./configure --enable-shared --enable-static --prefix=/app...
make; make install
dnf install CGAL-devel CGAL-qt5-devel
dnf --enablerepo=devel install SDL_image-devel
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=$buildFold -DCFITSIO_DIR=$...
cmake .. -DCMAKE_INSTALL_PREFIX=/apps/pyseg_system/sys/so...
make; make install
ls /apps/src/pyseg_system/sys/soft/disperse/latest/build/...
fieldconv mse netconv skelconv
conda create -n pyseg python=3.7 opencv=4.2 graph-tool=2....
conda activate pyseg
conda install beautifulsoup4=4.9 lxml=4.6 pillow=6.2 pywa...
pip install pyfits==3.5
PATH=/apps/pyenv/versions/anaconda3-2024.10-1/envs/pyseg/...
PYTHONPATH=/apps/src/pyseg_system/code
}}
終了行:
&color(red){みかんせい};
本家様 [[https://github.com/anmartinezs/pyseg_system>+htt...
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...
#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...
[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/anma...
[root@rockylinux9 src]# cd pyseg_system
[root@rockylinux9 pyseg_system]# git log -1
commit 6baf5f9aaa11ad41b99796e548e51fafa9b4330b (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:...
:
251.7 + /usr/local/pyseg_system/sys/soft/miniconda3/bin/c...
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): ...wor...
265.8 Solving environment: ...working... failed
508.0
508.0 LibMambaUnsatisfiableError: Encountered problems wh...
508.0 - nothing provides openssl >=1.1.1,<1.1.2.0a0 nee...
508.0 - nothing provides libopencv 4.2.0 py36_5 needed ...
:
Dockerfile:22
--------------------
21 |
22 | >>> RUN cd sys && chmod u+x *.sh && ./install_ubun...
23 | >>> && ./install_miniconda.sh && ./install_con...
24 | RUN cd sys && ./set_bashrc_env.sh
--------------------
ERROR: failed to solve: process "/bin/sh -c cd sys && chm...
[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...
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/anm...
[root@rockylinux9 apps]# cd pyseg_system/
[root@rockylinux9 pyseg_system]#
}}
#code(nonumber){{
/apps/pyseg_system/sys/soft /disperse/latest/build ...
/infrstr ...
./sys/install/disperse/latest/sources/cf...
/cfitsio
./sys/install/cgal/4.7/sources/CGAL-4.7....
cp /apps/pyseg_system/sys/install/disperse/latest/sources...
cd /apps/src
tar xf cfitsio_3.380.tar.gz
cd cfitsio/
./configure --enable-shared --enable-static --prefix=/app...
make; make install
dnf install CGAL-devel CGAL-qt5-devel
dnf --enablerepo=devel install SDL_image-devel
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=$buildFold -DCFITSIO_DIR=$...
cmake .. -DCMAKE_INSTALL_PREFIX=/apps/pyseg_system/sys/so...
make; make install
ls /apps/src/pyseg_system/sys/soft/disperse/latest/build/...
fieldconv mse netconv skelconv
conda create -n pyseg python=3.7 opencv=4.2 graph-tool=2....
conda activate pyseg
conda install beautifulsoup4=4.9 lxml=4.6 pillow=6.2 pywa...
pip install pyfits==3.5
PATH=/apps/pyenv/versions/anaconda3-2024.10-1/envs/pyseg/...
PYTHONPATH=/apps/src/pyseg_system/code
}}
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