BioPipelines をテンプレートにして作成
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開始行:
本家様 [[https://biopipelines.readthedocs.io/en/latest/>+...
github [[https://github.com/locbp-uzh/biopipelines>+https...
#code(nonumber){{
git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install miniforge3-26.3.2-1
source /apps/pyenv/versions/miniforge3-26.3.2-1/etc/profi...
conda update conda
(既に環境があるなら)
source /apps/pyenv/versions/miniforge3-26.3.2-1/etc/profi...
}}
#code(nonumber){{
root@ubuntu24:~# grep VERSION /etc/os-release
VERSION_ID="24.04"
VERSION="24.04.4 LTS (Noble Numbat)"
VERSION_CODENAME=noble
root@ubuntu24:~#
root@ubuntu24:~# cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX Open Kernel Module for x86_64 ...
GCC version: gcc version 13.3.0 (Ubuntu 13.3.0-6ubuntu2~...
root@ubuntu24:~# nvidia-smi -L
GPU 0: NVIDIA RTX PRO 2000 Blackwell (UUID: GPU-40660e37-...
root@ubuntu24:~#
root@ubuntu24:~# ls /usr/local/cuda-12.9/
bin extras gds-12.9 lib64 nsight-comp...
compute-sanitizer gds include libnvvp nsightee_pl...
root@ubuntu24:~#
}}
#code(nonumber){{
root@ubuntu24:~# cd /apps/
root@ubuntu24:/apps# git clone https://github.com/locbp-u...
root@ubuntu24:/apps# cd biopipelines
root@ubuntu24:/apps/biopipelines# ls
biopipelines config.local.yaml environments ...
config.cluster.yaml CONTRIBUTING.md example_pipelines...
config.colab.yaml docs LICENSE ...
root@ubuntu24:/apps/biopipelines# ls environments/
admet_ai.pip.txt dssp.yaml fra...
admet_ai.yaml dynamicbind.colab.yaml gem...
af2bind.yaml dynamicbind.pip.1.txt gem...
Aggrescan3D.colab.yaml dynamicbind.pip.2.txt gni...
Aggrescan3D.yaml dynamicbind.pip.colab.1.txt lig...
apbs.colab.yaml dynamicbind.pip.colab.2.txt lig...
apbs.yaml dynamicbind_relax.colab.yaml lig...
bioemu.yaml dynamicbind_relax.yaml Mut...
biopipelines.yaml dynamicbind.yaml neu...
Boltz2Env.pip.txt esmfold.cluster.yaml neu...
Boltz2Env.yaml esmfold.colab.yaml neu...
boltzgen.pip.txt esmfold.pip.colab.1.txt neu...
boltzgen.yaml esmfold.pip.colab.2.txt neu...
CABSflex.colab.yaml foundry.pip.txt neu...
CABSflex.yaml foundry.yaml neu...
diffdock.colab.yaml fpocket.colab.yaml neu...
diffdock.pip.colab.txt fpocket.yaml ope...
diffdock.pip.txt frame2seq.colab.yaml ope...
diffdock.yaml frame2seq.pip.colab.txt p2r...
dssp.colab.yaml frame2seq.pip.txt p2r...
root@ubuntu24:/apps/biopipelines#
root@ubuntu24:/apps/biopipelines# conda env create -f env...
root@ubuntu24:/apps/biopipelines# conda activate biopipel...
(biopipelines) root@ubuntu24:/apps/biopipelines#
(biopipelines) root@ubuntu24:/apps/biopipelines# conda list
:
ipython 9.14.0 pyh53cf698_...
:
numpy 2.4.6 py312h33ff5...
openbabel 3.1.1 py312hbfe45...
:
python 3.12.13 hd63d673_0_...
:
rdkit 2025.09.5 py312h3ecb6...
:
(biopipelines) root@ubuntu24:/apps/biopipelines#
(biopipelines) root@ubuntu24:/apps/biopipelines# conda se...
Loading channels: done
# Name Version Build Cha...
pytorch 2.11.0 cuda129_generic_py31...
pytorch 2.11.0 cuda129_generic_py31...
pytorch 2.11.0 cuda129_generic_py31...
pytorch 2.11.0 cuda129_generic_py31...
pytorch 2.11.0 cuda129_generic_py31...
pytorch 2.11.0 cuda129_mkl_py310_h5...
pytorch 2.11.0 cuda129_mkl_py311_h6...
pytorch 2.11.0 cuda129_mkl_py312_hb...
pytorch 2.11.0 cuda129_mkl_py313_hd...
pytorch 2.11.0 cuda129_mkl_py314_hf...
(biopipelines) root@ubuntu24:/apps/biopipelines#
(biopipelines) root@ubuntu24:/apps/biopipelines# conda in...
(biopipelines) root@ubuntu24:/apps/biopipelines# python -...
True
NVIDIA RTX PRO 2000 Blackwell
(biopipelines) root@ubuntu24:/apps/biopipelines#
}}
#code(nonumber){{
(biopipelines) root@ubuntu24:/apps/biopipelines# conda in...
(biopipelines) root@ubuntu24:/apps/biopipelines#
(biopipelines) root@ubuntu24:/apps/biopipelines# pytest t...
=========================================================...
platform linux -- Python 3.12.13, pytest-9.0.3, pluggy-1....
rootdir: /apps/biopipelines
configfile: pyproject.toml
collected 650 items / 146 deselected / 504 selected
tests/test_bayesian_adjuster.py .... ...
tests/test_cabsflex_colab.py ...... ...
tests/test_combinatorics.py ........................ ...
tests/test_consensus.py .... ...
tests/test_datastream.py ...................................
tests/test_folders.py .. ...
tests/test_id_map_utils.py .................................
tests/test_id_patterns.py ..................................
tests/test_internal_and_folder.py .............. ...
tests/test_ligand.py .............................. ...
tests/test_load_multiple_folder.py ... ...
tests/test_missing_propagation.py ..........................
tests/test_mock.py ................................. ...
tests/test_openbabel.py ..... ...
tests/test_panda.py .................... ...
tests/test_parallel.py ....... ...
tests/test_pdb.py ................................. ...
tests/test_pipeline_generation.py ..... ...
tests/test_pocket_validation_wiring.py ....... ...
tests/test_pool.py .............. ...
tests/test_provenance.py ................ ...
tests/test_remap.py .......... ...
tests/test_resolve_selection_in_sequence.py ..... ...
tests/test_sequence.py .............................. ...
tests/test_shell_safety.py .................................
tests/test_stream_slicers.py ................. ...
tests/test_table.py .................... ...
===================================================== 504...
(biopipelines) root@ubuntu24:/apps/biopipelines#
}}
使いたいアプリがあるなら
#code(nonumber){{
conda env update -n biopipelines -f environments/dssp.yaml
}}
とかで作った biopipelines 仮想実行環境に組み込むことはで...
実際の計算というかジョブの流し方は
#code(nonumber){{
pipeline:
- module: dssp
input_pdb: ./pdbs/1abc.pdb
output_dir: ./outputs/dssp
- module: plip
input_pdb: ./pdbs/1abc.pdb
output_dir: ./outputs/plip
}}
とか作って ./run に渡す
jupyterlab とか使った方がいいかも。でも複数のアプリをまと...
終了行:
本家様 [[https://biopipelines.readthedocs.io/en/latest/>+...
github [[https://github.com/locbp-uzh/biopipelines>+https...
#code(nonumber){{
git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install miniforge3-26.3.2-1
source /apps/pyenv/versions/miniforge3-26.3.2-1/etc/profi...
conda update conda
(既に環境があるなら)
source /apps/pyenv/versions/miniforge3-26.3.2-1/etc/profi...
}}
#code(nonumber){{
root@ubuntu24:~# grep VERSION /etc/os-release
VERSION_ID="24.04"
VERSION="24.04.4 LTS (Noble Numbat)"
VERSION_CODENAME=noble
root@ubuntu24:~#
root@ubuntu24:~# cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX Open Kernel Module for x86_64 ...
GCC version: gcc version 13.3.0 (Ubuntu 13.3.0-6ubuntu2~...
root@ubuntu24:~# nvidia-smi -L
GPU 0: NVIDIA RTX PRO 2000 Blackwell (UUID: GPU-40660e37-...
root@ubuntu24:~#
root@ubuntu24:~# ls /usr/local/cuda-12.9/
bin extras gds-12.9 lib64 nsight-comp...
compute-sanitizer gds include libnvvp nsightee_pl...
root@ubuntu24:~#
}}
#code(nonumber){{
root@ubuntu24:~# cd /apps/
root@ubuntu24:/apps# git clone https://github.com/locbp-u...
root@ubuntu24:/apps# cd biopipelines
root@ubuntu24:/apps/biopipelines# ls
biopipelines config.local.yaml environments ...
config.cluster.yaml CONTRIBUTING.md example_pipelines...
config.colab.yaml docs LICENSE ...
root@ubuntu24:/apps/biopipelines# ls environments/
admet_ai.pip.txt dssp.yaml fra...
admet_ai.yaml dynamicbind.colab.yaml gem...
af2bind.yaml dynamicbind.pip.1.txt gem...
Aggrescan3D.colab.yaml dynamicbind.pip.2.txt gni...
Aggrescan3D.yaml dynamicbind.pip.colab.1.txt lig...
apbs.colab.yaml dynamicbind.pip.colab.2.txt lig...
apbs.yaml dynamicbind_relax.colab.yaml lig...
bioemu.yaml dynamicbind_relax.yaml Mut...
biopipelines.yaml dynamicbind.yaml neu...
Boltz2Env.pip.txt esmfold.cluster.yaml neu...
Boltz2Env.yaml esmfold.colab.yaml neu...
boltzgen.pip.txt esmfold.pip.colab.1.txt neu...
boltzgen.yaml esmfold.pip.colab.2.txt neu...
CABSflex.colab.yaml foundry.pip.txt neu...
CABSflex.yaml foundry.yaml neu...
diffdock.colab.yaml fpocket.colab.yaml neu...
diffdock.pip.colab.txt fpocket.yaml ope...
diffdock.pip.txt frame2seq.colab.yaml ope...
diffdock.yaml frame2seq.pip.colab.txt p2r...
dssp.colab.yaml frame2seq.pip.txt p2r...
root@ubuntu24:/apps/biopipelines#
root@ubuntu24:/apps/biopipelines# conda env create -f env...
root@ubuntu24:/apps/biopipelines# conda activate biopipel...
(biopipelines) root@ubuntu24:/apps/biopipelines#
(biopipelines) root@ubuntu24:/apps/biopipelines# conda list
:
ipython 9.14.0 pyh53cf698_...
:
numpy 2.4.6 py312h33ff5...
openbabel 3.1.1 py312hbfe45...
:
python 3.12.13 hd63d673_0_...
:
rdkit 2025.09.5 py312h3ecb6...
:
(biopipelines) root@ubuntu24:/apps/biopipelines#
(biopipelines) root@ubuntu24:/apps/biopipelines# conda se...
Loading channels: done
# Name Version Build Cha...
pytorch 2.11.0 cuda129_generic_py31...
pytorch 2.11.0 cuda129_generic_py31...
pytorch 2.11.0 cuda129_generic_py31...
pytorch 2.11.0 cuda129_generic_py31...
pytorch 2.11.0 cuda129_generic_py31...
pytorch 2.11.0 cuda129_mkl_py310_h5...
pytorch 2.11.0 cuda129_mkl_py311_h6...
pytorch 2.11.0 cuda129_mkl_py312_hb...
pytorch 2.11.0 cuda129_mkl_py313_hd...
pytorch 2.11.0 cuda129_mkl_py314_hf...
(biopipelines) root@ubuntu24:/apps/biopipelines#
(biopipelines) root@ubuntu24:/apps/biopipelines# conda in...
(biopipelines) root@ubuntu24:/apps/biopipelines# python -...
True
NVIDIA RTX PRO 2000 Blackwell
(biopipelines) root@ubuntu24:/apps/biopipelines#
}}
#code(nonumber){{
(biopipelines) root@ubuntu24:/apps/biopipelines# conda in...
(biopipelines) root@ubuntu24:/apps/biopipelines#
(biopipelines) root@ubuntu24:/apps/biopipelines# pytest t...
=========================================================...
platform linux -- Python 3.12.13, pytest-9.0.3, pluggy-1....
rootdir: /apps/biopipelines
configfile: pyproject.toml
collected 650 items / 146 deselected / 504 selected
tests/test_bayesian_adjuster.py .... ...
tests/test_cabsflex_colab.py ...... ...
tests/test_combinatorics.py ........................ ...
tests/test_consensus.py .... ...
tests/test_datastream.py ...................................
tests/test_folders.py .. ...
tests/test_id_map_utils.py .................................
tests/test_id_patterns.py ..................................
tests/test_internal_and_folder.py .............. ...
tests/test_ligand.py .............................. ...
tests/test_load_multiple_folder.py ... ...
tests/test_missing_propagation.py ..........................
tests/test_mock.py ................................. ...
tests/test_openbabel.py ..... ...
tests/test_panda.py .................... ...
tests/test_parallel.py ....... ...
tests/test_pdb.py ................................. ...
tests/test_pipeline_generation.py ..... ...
tests/test_pocket_validation_wiring.py ....... ...
tests/test_pool.py .............. ...
tests/test_provenance.py ................ ...
tests/test_remap.py .......... ...
tests/test_resolve_selection_in_sequence.py ..... ...
tests/test_sequence.py .............................. ...
tests/test_shell_safety.py .................................
tests/test_stream_slicers.py ................. ...
tests/test_table.py .................... ...
===================================================== 504...
(biopipelines) root@ubuntu24:/apps/biopipelines#
}}
使いたいアプリがあるなら
#code(nonumber){{
conda env update -n biopipelines -f environments/dssp.yaml
}}
とかで作った biopipelines 仮想実行環境に組み込むことはで...
実際の計算というかジョブの流し方は
#code(nonumber){{
pipeline:
- module: dssp
input_pdb: ./pdbs/1abc.pdb
output_dir: ./outputs/dssp
- module: plip
input_pdb: ./pdbs/1abc.pdb
output_dir: ./outputs/plip
}}
とか作って ./run に渡す
jupyterlab とか使った方がいいかも。でも複数のアプリをまと...
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