miffi をテンプレートにして作成
[
トップ
] [
新規
|
一覧
|
検索
|
最終更新
|
ヘルプ
|
ログイン
]
開始行:
本家様 [[https://github.com/ando-lab/miffi>+https://githu...
pipy[[https://pypi.org/project/miffi/>+https://pypi.org/p...
Cryo-EM micrograph filtering utilizing Fourier space info...
各自のホームディレクトリに各種pythonアプリの実行環境を用...
pyenvでOS提供のpython環境から離れ、そのpyenv上にconda環境...
ここでは「/apps/pyenv」を起点としています
#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 miniforge3-26.1.0-0
source /apps/pyenv/versions/miniforge3-26.1.0-0/etc/profi...
conda update -n base -c conda-forge conda
}}
既にpyenv/conda 環境があるなら
#code(nonumber){{
source /apps/pyenv/versions/<conda>/etc/profile.d/conda.sh
}}
として「pyenv-conda」環境を整備します
っで、
#code(nonumber){{
conda create -n miffi python=3.9
conda activate miffi
cd /apps/src
git clone https://github.com/ando-lab/miffi.git
cd miffi
pip install .
mkdir /apps/miffi
miffi download -d /apps/miffi
conda deactivate
}}
Environment-modules
「/apps/modulefiles/miffi」
#code(nonumber){{
#%Module
set root /apps/pyenv/versions/miniforge3-26.1.0-...
prepend-path PATH $root/bin
prepend-path LD_LIBRARY_PATH $root/lib
}}
一応conda list
#code(nonumber){{
# packages in environment at /apps/pyenv/versions/minifor...
#
# Name Version Build...
_openmp_mutex 4.5 20_gn...
annotated-doc 0.0.4 pypi_...
anyio 4.12.1 pypi_...
argon2-cffi 25.1.0 pypi_...
argon2-cffi-bindings 25.1.0 pypi_...
arrow 1.4.0 pypi_...
asttokens 3.0.1 pypi_...
async-lru 2.0.5 pypi_...
attrs 25.4.0 pypi_...
babel 2.18.0 pypi_...
beautifulsoup4 4.14.3 pypi_...
bleach 6.2.0 pypi_...
bzip2 1.0.8 hda65...
ca-certificates 2026.2.25 hbd8a...
certifi 2026.2.25 pypi_...
cffi 2.0.0 pypi_...
charset-normalizer 3.4.6 pypi_...
click 8.1.8 pypi_...
comm 0.2.3 pypi_...
contourpy 1.3.0 pypi_...
cycler 0.12.1 pypi_...
debugpy 1.8.20 pypi_...
decorator 5.2.1 pypi_...
defusedxml 0.7.1 pypi_...
exceptiongroup 1.3.1 pypi_...
executing 2.2.1 pypi_...
fastjsonschema 2.21.2 pypi_...
filelock 3.19.1 pypi_...
fonttools 4.60.2 pypi_...
fqdn 1.5.1 pypi_...
fsspec 2025.10.0 pypi_...
h11 0.16.0 pypi_...
hf-xet 1.4.2 pypi_...
httpcore 1.0.9 pypi_...
httpx 0.28.1 pypi_...
huggingface-hub 1.7.1 pypi_...
icu 78.3 h33c6...
idna 3.11 pypi_...
importlib-metadata 8.7.1 pypi_...
importlib-resources 6.5.2 pypi_...
ipykernel 6.31.0 pypi_...
ipython 8.18.1 pypi_...
ipywidgets 8.1.8 pypi_...
isoduration 20.11.0 pypi_...
jedi 0.19.2 pypi_...
jinja2 3.1.6 pypi_...
json5 0.13.0 pypi_...
jsonpointer 3.0.0 pypi_...
jsonschema 4.25.1 pypi_...
jsonschema-specifications 2025.9.1 pypi_...
jupyter-client 8.6.3 pypi_...
jupyter-core 5.8.1 pypi_...
jupyter-events 0.12.0 pypi_...
jupyter-lsp 2.3.0 pypi_...
jupyter-server 2.17.0 pypi_...
jupyter-server-terminals 0.5.4 pypi_...
jupyterlab 4.5.6 pypi_...
jupyterlab-pygments 0.3.0 pypi_...
jupyterlab-server 2.28.0 pypi_...
jupyterlab-widgets 3.0.16 pypi_...
kiwisolver 1.4.7 pypi_...
lark 1.3.1 pypi_...
ld_impl_linux-64 2.45.1 defau...
libexpat 2.7.4 hecca...
libffi 3.5.2 h3435...
libgcc 15.2.0 he0fe...
libgcc-ng 15.2.0 h69a7...
libgomp 15.2.0 he0fe...
liblzma 5.8.2 hb03c...
libnsl 2.0.1 hb9d3...
libsqlite 3.52.0 hf4e2...
libstdcxx 15.2.0 h934c...
libuuid 2.41.3 h5347...
libxcrypt 4.4.36 hd590...
libzlib 1.3.1 hb9d3...
markdown-it-py 3.0.0 pypi_...
markupsafe 3.0.3 pypi_...
matplotlib 3.9.4 pypi_...
matplotlib-inline 0.2.1 pypi_...
mdurl 0.1.2 pypi_...
miffi 1.0.2.dev5+g697c72545 pypi_...
mistune 3.2.0 pypi_...
mpmath 1.3.0 pypi_...
mrcfile 1.5.4 pypi_...
nbclient 0.10.2 pypi_...
nbconvert 7.17.0 pypi_...
nbformat 5.10.4 pypi_...
ncurses 6.5 h2d0b...
nest-asyncio 1.6.0 pypi_...
networkx 3.2.1 pypi_...
notebook-shim 0.2.4 pypi_...
numpy 2.0.2 pypi_...
nvidia-cublas-cu12 12.8.4.1 pypi_...
nvidia-cuda-cupti-cu12 12.8.90 pypi_...
nvidia-cuda-nvrtc-cu12 12.8.93 pypi_...
nvidia-cuda-runtime-cu12 12.8.90 pypi_...
nvidia-cudnn-cu12 9.10.2.21 pypi_...
nvidia-cufft-cu12 11.3.3.83 pypi_...
nvidia-cufile-cu12 1.13.1.3 pypi_...
nvidia-curand-cu12 10.3.9.90 pypi_...
nvidia-cusolver-cu12 11.7.3.90 pypi_...
nvidia-cusparse-cu12 12.5.8.93 pypi_...
nvidia-cusparselt-cu12 0.7.1 pypi_...
nvidia-nccl-cu12 2.27.3 pypi_...
nvidia-nvjitlink-cu12 12.8.93 pypi_...
nvidia-nvtx-cu12 12.8.90 pypi_...
openssl 3.6.1 h35e6...
overrides 7.7.0 pypi_...
packaging 26.0 pypi_...
pandas 2.3.3 pypi_...
pandocfilters 1.5.1 pypi_...
parso 0.8.6 pypi_...
pexpect 4.9.0 pypi_...
pillow 11.3.0 pypi_...
pip 25.2 pyh8b...
platformdirs 4.4.0 pypi_...
prometheus-client 0.24.1 pypi_...
prompt-toolkit 3.0.52 pypi_...
psutil 7.2.2 pypi_...
ptyprocess 0.7.0 pypi_...
pure-eval 0.2.3 pypi_...
pyarrow 21.0.0 pypi_...
pycparser 2.23 pypi_...
pygments 2.19.2 pypi_...
pyparsing 3.3.2 pypi_...
python 3.9.23 hc30a...
python-dateutil 2.9.0.post0 pypi_...
python-json-logger 4.0.0 pypi_...
pytz 2026.1.post1 pypi_...
pyyaml 6.0.3 pypi_...
pyzmq 27.1.0 pypi_...
readline 8.3 h853b...
referencing 0.36.2 pypi_...
requests 2.32.5 pypi_...
rfc3339-validator 0.1.4 pypi_...
rfc3986-validator 0.1.1 pypi_...
rfc3987-syntax 1.1.0 pypi_...
rich 14.3.3 pypi_...
rpds-py 0.27.1 pypi_...
safetensors 0.7.0 pypi_...
send2trash 2.1.0 pypi_...
setuptools 80.9.0 pyhff...
shellingham 1.5.4 pypi_...
six 1.17.0 pypi_...
soupsieve 2.8.3 pypi_...
stack-data 0.6.3 pypi_...
starfile 0.5.13 pypi_...
sympy 1.14.0 pypi_...
terminado 0.18.1 pypi_...
timm 1.0.25 pypi_...
tinycss2 1.4.0 pypi_...
tk 8.6.13 noxft...
tomli 2.4.0 pypi_...
torch 2.8.0 pypi_...
torchvision 0.23.0 pypi_...
tornado 6.5.5 pypi_...
tqdm 4.67.3 pypi_...
traitlets 5.14.3 pypi_...
triton 3.4.0 pypi_...
typer 0.23.2 pypi_...
typing-extensions 4.15.0 pypi_...
tzdata 2025.3 pypi_...
uri-template 1.3.0 pypi_...
urllib3 2.6.3 pypi_...
wcwidth 0.6.0 pypi_...
webcolors 24.11.1 pypi_...
webencodings 0.5.1 pypi_...
websocket-client 1.9.0 pypi_...
wheel 0.45.1 pyhd8...
widgetsnbextension 4.0.15 pypi_...
zipp 3.23.0 pypi_...
zstd 1.5.7 hb78e...
}}
終了行:
本家様 [[https://github.com/ando-lab/miffi>+https://githu...
pipy[[https://pypi.org/project/miffi/>+https://pypi.org/p...
Cryo-EM micrograph filtering utilizing Fourier space info...
各自のホームディレクトリに各種pythonアプリの実行環境を用...
pyenvでOS提供のpython環境から離れ、そのpyenv上にconda環境...
ここでは「/apps/pyenv」を起点としています
#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 miniforge3-26.1.0-0
source /apps/pyenv/versions/miniforge3-26.1.0-0/etc/profi...
conda update -n base -c conda-forge conda
}}
既にpyenv/conda 環境があるなら
#code(nonumber){{
source /apps/pyenv/versions/<conda>/etc/profile.d/conda.sh
}}
として「pyenv-conda」環境を整備します
っで、
#code(nonumber){{
conda create -n miffi python=3.9
conda activate miffi
cd /apps/src
git clone https://github.com/ando-lab/miffi.git
cd miffi
pip install .
mkdir /apps/miffi
miffi download -d /apps/miffi
conda deactivate
}}
Environment-modules
「/apps/modulefiles/miffi」
#code(nonumber){{
#%Module
set root /apps/pyenv/versions/miniforge3-26.1.0-...
prepend-path PATH $root/bin
prepend-path LD_LIBRARY_PATH $root/lib
}}
一応conda list
#code(nonumber){{
# packages in environment at /apps/pyenv/versions/minifor...
#
# Name Version Build...
_openmp_mutex 4.5 20_gn...
annotated-doc 0.0.4 pypi_...
anyio 4.12.1 pypi_...
argon2-cffi 25.1.0 pypi_...
argon2-cffi-bindings 25.1.0 pypi_...
arrow 1.4.0 pypi_...
asttokens 3.0.1 pypi_...
async-lru 2.0.5 pypi_...
attrs 25.4.0 pypi_...
babel 2.18.0 pypi_...
beautifulsoup4 4.14.3 pypi_...
bleach 6.2.0 pypi_...
bzip2 1.0.8 hda65...
ca-certificates 2026.2.25 hbd8a...
certifi 2026.2.25 pypi_...
cffi 2.0.0 pypi_...
charset-normalizer 3.4.6 pypi_...
click 8.1.8 pypi_...
comm 0.2.3 pypi_...
contourpy 1.3.0 pypi_...
cycler 0.12.1 pypi_...
debugpy 1.8.20 pypi_...
decorator 5.2.1 pypi_...
defusedxml 0.7.1 pypi_...
exceptiongroup 1.3.1 pypi_...
executing 2.2.1 pypi_...
fastjsonschema 2.21.2 pypi_...
filelock 3.19.1 pypi_...
fonttools 4.60.2 pypi_...
fqdn 1.5.1 pypi_...
fsspec 2025.10.0 pypi_...
h11 0.16.0 pypi_...
hf-xet 1.4.2 pypi_...
httpcore 1.0.9 pypi_...
httpx 0.28.1 pypi_...
huggingface-hub 1.7.1 pypi_...
icu 78.3 h33c6...
idna 3.11 pypi_...
importlib-metadata 8.7.1 pypi_...
importlib-resources 6.5.2 pypi_...
ipykernel 6.31.0 pypi_...
ipython 8.18.1 pypi_...
ipywidgets 8.1.8 pypi_...
isoduration 20.11.0 pypi_...
jedi 0.19.2 pypi_...
jinja2 3.1.6 pypi_...
json5 0.13.0 pypi_...
jsonpointer 3.0.0 pypi_...
jsonschema 4.25.1 pypi_...
jsonschema-specifications 2025.9.1 pypi_...
jupyter-client 8.6.3 pypi_...
jupyter-core 5.8.1 pypi_...
jupyter-events 0.12.0 pypi_...
jupyter-lsp 2.3.0 pypi_...
jupyter-server 2.17.0 pypi_...
jupyter-server-terminals 0.5.4 pypi_...
jupyterlab 4.5.6 pypi_...
jupyterlab-pygments 0.3.0 pypi_...
jupyterlab-server 2.28.0 pypi_...
jupyterlab-widgets 3.0.16 pypi_...
kiwisolver 1.4.7 pypi_...
lark 1.3.1 pypi_...
ld_impl_linux-64 2.45.1 defau...
libexpat 2.7.4 hecca...
libffi 3.5.2 h3435...
libgcc 15.2.0 he0fe...
libgcc-ng 15.2.0 h69a7...
libgomp 15.2.0 he0fe...
liblzma 5.8.2 hb03c...
libnsl 2.0.1 hb9d3...
libsqlite 3.52.0 hf4e2...
libstdcxx 15.2.0 h934c...
libuuid 2.41.3 h5347...
libxcrypt 4.4.36 hd590...
libzlib 1.3.1 hb9d3...
markdown-it-py 3.0.0 pypi_...
markupsafe 3.0.3 pypi_...
matplotlib 3.9.4 pypi_...
matplotlib-inline 0.2.1 pypi_...
mdurl 0.1.2 pypi_...
miffi 1.0.2.dev5+g697c72545 pypi_...
mistune 3.2.0 pypi_...
mpmath 1.3.0 pypi_...
mrcfile 1.5.4 pypi_...
nbclient 0.10.2 pypi_...
nbconvert 7.17.0 pypi_...
nbformat 5.10.4 pypi_...
ncurses 6.5 h2d0b...
nest-asyncio 1.6.0 pypi_...
networkx 3.2.1 pypi_...
notebook-shim 0.2.4 pypi_...
numpy 2.0.2 pypi_...
nvidia-cublas-cu12 12.8.4.1 pypi_...
nvidia-cuda-cupti-cu12 12.8.90 pypi_...
nvidia-cuda-nvrtc-cu12 12.8.93 pypi_...
nvidia-cuda-runtime-cu12 12.8.90 pypi_...
nvidia-cudnn-cu12 9.10.2.21 pypi_...
nvidia-cufft-cu12 11.3.3.83 pypi_...
nvidia-cufile-cu12 1.13.1.3 pypi_...
nvidia-curand-cu12 10.3.9.90 pypi_...
nvidia-cusolver-cu12 11.7.3.90 pypi_...
nvidia-cusparse-cu12 12.5.8.93 pypi_...
nvidia-cusparselt-cu12 0.7.1 pypi_...
nvidia-nccl-cu12 2.27.3 pypi_...
nvidia-nvjitlink-cu12 12.8.93 pypi_...
nvidia-nvtx-cu12 12.8.90 pypi_...
openssl 3.6.1 h35e6...
overrides 7.7.0 pypi_...
packaging 26.0 pypi_...
pandas 2.3.3 pypi_...
pandocfilters 1.5.1 pypi_...
parso 0.8.6 pypi_...
pexpect 4.9.0 pypi_...
pillow 11.3.0 pypi_...
pip 25.2 pyh8b...
platformdirs 4.4.0 pypi_...
prometheus-client 0.24.1 pypi_...
prompt-toolkit 3.0.52 pypi_...
psutil 7.2.2 pypi_...
ptyprocess 0.7.0 pypi_...
pure-eval 0.2.3 pypi_...
pyarrow 21.0.0 pypi_...
pycparser 2.23 pypi_...
pygments 2.19.2 pypi_...
pyparsing 3.3.2 pypi_...
python 3.9.23 hc30a...
python-dateutil 2.9.0.post0 pypi_...
python-json-logger 4.0.0 pypi_...
pytz 2026.1.post1 pypi_...
pyyaml 6.0.3 pypi_...
pyzmq 27.1.0 pypi_...
readline 8.3 h853b...
referencing 0.36.2 pypi_...
requests 2.32.5 pypi_...
rfc3339-validator 0.1.4 pypi_...
rfc3986-validator 0.1.1 pypi_...
rfc3987-syntax 1.1.0 pypi_...
rich 14.3.3 pypi_...
rpds-py 0.27.1 pypi_...
safetensors 0.7.0 pypi_...
send2trash 2.1.0 pypi_...
setuptools 80.9.0 pyhff...
shellingham 1.5.4 pypi_...
six 1.17.0 pypi_...
soupsieve 2.8.3 pypi_...
stack-data 0.6.3 pypi_...
starfile 0.5.13 pypi_...
sympy 1.14.0 pypi_...
terminado 0.18.1 pypi_...
timm 1.0.25 pypi_...
tinycss2 1.4.0 pypi_...
tk 8.6.13 noxft...
tomli 2.4.0 pypi_...
torch 2.8.0 pypi_...
torchvision 0.23.0 pypi_...
tornado 6.5.5 pypi_...
tqdm 4.67.3 pypi_...
traitlets 5.14.3 pypi_...
triton 3.4.0 pypi_...
typer 0.23.2 pypi_...
typing-extensions 4.15.0 pypi_...
tzdata 2025.3 pypi_...
uri-template 1.3.0 pypi_...
urllib3 2.6.3 pypi_...
wcwidth 0.6.0 pypi_...
webcolors 24.11.1 pypi_...
webencodings 0.5.1 pypi_...
websocket-client 1.9.0 pypi_...
wheel 0.45.1 pyhd8...
widgetsnbextension 4.0.15 pypi_...
zipp 3.23.0 pypi_...
zstd 1.5.7 hb78e...
}}
ページ名:
1
![[PukiWiki]](image/picc.png "[PukiWiki]")
