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Update Dockerfile and docker-compose.yaml. By default, container can use cifs to map network drives so no need to install, and added bash command to docker compose file to run both jupyterlab and dash board simultanously

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florez_j
2025-04-02 14:09:44 +02:00
parent c6b010702c
commit 73648ebe31
2 changed files with 56 additions and 48 deletions
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96
Dockerfile
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@ -1,46 +1,50 @@
# Get additional info about the Dockerfile at https://docs.docker.com/reference/dockerfile/ # Get additional info about the Dockerfile at https://docs.docker.com/reference/dockerfile/
FROM continuumio/miniconda3:latest FROM continuumio/miniconda3:latest
# Define the name of the environment # Define the name of the environment
ARG ENV_NAME=apog_penv ARG ENV_NAME=apog_penv
ENV ENV_NAME=apog_penv ENV ENV_NAME=apog_penv
# Set the working directory # Set the working directory
WORKDIR /acsmdc WORKDIR /acsmdc
# Use mamba if available for faster installation #RUN apt-get update && apt-get install -y cifs-utils
RUN conda install -y -n base -c conda-forge mamba && \
mamba create -y -n $ENV_NAME -c conda-forge -c defaults python=3.11 \ # Use mamba if available for faster installation
jupyter numpy h5py pandas matplotlib plotly=5.24 scipy pip && \ RUN conda install -y -n base -c conda-forge mamba && \
conda clean --all -y && rm -rf /root/.cache/pip mamba create -y -n $ENV_NAME -c conda-forge -c defaults python=3.11 \
jupyter numpy h5py pandas matplotlib plotly=5.24 scipy pip && \
# Activate the environment and install additional pip packages conda clean --all -y && rm -rf /root/.cache/pip
RUN conda run -n $ENV_NAME pip install pybis==1.35 igor2 ipykernel sphinx dash dash-bootstrap-components
# Activate the environment and install additional pip packages
# Set the default environment when the container starts RUN conda run -n $ENV_NAME pip install pybis==1.35 igor2 ipykernel sphinx dash dash-bootstrap-components
ENV CONDA_DEFAULT_ENV=$ENV_NAME
ENV PATH=/opt/conda/envs/$ENV_NAME/bin:$PATH # Set the default environment when the container starts
ENV CONDA_DEFAULT_ENV=$ENV_NAME
# Create necessary directories for VOLUME ENV PATH=/opt/conda/envs/$ENV_NAME/bin:$PATH
RUN mkdir -p /acsmdc/data /acsmdc/figures /acsmdc/pipelines/params
# Create necessary directories for VOLUME
# Copy project files, excluding certain directories (handled via .dockerignore) RUN mkdir -p /acsmdc/data /acsmdc/figures /acsmdc/pipelines/params
COPY . /acsmdc #RUN mkdir -p /mnt/lac_ord
# Copy and install dependencies from requirements.txt # Copy project files, excluding certain directories (handled via .dockerignore)
COPY requirements.txt /acsmdc/requirements.txt COPY . /acsmdc
RUN conda run -n $ENV_NAME pip install -r /acsmdc/requirements.txt
# Copy and install dependencies from requirements.txt
# Define volumes for excluded directories COPY requirements.txt /acsmdc/requirements.txt
VOLUME ["/acsmdc/data", "/acsmdc/figures", "/acsmdc/pipelines/params"] RUN conda run -n $ENV_NAME pip install -r /acsmdc/requirements.txt
# Add JupyterLab # Define volumes for excluded directories
RUN pip install --no-cache-dir jupyterlab VOLUME ["/acsmdc/data", "/acsmdc/figures", "/acsmdc/pipelines/params"]
#RUN pip install pipx
#RUN pipx install renku # Add JupyterLab
# Add any other packages needed for JupyterLab RUN pip install --no-cache-dir jupyterlab
#RUN pip install --no-cache-dir matplotlib scikit-learn #RUN pip install pipx
#RUN pipx install renku
# If you want to set JupyterLab as the default command # Add any other packages needed for JupyterLab
CMD ["jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root", "--NotebookApp.token='my-token'"] #RUN pip install --no-cache-dir matplotlib scikit-learn
# If you want to set JupyterLab as the default command
#CMD ["jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root", "--NotebookApp.token='my-token'"]
CMD ["/bin/bash"]

8
docker-compose.yaml
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@ -1,5 +1,5 @@
services: services:
data_processor: datachain_processor:
image: datachain_processor image: datachain_processor
container_name: datachain_processor container_name: datachain_processor
restart: unless-stopped restart: unless-stopped
@ -13,7 +13,11 @@ services:
- ./figures:/acsmdc/figures - ./figures:/acsmdc/figures
- ./pipelines/params:/acsmdc/pipelines/params - ./pipelines/params:/acsmdc/pipelines/params
- lac_ord:/mnt/network/lac_ord:rw - lac_ord:/mnt/network/lac_ord:rw
command: ["jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root", "--NotebookApp.token='my-token'"] command: >
bash -c "
jupyter lab --ip=0.0.0.0 --port=8888 --no-browser --allow-root --NotebookApp.token='my-token' &
python /acsmdc/app/data_flagging_app.py
"
volumes: volumes:
lac_ord: lac_ord: