Renamed Dockerfile to avoid conflicts with project rekurization/init

Dockerfile.acsmchain

@@ -0,0 +1,50 @@
+# Get additional info about the Dockerfile at https://docs.docker.com/reference/dockerfile/ 
+
+FROM continuumio/miniconda3:latest
+
+# Define the name of the environment
+ARG ENV_NAME=apog_penv
+ENV ENV_NAME=apog_penv
+
+# Set the working directory
+WORKDIR /acsmdc
+
+#RUN apt-get update && apt-get install -y cifs-utils
+
+# Use mamba if available for faster installation
+RUN conda install -y -n base -c conda-forge mamba && \
+    mamba create -y -n $ENV_NAME -c conda-forge python=3.11 \
+    jupyter numpy h5py pandas matplotlib plotly=5.24 scipy pip && \
+    conda clean --all -y && rm -rf /root/.cache/pip
+
+# Activate the environment and install additional pip packages
+RUN conda run -n $ENV_NAME pip install pybis==1.35 igor2 ipykernel sphinx dash dash-bootstrap-components
+
+# Set the default environment when the container starts
+ENV CONDA_DEFAULT_ENV=$ENV_NAME
+ENV PATH=/opt/conda/envs/$ENV_NAME/bin:$PATH
+
+# Create necessary directories for VOLUME
+RUN mkdir -p /acsmdc/data /acsmdc/figures /acsmdc/pipelines/params
+#RUN mkdir -p /mnt/lac_ord
+
+# Copy project files, excluding certain directories (handled via .dockerignore)
+COPY . /acsmdc
+
+# Copy and install dependencies from requirements.txt
+COPY requirements.txt /acsmdc/requirements.txt
+RUN conda run -n $ENV_NAME pip install -r /acsmdc/requirements.txt
+
+# Define volumes for excluded directories
+VOLUME ["/acsmdc/data", "/acsmdc/figures", "/acsmdc/pipelines/params"]
+
+# Add JupyterLab
+RUN pip install --no-cache-dir jupyterlab
+#RUN pip install pipx
+#RUN pipx install renku
+# Add any other packages needed for JupyterLab
+#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"]