Update Dockerfile

Author: egagli

Dockerfile

@@ -1,23 +1,52 @@
 # Dockerfile
 FROM continuumio/miniconda3:latest
 
+# Create non-root user similar to jupyter's default 'jovyan'
+RUN useradd -ms /bin/bash jovyan
+USER root
+
 # Copy environment files
 COPY environment.yml /tmp/environment.yml
 COPY apt.txt /tmp/apt.txt
 
 # Install system dependencies
 RUN apt-get update && \
-    xargs apt-get install -y < /tmp/apt.txt && \
+    grep -v '^#' /tmp/apt.txt | xargs apt-get install -y && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
 # Create conda environment
 RUN conda env create -f /tmp/environment.yml && \
     conda clean -afy
 
+# Add jupyterlab to environment
+RUN conda install -n gda -c conda-forge jupyterlab && \
+    conda clean -afy
+
 # Add conda environment to PATH
-ENV PATH /opt/conda/envs/$(head -1 /tmp/environment.yml | cut -d' ' -f2)/bin:$PATH
+ENV PATH /opt/conda/envs/gda/bin:$PATH
+
+# Set up work directory and permissions
+WORKDIR /home/jovyan
+RUN chown -R jovyan:jovyan /home/jovyan
+
+# Switch to non-root user
+USER jovyan
+
+# Expose Jupyter port
+EXPOSE 8888
+
+# Start JupyterLab
+CMD ["jupyter", "lab", "--ip", "0.0.0.0", "--no-browser", "--ServerApp.token=''"]
 
-# Set the shell to bash
-SHELL ["/bin/bash", "-c"]
-ENTRYPOINT ["bash"]
+---
+# docker-compose.yml
+version: "3.9"
+services:
+  jupyterlab:
+    image: "ghcr.io/uw-gda/uwgda-image-living:latest"
+    ports:
+      - "8888:8888"
+    volumes:
+      - ${PWD}:/home/jovyan
+    user: "1000:1000"  # This matches typical Linux UID:GID for first user