Update Dockerfile

Dockerfile

@@ -1,14 +1,61 @@
+# Use the R base image
 FROM rocker/r-base:latest
 
+# Switch to /code as our working directory
 WORKDIR /code
 
+# ------------------------------------------------------------------------------
+# 1) Install system dependencies + Miniconda
+# ------------------------------------------------------------------------------
+RUN apt-get update -y && \
+    apt-get install -y --no-install-recommends \
+        wget \
+        bzip2 \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install Miniconda to /opt/conda
+RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /tmp/miniconda.sh \
+    && /bin/bash /tmp/miniconda.sh -b -p /opt/conda \
+    && rm /tmp/miniconda.sh \
+    && /opt/conda/bin/conda clean -afy
+
+# Make sure conda is on PATH
+ENV PATH=/opt/conda/bin:$PATH
+
+# ------------------------------------------------------------------------------
+# 2) Install required R packages
+#    (We add reticulate + a few extras such as DT and shinydashboard
+#     since your app uses them.)
+# ------------------------------------------------------------------------------
 RUN install2.r --error \
     shiny \
     dplyr \
     ggplot2 \
     readr \
-    ggExtra
-    
+    ggExtra \
+    DT \
+    shinydashboard \
+    reticulate \
+    remotes
+
+# ------------------------------------------------------------------------------
+# 3) Copy your local code (including app.R and CODEBASE) into the container
+# ------------------------------------------------------------------------------
 COPY . .
 
-CMD ["R", "--quiet", "-e", "shiny::runApp(host='0.0.0.0', port=7860)"]
+# If your `fastrerandomize` package is on GitHub and not installed yet,
+# uncomment and adjust the GitHub URL as appropriate:
+# RUN Rscript -e "remotes::install_github('cjerzak/fastrerandomize-software/fastrerandomize')"
+
+# ------------------------------------------------------------------------------
+# 4) (Optional) Pre-build the conda environment inside the Docker image
+#    by calling your 'build_backend()' function. 
+#    This ensures that JAX/numpy are already installed.
+# ------------------------------------------------------------------------------
+RUN Rscript -e "source('CODEBASE'); build_backend(conda_env='fastrerandomize', conda='auto')"
+
+# ------------------------------------------------------------------------------
+# 5) Expose the Shiny port and set default command to run the Shiny app
+# ------------------------------------------------------------------------------
+EXPOSE 7860
+CMD ["R", "--quiet", "-e", "shiny::runApp('/code', host='0.0.0.0', port=7860)"]