Update Dockerfile

Dockerfile

@@ -1,28 +1,19 @@
-# Stage 1: Generate SSH key pair and clone repository
+# Stage 1: Base image for building
 FROM rocker/shiny:4.0.0 AS builder
 
 # Install git and openssh-client
 RUN apt-get update && apt-get install -y git openssh-client
 
-# Generate SSH key pair
-RUN ssh-keygen -t rsa -b 4096 -C "your_email@example.com" -f /root/.ssh/id_rsa -N ''
-
-# Add GitHub to known hosts
-RUN ssh-keyscan github.com >> /root/.ssh/known_hosts
-
-# Clone the repository
-ARG UN
-ARG FILE
-RUN git clone git@github.com:${UN}/${FILE}.git /srv/shiny-server/app
-
-
 # Stage 2: Final image
 FROM rocker/shiny:4.0.0
 
-# Copy application from builder stage
-COPY --from=builder /srv/shiny-server/app /srv/shiny-server/app
+# Copy installed packages from builder stage
+COPY --from=builder /usr/local/lib/R/site-library/ /usr/local/lib/R/site-library/
+
+# Copy installed system packages from builder stage
+COPY --from=builder /var/lib/apt/lists/ /var/lib/apt/lists/
 
-# Set working directory
+# Set up working directory
 WORKDIR /srv/shiny-server/app
 
 # Install additional R packages
@@ -35,6 +26,22 @@ RUN install2.r --error \
     zoo \
     dplyr
 
+# Arguments
+ARG UN
+ARG FILE
+ARG PAT
+
+# Create SSH directory
+RUN mkdir -p /root/.ssh
+
+# Copy the SSH private key into the container
+RUN echo "$PAT" > /root/.ssh/id_rsa \
+    && chmod 600 /root/.ssh/id_rsa \
+    && ssh-keyscan github.com >> /root/.ssh/known_hosts
+
+# Clone the repository using SSH
+RUN git clone git@github.com:${UN}/${FILE}.git /srv/shiny-server/app
+
 # Set Auth0 config file path
 RUN echo "options(auth0_find_config_file = '/srv/shiny-server/app/_auth0.yml')" > /usr/local/lib/R/etc/Rprofile.site