Enhance documentation and automate R package management

Update documentation to reflect that all tools are provided via a builder Docker image

- Simplify prerequisites section in Readme.md
- Add detailed explanation of the builder image and its role
- Document R package caching mechanism for faster builds
- Update start-jupyterhub.sh to build and use the builder image
- Add Dockerfile.builder to provide the build environment
- Implement automatic R dependency detection and installation
- Update Slides.qmd to use gt package for better table formatting

obijupyterhub/Dockerfile.builder

@@ -0,0 +1,68 @@
+# Dockerfile.builder
+# Image containing all tools needed to prepare the OBIJupyterHub stack
+# This allows the host system to only require Docker to be installed
+
+FROM ubuntu:24.04
+
+LABEL maintainer="OBIJupyterHub"
+LABEL description="Builder image for OBIJupyterHub preparation tasks"
+
+# Avoid interactive prompts during package installation
+ENV DEBIAN_FRONTEND=noninteractive
+ENV TZ=Etc/UTC
+
+# Install base dependencies and R
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+       ca-certificates \
+       curl \
+       wget \
+       git \
+       rsync \
+       python3 \
+       r-base \
+       r-base-dev \
+       libcurl4-openssl-dev \
+       libssl-dev \
+       libxml2-dev \
+       libfontconfig1-dev \
+       libharfbuzz-dev \
+       libfribidi-dev \
+       libfreetype6-dev \
+       libpng-dev \
+       libtiff5-dev \
+       libjpeg-dev \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install the attachment package in a separate location (not overwritten by volume mount)
+# This ensures attachment is always available even when site-library is mounted as a volume
+ENV R_LIBS_BUILDER=/opt/R/builder-packages
+RUN mkdir -p ${R_LIBS_BUILDER} \
+    && R -e "install.packages('attachment', lib='${R_LIBS_BUILDER}', repos='https://cloud.r-project.org/')"
+
+# Install Hugo (extended version for SCSS support)
+# Detect architecture and download appropriate binary
+ARG HUGO_VERSION=0.140.2
+RUN ARCH=$(dpkg --print-architecture) \
+    && case "$ARCH" in \
+         amd64) HUGO_ARCH="amd64" ;; \
+         arm64) HUGO_ARCH="arm64" ;; \
+         *) echo "Unsupported architecture: $ARCH" && exit 1 ;; \
+       esac \
+    && curl -fsSL "https://github.com/gohugoio/hugo/releases/download/v${HUGO_VERSION}/hugo_extended_${HUGO_VERSION}_linux-${HUGO_ARCH}.tar.gz" \
+       | tar -xz -C /usr/local/bin hugo \
+    && chmod +x /usr/local/bin/hugo
+
+# Install Quarto using the official .deb package (handles all dependencies properly)
+ARG QUARTO_VERSION=1.6.42
+RUN ARCH=$(dpkg --print-architecture) \
+    && curl -fsSL -o /tmp/quarto.deb "https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-${ARCH}.deb" \
+    && dpkg -i /tmp/quarto.deb \
+    && rm /tmp/quarto.deb
+
+# Create working directory
+WORKDIR /workspace
+
+# Default command
+CMD ["/bin/bash"]