Image multistage

Dockerfile

@@ -1,47 +1,49 @@
-FROM jupyter/base-notebook:latest
+# ---------- Stage 1 : builder ----------
+FROM jupyter/base-notebook:latest AS builder
 
 USER root
 
-# Install R and system dependencies
+# Install system dependencies for R, build tools and Go/Rust
 RUN apt-get update && apt-get install -y \
-    r-base \
-    r-base-dev \
-    libcurl4-openssl-dev \
-    libssl-dev \
-    libxml2-dev \
-    git \
-    build-essential \
-    curl \
+    r-base r-base-dev \
+    libcurl4-openssl-dev libssl-dev libxml2-dev \
+    build-essential git curl \
     && apt-get clean && rm -rf /var/lib/apt/lists/*
 
-# Install R kernel for Jupyter (as root)
+# Install R kernel + useful packages
 RUN R -e "install.packages('IRkernel', repos='http://cran.rstudio.com/')" && \
-    R -e "IRkernel::installspec(user = FALSE)"
+    R -e "IRkernel::installspec(user = FALSE)" && \
+    R -e "install.packages(c('tidyverse','vegan','ade4'), repos='http://cran.rstudio.com/')"
 
-# Install some useful R packages for labs
-RUN R -e "install.packages(c('tidyverse', 'vegan', 'ade4'), repos='http://cran.rstudio.com/')"
+# Install bash kernel
+RUN pip install bash_kernel && python -m bash_kernel.install --sys-prefix
 
-# Install bash kernel (as root also)
-RUN pip install bash_kernel && \
-    python -m bash_kernel.install --sys-prefix
-
-# Install obitools4 (written in Go)
+# Install obitools4
 RUN curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash
 
 # Install csvkit
 RUN pip install csvkit
 
-# Install csvlens
-RUN curl https://sh.rustup.rs -sSf | bash -s -- -y \
-    && . $HOME/.cargo/env \
-    && cargo install csvlens \
-    && mv $HOME/.cargo/bin/csvlens /usr/local/bin/ \
-    && rm -rf $HOME/.cargo $HOME/.rustup
+# Install csvlens via Rust
+RUN curl https://sh.rustup.rs -sSf | bash -s -- -y && \
+    . $HOME/.cargo/env && \
+    cargo install csvlens
 
-# Create necessary directories with proper permissions
+RUN apt-get update && apt-get install -y ruby ruby-dev build-essential \
+    && gem install youplot
+
+# Copy csvlens to /usr/local/bin for final use
+RUN cp $HOME/.cargo/bin/csvlens /usr/local/bin/
+
+# Set permissions for Jupyter user
 RUN mkdir -p /home/${NB_USER}/.local/share/jupyter && \
-    chown -R ${NB_UID}:${NB_GID} /home/${NB_USER}
+    chown -R ${NB_UID}:${NB_GID} /home/${NB_USER} 
 
-USER ${NB_UID}
+# Switch back to Jupyter user
+USER ${NB_UID}:${NB_GID}
+WORKDIR /home/${NB_USER}/work
 
-WORKDIR /home/${NB_USER}
+# Environment variables
+ENV PATH="/home/${NB_USER}/work/course/bin:${PATH}"
+ENV R_LIBS_USER="/home/${NB_USER}/work/R_packages"
+ENV R_LIBS_SITE="/home/${NB_USER}/work/course/R_packages:/usr/local/lib/R/site-library:/usr/lib/R/site-library"