Downsize the student image

obijupyterhub/Dockerfile

@@ -1,40 +1,53 @@
-# ---------- Stage 1 : builder ----------
-FROM jupyter/base-notebook:latest AS builder
+# ---------- Stage 1 : builder pour csvlens ----------
+FROM jupyter/base-notebook:latest AS rust-builder
 
 USER root
 
-# Install system dependencies for R, build tools and Go/Rust
+# Installer seulement les dépendances pour compiler csvlens
 RUN apt-get update && apt-get install -y \
-    r-base r-base-dev \
-    libcurl4-openssl-dev libssl-dev libxml2-dev \
-    build-essential git curl \
-    texlive-xetex texlive-fonts-recommended texlive-plain-generic \
-    && apt-get clean && rm -rf /var/lib/apt/lists/*
+    curl build-essential zlib1g-dev unzip \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
 
-# Install R kernel + useful packages
-RUN R -e "install.packages('IRkernel', repos='http://cran.rstudio.com/')" && \
-    R -e "IRkernel::installspec(user = FALSE)" && \
-    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
+# Installer Rust et compiler csvlens
+RUN curl https://sh.rustup.rs -sSf | bash -s -- -y
+RUN . $HOME/.cargo/env && cargo install csvlens
 
 # Install obitools4
-RUN curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash
+RUN TEMP=. curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh \
+    | bash -s -- --install-dir $HOME/obitools-build \
+    && cp $HOME/obitools-build/bin/* /usr/local/bin
+RUN ls -l /usr/local/bin
 
-# Install csvkit
-RUN pip install csvkit
 
-# Install csvlens via Rust
-RUN curl https://sh.rustup.rs -sSf | bash -s -- -y && \
-    . $HOME/.cargo/env && \
-    cargo install csvlens
+# ---------- Stage 2 : image finale ----------
+FROM jupyter/base-notebook:latest
 
-RUN apt-get update && apt-get install -y ruby ruby-dev build-essential \
-    && gem install youplot
+USER root
 
-# Copy csvlens to /usr/local/bin for final use
-RUN cp $HOME/.cargo/bin/csvlens /usr/local/bin/
+# Installer seulement les dépendances d'exécution (sans build-essential)
+RUN apt-get update && apt-get install -y \
+    r-base \
+    libcurl4-openssl-dev libssl-dev libxml2-dev \
+    curl \
+    texlive-xetex texlive-fonts-recommended texlive-plain-generic \
+    ruby ruby-dev \
+    vim nano \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# Installer R et packages
+RUN R -e "install.packages(c('IRkernel','tidyverse','vegan','ade4','BiocManager','remotes'), repos='http://cran.rstudio.com/')" && \
+    R -e "BiocManager::install('biomformat')" && \
+    R -e "remotes::install_github('metabaRfactory/metabaR')" && \
+    R -e "IRkernel::installspec(user = FALSE)" && \
+    rm -rf /tmp/Rtmp*
+
+# Installer les autres outils
+RUN pip install --no-cache-dir bash_kernel csvkit && \
+    python -m bash_kernel.install --sys-prefix
+
+RUN gem install youplot
 
 # Set permissions for Jupyter user
 RUN mkdir -p /home/${NB_USER}/.local/share/jupyter && \
@@ -43,12 +56,14 @@ RUN mkdir -p /home/${NB_USER}/.local/share/jupyter && \
 COPY start-notebook.sh /usr/local/bin/start-notebook.sh
 RUN chmod +x /usr/local/bin/start-notebook.sh
 
+# Copier uniquement le binaire csvlens du builder
+COPY --from=rust-builder /home/jovyan/.cargo/bin/csvlens /usr/local/bin/
+COPY --from=rust-builder /usr/local/bin/* /usr/local/bin/
+
 # Switch back to Jupyter user
 USER ${NB_UID}:${NB_GID}
 WORKDIR /home/${NB_USER}/work
 
-# 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"
-

obijupyterhub/jupyterhub_config.py

@@ -76,6 +76,7 @@ c.DockerSpawner.volume_driver_opts = {
     'device': '/volumes',
     'o': 'bind'
 }
+
 # Memory and CPU configuration (adjust according to your needs)
 c.DockerSpawner.mem_limit = '2G'
 c.DockerSpawner.cpu_limit = 1.0