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