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