48 lines
1.3 KiB
Docker
48 lines
1.3 KiB
Docker
FROM jupyter/base-notebook:latest
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USER root
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# Install R and system dependencies
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RUN apt-get update && apt-get install -y \
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r-base \
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r-base-dev \
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libcurl4-openssl-dev \
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libssl-dev \
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libxml2-dev \
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git \
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build-essential \
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curl \
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&& apt-get clean && rm -rf /var/lib/apt/lists/*
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# Install R kernel for Jupyter (as root)
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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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# Install some useful R packages for labs
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RUN R -e "install.packages(c('tidyverse', 'vegan', 'ade4'), repos='http://cran.rstudio.com/')"
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# Install bash kernel (as root also)
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RUN pip install bash_kernel && \
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python -m bash_kernel.install --sys-prefix
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# Install obitools4 (written in Go)
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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
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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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&& mv $HOME/.cargo/bin/csvlens /usr/local/bin/ \
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&& rm -rf $HOME/.cargo $HOME/.rustup
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# Create necessary directories with proper permissions
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RUN mkdir -p /home/${NB_USER}/.local/share/jupyter && \
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chown -R ${NB_UID}:${NB_GID} /home/${NB_USER}
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USER ${NB_UID}
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WORKDIR /home/${NB_USER}
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