Building a Bioinformatics Docker Environment with Python, R, and Jupyter Lab

# docker build --build-arg UID=$(id -u) --build-arg GID=$(id -g) --build-arg USERNAME=biouser -t ubuntu-nonroot .

# FROM ubuntu:jammy
FROM ubuntu:25.04

# Install common packages
# Replace Ubuntu mirrors with Tsinghua
# ubuntu:jammy: /etc/apt/sources.list
RUN sed -i 's|archive.ubuntu.com|mirrors.tuna.tsinghua.edu.cn|g' /etc/apt/sources.list.d/ubuntu.sources \
    && sed -i 's|security.ubuntu.com|mirrors.tuna.tsinghua.edu.cn|g' /etc/apt/sources.list.d/ubuntu.sources \
    && apt update

# passwd is for delluser and delgroup
RUN apt install -y sudo adduser

# Create a non-root user
ARG USERNAME=biouser
ARG UID=1000
ARG GID=1000

# --remove-home ubuntu requires perl, so skip
RUN deluser ubuntu || true \
    && delgroup ubuntu || true \
    && groupadd -g 1000 biouser \
    && useradd -m -u 1000 -g biouser -s /bin/bash biouser \
    && echo "biouser ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers

# RUN groupadd -g $GID $USERNAME \
#     && useradd -m -u $UID -g $USERNAME -s /bin/bash $USERNAME \
#     && echo "$USERNAME ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers

# Switch to the new user
USER $USERNAME
WORKDIR /home/$USERNAME
ENV HOME=/home/$USERNAME

# need relogin and apt update to populate the database
RUN sudo apt install -y command-not-found
RUN sudo apt update

# to avoid tzdata require input in the following apt installation
ENV TZ=Asia/Shanghai
RUN sudo ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ | sudo tee /etc/timezone

RUN sudo apt install \
    nano vim \
    build-essential cmake \
    -y

# ------------------------------------------------------------------- python
RUN sudo apt install -y python3 python3-pip python3-virtualenv

# RUN pip config set global.index-url https://mirrors.cloud.tencent.com/pypi/simple
RUN pip config set global.index-url https://pypi.tuna.tsinghua.edu.cn/simple

# pip install some binaries to .local/bin folder
ENV PATH=$HOME/pyenvs/bio/bin:$HOME/.local/bin:$PATH

ENV BIOPY=$HOME/pyenvs/bio
RUN virtualenv $BIOPY
RUN echo "source $HOME/pyenvs/bio/bin/activate" >> $HOME/.bashrc

# ------------------------------------------------------------------- jupyter
RUN $BIOPY/bin/pip install jupyterlab

ENV JUPYTER_CONFIG_DIR=$HOME/.jupyter
RUN mkdir -p $JUPYTER_CONFIG_DIR

# Set hashed password
RUN echo '{ \
  "IdentityProvider": { \
    "hashed_password": "<replace with password genreation by jupyter server password>" \
  } \
}' > $JUPYTER_CONFIG_DIR/jupyter_server_config.json

# ------------------------------------------------------------------- R core
RUN sudo apt install -y r-base r-base-dev

# Speed up R compilation
RUN echo "MAKEFLAGS=-j$(nproc)" | sudo tee -a /etc/R/Makeconf
ENV MAKEFLAGS="-j8"

# the default repos sometimes cause download error, the tsinghua is very stable
RUN R_VERSION=$(Rscript -e 'cat(paste0(R.version$major, ".", strsplit(R.version$minor, "[.]")[[1]][1]))') && \
    mkdir -p ~/R/x86_64-pc-linux-gnu-library/${R_VERSION} && \
    echo ".libPaths('~/R/x86_64-pc-linux-gnu-library/${R_VERSION}')" >> ~/.Rprofile

RUN echo 'options(repos = c(CRAN = "https://mirrors.tuna.tsinghua.edu.cn/CRAN/"))' >> ~/.Rprofile

RUN Rscript -e 'install.packages("IRkernel"); IRkernel::installspec(user = TRUE)'

# ------------------------------------------------------------------- R application
# required by Seurat (as the installation message hint)
RUN sudo apt install -y libcurl4-openssl-dev libssl-dev
# Matrix is already bundled with R-base
RUN Rscript -e 'install.packages("Seurat")'

RUN Rscript -e 'install.packages(c("ggplot2", "data.table"))'

RUN sudo apt install -y libudunits2-dev libssl-dev cmake libgdal-dev libgeos-dev libproj-dev libsqlite3-dev libudunits2-dev
RUN Rscript -e 'install.packages("sf")'

# ------------------------------------------------------------------- jupyter service

ENV JUPYTER_PORT=8889
# set SHELL and -l (login shell) to make the terminal in jupyter with normal prompt
ENV SHELL=/bin/bash
CMD ["bash", "-lc", "jupyter lab --ip=0.0.0.0 --port=$JUPYTER_PORT --no-browser --notebook-dir=/"]

# Keep container alive for background dev
# CMD ["sleep", "infinity"]

version: "3.9"

services:
  # =========================================================
  # Development profile: full rebuilds, uses local Dockerfile
  # =========================================================
  biodev:
    build:
      context: .
      dockerfile: Dockerfile
      args:
        UID: ${UID:-1000}
        GID: ${GID:-1000}
        USERNAME: biouser
    image: bio:dev
    container_name: bio-dev
    hostname: docker-dev
    profiles: ["dev"]
    environment:
      - JUPYTER_PORT=8887
    extra_hosts:
      - "docker-dev:127.0.0.1"
    volumes:
      - /work:/work
    working_dir: /work
    tty: true
    network_mode: host
    shm_size: "2g"

  # =========================================================
  # Release profile: use prebuilt stable image
  # =========================================================
  biorelease:
    build:
      context: .
      dockerfile: Dockerfile
      args:
        UID: ${UID:-1000}
        GID: ${GID:-1000}
        USERNAME: biouser  
    image: bio:release
    container_name: bio-release
    hostname: docker
    profiles: ["release"]
    restart: unless-stopped
    environment:
      - JUPYTER_PORT=8889
    extra_hosts:
      - "docker:127.0.0.1"
    volumes:
      - /work:/work
    working_dir: /work
    tty: true
    network_mode: host
    shm_size: "2g"