Dockerfile

FROM ubuntu:22.04

# Set noninteractive mode to prevent prompts during installation
ENV DEBIAN_FRONTEND=noninteractive

# Install required system dependencies
RUN apt-get update && apt-get install -y \
    wget \
    sudo \
    curl \
    git \
    build-essential \
    libcurl4-openssl-dev \
    libssl-dev \
    libxml2-dev \
    libxt-dev \
    pandoc \
    libclang-dev \
    libpq-dev \
    libgit2-dev \
    gdebi-core \
    psmisc \
    && rm -rf /var/lib/apt/lists/*

# Create an RStudio user with sudo access
RUN useradd -m -s /bin/bash rstudio && echo "rstudio:rstudio" | chpasswd && \
    usermod -aG sudo rstudio

# Set working directory
WORKDIR /root

# Install Miniconda
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh && \
    bash miniconda.sh -b -p /opt/miniconda && \
    rm miniconda.sh

# Set environment variables for Conda
ENV PATH="/opt/miniconda/bin:$PATH"

# Create .condarc file for channel priority
RUN echo "channels:\n  - conda-forge\n  - bioconda\n  - defaults\n  - r" > /root/.condarc

# Create Conda environment and install dependencies
RUN conda create --name neuroestimator -y \
    r-essentials \
    tensorflow=1.15.0 \
    tensorflow-estimator=1.15.1 \
    r-keras=2.3.0.0 \
    r-tensorflow=2.2.0 \
    h5py=2.10.0 \
    hdf5=1.10.6 \
    r-dplyr=1.0.9 \
    r-base \
    r-remotes \
    'r-reticulate<=1.24'

# Install RStudio Server
RUN wget https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2024.12.1-563-amd64.deb -O rstudio-server.deb && \
    dpkg -i rstudio-server.deb || apt-get -f install -y && \
    rm rstudio-server.deb

# Ensure RStudio uses Conda's R
RUN echo 'export RSTUDIO_WHICH_R="/opt/miniconda/envs/neuroestimator/bin/R"' >> /etc/profile.d/rstudio.sh

# Install NEUROeSTIMator in the Conda environment
RUN conda run -n neuroestimator R -e "remotes::install_git('https://research-git.uiowa.edu/michaelson-lab-public/neuroestimator')"

# Ensure Conda environment is activated on container start
SHELL ["/bin/bash", "-c"]

# Expose RStudio Server port
EXPOSE 8787

# Set the entrypoint to start RStudio Server
ENTRYPOINT ["/bin/bash", "-c", "source activate neuroestimator && /usr/lib/rstudio-server/bin/rserver --server-user=$(whoami) --server-daemonize=0"]