Dockerfile

FROM rocker/shiny:latest

# Set working directory inside container
WORKDIR /code

# Install additional system dependencies including libglpk for igraph
RUN apt-get update && apt-get install -y \
    libcurl4-openssl-dev \
    libssl-dev \
    libxml2-dev \
    libnlopt-dev \
    libicu-dev \
    libgdal-dev \
    libgeos-dev \
    libproj-dev \
    libv8-dev \
    libnode-dev \
    libglpk-dev \
    libglpk40 \
    zlib1g-dev \
    libbz2-dev \
    liblzma-dev \
    && rm -rf /var/lib/apt/lists/*

# Install DT dependencies first
RUN install2.r --error \
    htmltools \
    htmlwidgets \
    jsonlite \
    crosstalk \
    magrittr \
    promises

# Then install the main packages (excluding QTLseqr and vcfR for now)
RUN install2.r --error \
    nloptr \
    lme4 \
    emmeans \
    readxl \
    plotly \
    shinyjs \
    shinyWidgets \
    DT \
    RColorBrewer \
    ggrepel \
    openxlsx

# Install tidyverse and igraph
RUN install2.r --error tidyverse igraph

# Install data.table separately
RUN install2.r --error data.table

# Install BiocManager
RUN R -e "install.packages('BiocManager', repos='https://cloud.r-project.org/')"

# Install Bioconductor dependencies
RUN R -e "BiocManager::install(c('GenomicRanges', 'IRanges', 'S4Vectors', 'Biostrings', 'Rsamtools', 'GenomeInfoDb'), ask=FALSE, update=FALSE)"

# Install vcfR package
RUN install2.r --error vcfR

# Install remotes for GitHub installations
RUN install2.r --error remotes

# Install QTLseqr from GitHub
RUN R -e "remotes::install_github('bmansfeld/QTLseqr', upgrade='never', dependencies=FALSE)"

# Create www directory and health file directly
RUN mkdir -p /code/www && echo "OK" > /code/www/health

# Copy app code
COPY app.R /code/

# Expose the port Shiny will run on
EXPOSE 7860

# Run the app with corrected host address
CMD ["R", "--quiet", "-e", "shiny::runApp('/code', host='0.0.0.0', port=7860)"]