softwareDevelopment/linkage_mapping

1FROM rocker/shiny:latest2 3# Set working directory inside container4WORKDIR /code5 6# Install additional system dependencies including libglpk for igraph7RUN apt-get update && apt-get install -y \8    libcurl4-openssl-dev \9    libssl-dev \10    libxml2-dev \11    libnlopt-dev \12    libicu-dev \13    libgdal-dev \14    libgeos-dev \15    libproj-dev \16    libv8-dev \17    libnode-dev \18    libglpk-dev \19    libglpk40 \20    zlib1g-dev \21    libbz2-dev \22    liblzma-dev \23    && rm -rf /var/lib/apt/lists/*24 25# Install DT dependencies first26RUN install2.r --error \27    htmltools \28    htmlwidgets \29    jsonlite \30    crosstalk \31    magrittr \32    promises33 34# Then install the main packages (excluding QTLseqr and vcfR for now)35RUN install2.r --error \36    nloptr \37    lme4 \38    emmeans \39    readxl \40    plotly \41    shinyjs \42    shinyWidgets \43    DT \44    RColorBrewer \45    ggrepel \46    openxlsx47 48# Install tidyverse and igraph49RUN install2.r --error tidyverse igraph50 51# Install data.table separately52RUN install2.r --error data.table53 54# Install BiocManager55RUN R -e "install.packages('BiocManager', repos='https://cloud.r-project.org/')"56 57# Install Bioconductor dependencies58RUN R -e "BiocManager::install(c('GenomicRanges', 'IRanges', 'S4Vectors', 'Biostrings', 'Rsamtools', 'GenomeInfoDb'), ask=FALSE, update=FALSE)"59 60# Install vcfR package61RUN install2.r --error vcfR62 63# Install remotes for GitHub installations64RUN install2.r --error remotes65 66# Install QTLseqr from GitHub67RUN R -e "remotes::install_github('bmansfeld/QTLseqr', upgrade='never', dependencies=FALSE)"68 69# Create www directory and health file directly70RUN mkdir -p /code/www && echo "OK" > /code/www/health71 72# Copy app code73COPY app.R /code/74 75# Expose the port Shiny will run on76EXPOSE 786077 78# Run the app with corrected host address79CMD ["R", "--quiet", "-e", "shiny::runApp('/code', host='0.0.0.0', port=7860)"]