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Dockerfile
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# Use RStudio as base image
FROM rocker/rstudio:4
# Set the working directory
WORKDIR /app
# Install system libraries required for R packages
RUN apt-get update && apt-get install -y \
libcurl4-openssl-dev \
libssl-dev \
libxml2-dev \
libpng-dev \
libmagick++-dev \
zlib1g-dev \
default-jdk \
libnetcdf-dev
# Install BiocManager and remotes
RUN R -e "install.packages(c('BiocManager', 'remotes'), repos='http://cran.rstudio.com/')"
# Install patRoon dependencies
RUN R -e "BiocManager::install(c('ncdf4', 'rJava', 'magick', 'mzR', 'rcdklibs', 'MSnbase', 'rcdk', 'xcms', 'CAMERA'), dependencies = TRUE)"
# Install patRoon
RUN R -e "BiocManager::install('rickhelmus/patRoon', dependencies = TRUE)"
# Install StreamFind
RUN R -e "BiocManager::install('odea-project/StreamFind', dependencies = TRUE)"
# Install StreamFindData
RUN R -e "BiocManager::install('odea-project/StreamFindData')"
# Copy the start.sh script to the container
COPY start.sh /start.sh
# Give execute permission to the script
RUN chmod +x /start.sh
ENTRYPOINT ["/start.sh"]