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Dockerfile
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FROM rocker/r-base
LABEL maintainer "Sebastian Didusch <[email protected]>"
# system libraries of general use
RUN apt-get update && apt-get install -y \
sudo \
pandoc \
libcairo2-dev \
libxt-dev \
libssl-dev \
libssh2-1-dev \
libcurl4-openssl-dev \
libxml2-dev \
libxslt-dev
# basic shiny functionality
RUN R -e "install.packages(c('shiny', 'rmarkdown', 'shinyjs', 'shinymanager', 'shinyBS', 'DT', 'shinycssloaders', 'bslib', 'profvis', 'colourpicker', 'shinyalert'), repos='https://cloud.r-project.org/')"
RUN R -e "install.packages(c('reshape2', 'igraph', 'visNetwork', 'UpSetR', 'dplyr', 'pheatmap', 'DT', 'data.table', 'RColorBrewer', 'Rmisc', 'eulerr'), repos='https://cloud.r-project.org/')"
RUN R -e "install.packages(c('heatmaply', 'ggfortify', 'colourvalues', 'pryr'), repos='https://cloud.r-project.org/')"
RUN R -e "install.packages(c('tidyr', 'Cairo', 'cowplot'), repos='https://cloud.r-project.org/')"
# install dependencies from bioconductor
RUN R -e "install.packages('BiocManager'); library('BiocManager'); BiocManager::install(c('limma', 'DEqMS', 'gprofiler2', 'vsn'))"
# copy the app to the image
RUN mkdir /root/amica
COPY amica /root/amica
COPY Rprofile.site /usr/lib/R/etc/
EXPOSE 3838
CMD ["R", "-e", "shiny::runApp('/root/amica')"]