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Update Dockerfile
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‎fea/Dockerfile‎

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FROM rocker/r-ver:4.5.2
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MAINTAINER Marta Bica <mbica.compbio@gmail.com>
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RUN apt-get update && apt-get -y upgrade && apt-get -y autoremove
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RUN apt-get install -y curl
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RUN apt-get install -y libcurl4-openssl-dev
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RUN apt-get install -y libssl-dev
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RUN apt-get install -y libxml2-dev
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RUN apt-get install -y libgeos-dev
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RUN apt-get install -y libglpk40 libglpk-dev
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RUN apt-get install -y libicu-dev
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RUN R -e "install.packages('curl', type='source')"
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# Install R packages
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RUN R -e 'install.packages("cowplot", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-29")'
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RUN R -e 'install.packages("data.table", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("dplyr", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("DT", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("ff", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("ggfun", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("ggplot2", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("ggplotify", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("ggpubr", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("ggrepel", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("ggridges", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("gridExtra", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("magrittr", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("Matrix", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("matrixStats", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("msigdbr", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("patchwork", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("plotly", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("reshape2", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("Seurat", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("shiny", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("shinycssloaders", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("shinydashboard", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("shinyjs", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("shinythemes", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("stringr", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("tidytree", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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RUN R -e 'install.packages("BiocManager")'
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RUN R -e 'BiocManager::install("scuttle")'
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RUN R -e 'BiocManager::install("BiocSingular")'
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RUN R -e 'BiocManager::install("fgsea")'
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RUN R -e 'BiocManager::install("markeR")'
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RUN R -e 'install.packages("devtools")'
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RUN R -e 'remotes::install_github("YuLab-SMU/ggtree")'
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RUN R -e 'devtools::install_github("XiaoLuo-boy/ggheatmap")'
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RUN R -e 'install.packages("gplots", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2026-01-24")'
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MAINTAINER Marta Bica <mbica.compbio@gmail.com>
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# Set the working directory
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# System dependencies
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RUN apt-get update && apt-get install -y \
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curl \
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libcurl4-openssl-dev \
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libssl-dev \
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libxml2-dev \
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libgeos-dev \
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libglpk40 \
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libglpk-dev \
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libicu-dev \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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# Force R to build from source (avoids binary mismatch issues)
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RUN R -e "options(pkgType='source')"
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# CRAN packages
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RUN R -e "install.packages(c(
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'cowplot','data.table','dplyr','DT','ff','ggfun','ggplot2','ggplotify',
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'ggpubr','ggrepel','ggridges','gridExtra','magrittr','Matrix',
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'matrixStats','msigdbr','patchwork','plotly','reshape2','Seurat',
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'shiny','shinycssloaders','shinydashboard','shinyjs','shinythemes',
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'stringr','tidytree','gplots'
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))"
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# Bioconductor packages
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RUN R -e "install.packages('BiocManager')"
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RUN R -e "BiocManager::install(c('scuttle','BiocSingular','fgsea','markeR'))"
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# GitHub packages
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RUN R -e "install.packages('devtools')"
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RUN R -e "remotes::install_github('YuLab-SMU/ggtree')"
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RUN R -e "devtools::install_github('XiaoLuo-boy/ggheatmap')"
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# App setup
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WORKDIR /home/app
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# Copy the app directory into the image
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COPY . /home/app
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# Expose the port
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EXPOSE 3838
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# Command to run the Shiny app
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CMD ["R", "-e", "shiny::runApp('/home/app', host='0.0.0.0', port=3838)"]

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