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Update Dockerfile
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‎dea/Dockerfile‎

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FROM rocker/r-ver:4.1.2
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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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ENV RSPM=https://packagemanager.rstudio.com/cran/__linux__/focal/2022-05-20
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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 update && apt-get -y upgrade && apt-get -y autoremove
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RUN apt-get install -y libglpk40 libglpk-dev
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RUN apt-get install -y 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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# CRAN packages (consistent snapshot)
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RUN R -e 'install.packages(c( \
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"cowplot","data.table","dplyr","DT","ff","ggfun","ggplot2","ggplotify","ggpubr", \
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"ggrepel","ggridges","gridExtra","magrittr","Matrix","matrixStats","msigdbr", \
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"patchwork","plotly","reshape2","Seurat","shiny","shinycssloaders", \
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"shinydashboard","shinyjs","shinythemes","stringi","stringr","tidytree","gplots","remotes" \
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), repos=Sys.getenv("RSPM"))'
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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/2024-04-20")'
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RUN R -e 'install.packages("data.table", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
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RUN R -e 'install.packages("dplyr", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
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RUN R -e 'install.packages("DT", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
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RUN R -e 'install.packages("ff", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
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RUN R -e 'install.packages("ggfun", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-10-27")'
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RUN R -e 'install.packages("ggplot2", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-12-23")'
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RUN R -e 'install.packages("ggplotify", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-10-20")'
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RUN R -e 'install.packages("ggpubr", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-09-19")'
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RUN R -e 'install.packages("ggrepel", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-10-20")'
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RUN R -e 'install.packages("ggridges", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-10-20")'
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RUN R -e 'install.packages("gridExtra", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
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RUN R -e 'install.packages("magrittr", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-12-23")'
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RUN R -e 'install.packages("Matrix", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-01-20")'
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RUN R -e 'install.packages("matrixStats", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
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RUN R -e 'install.packages("msigdbr", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-12-07")'
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RUN R -e 'install.packages("patchwork", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-10-20")'
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RUN R -e 'install.packages("plotly", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-04-20")'
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RUN R -e 'install.packages("reshape2", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
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RUN R -e 'install.packages("Seurat", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2022-05-20")'
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RUN R -e 'install.packages("shiny", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2021-04-23")'
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RUN R -e 'install.packages("shinycssloaders", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2021-04-23")'
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RUN R -e 'install.packages("shinydashboard", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2021-04-23")'
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RUN R -e 'install.packages("shinyjs", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2021-04-23")'
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RUN R -e 'install.packages("shinythemes", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
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RUN R -e 'install.packages("stringi", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
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RUN R -e 'install.packages("stringr", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
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RUN R -e 'install.packages("tidytree", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-04-20")'
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# Bioconductor (locked to R 4.1)
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RUN R -e 'install.packages("BiocManager", repos=Sys.getenv("RSPM"))'
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RUN R -e 'BiocManager::install(version="3.14", ask=FALSE)'
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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(c("ggtree","scuttle","BiocSingular","fgsea"), ask=FALSE)'
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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/2024-10-20")'
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# GitHub package without pulling incompatible deps
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RUN R -e 'remotes::install_github("XiaoLuo-boy/ggheatmap", dependencies=FALSE)'
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# Set the working directory
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WORKDIR /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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# Run app
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CMD ["R", "-e", "shiny::runApp('/home/app', host='0.0.0.0', port=3838)"]

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