Update Dockerfile

Author: martabica

dea/Dockerfile

@@ -15,24 +15,53 @@ RUN apt-get install -y libgeos-dev
 
 RUN apt-get install -y libglpk40 libglpk-dev
 
-RUN apt-get install -y libpng-dev
 
-# Install renv
-RUN R -e "install.packages('renv', repos='https://cloud.r-project.org')"
-      
+# Install R packages
+RUN R -e 'install.packages("cowplot", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-04-20")'
+RUN R -e 'install.packages("data.table", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
+RUN R -e 'install.packages("dplyr", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
+RUN R -e 'install.packages("DT", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
+RUN R -e 'install.packages("ff", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
+RUN R -e 'install.packages("ggfun", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-10-27")'
+RUN R -e 'install.packages("ggplot2", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-12-23")'
+RUN R -e 'install.packages("ggplotify", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-10-20")'
+RUN R -e 'install.packages("ggpubr", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-09-19")'
+RUN R -e 'install.packages("ggrepel", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-10-20")'
+RUN R -e 'install.packages("ggridges", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-10-20")'
+RUN R -e 'install.packages("gridExtra", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
+RUN R -e 'install.packages("magrittr", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-12-23")'
+RUN R -e 'install.packages("Matrix", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-01-20")'
+RUN R -e 'install.packages("matrixStats", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
+RUN R -e 'install.packages("msigdbr", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-12-07")'
+RUN R -e 'install.packages("patchwork", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-10-20")'
+RUN R -e 'install.packages("plotly", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-04-20")'
+RUN R -e 'install.packages("reshape2", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
+RUN R -e 'install.packages("Seurat", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2022-05-20")'
+RUN R -e 'install.packages("shiny", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2021-04-23")'
+RUN R -e 'install.packages("shinycssloaders", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2021-04-23")'
+RUN R -e 'install.packages("shinydashboard", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2021-04-23")'
+RUN R -e 'install.packages("shinyjs", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2021-04-23")'
+RUN R -e 'install.packages("shinythemes", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
+RUN R -e 'install.packages("stringi", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
+RUN R -e 'install.packages("stringr", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2023-04-20")'
+RUN R -e 'install.packages("tidytree", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-04-20")'
+
+RUN R -e 'install.packages("BiocManager")'
+RUN R -e 'BiocManager::install("scuttle")'
+RUN R -e 'BiocManager::install("BiocSingular")'
+RUN R -e 'BiocManager::install("fgsea")'
+
+RUN R -e 'install.packages("devtools")'
+RUN R -e 'remotes::install_github("YuLab-SMU/ggtree")'
+RUN R -e 'devtools::install_github("XiaoLuo-boy/ggheatmap")' 
+RUN R -e 'install.packages("gplots", repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2024-10-20")'
+
 # Set the working directory
 WORKDIR /home/app
 
 # Copy the app directory into the image
 COPY . /home/app
 
-ENV RENV_DOWNLOAD_METHOD=libcurl
-
-# Restore the environment exactly
-RUN R -e "renv::restore()"
-
-RUN R -e 'devtools::install_github("XiaoLuo-boy/ggheatmap")' 
-
 # Expose the port
 EXPOSE 3838