Merge remote-tracking branch 'origin/devel' into devel

Dockerfile

@@ -1,18 +1,40 @@
 # Base R Shiny image
-FROM rocker/shiny
+FROM rocker/shiny:4.4.0
+
+# Install system dependencies for GSL and GLPK
+RUN apt-get update && apt-get install -y \
+    libgsl-dev \
+    libglpk-dev
+
+# Install R dependencies early to leverage Docker layer caching
+RUN R -e "install.packages(c('devtools', 'BiocManager'))"
+
+RUN R -e "if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager'); BiocManager::install(version='devel', ask=FALSE); BiocManager::install('iSEEtree')"
+
+# Install necessary Bioconductor and CRAN packages
+RUN R -e "BiocManager::install(c('iSEE', 'iSEEtree', 'mia', 'biomformat', 'SummarizedExperiment', 'SingleCellExperiment', 'TreeSummarizedExperiment', 'shiny', 'shinyjs', 'methods', 'utils'))"
 
 # Set the working directory
 WORKDIR /srv/shiny-server
 
-# Copy the entire package to the working directory
+# Copy the DESCRIPTION file first to leverage Docker cache if dependencies haven't changed
+COPY DESCRIPTION .
+
+# Install the dependencies based on the DESCRIPTION file
+RUN R -e "remotes::install_deps(dependencies = TRUE)"
+
+# Copy the rest of the package code
 COPY . .
 
-# Install R dependencies from the DESCRIPTION file
-RUN R -e "install.packages(c('remotes', 'BiocManager'))"
-RUN R -e "remotes::install_local(dependencies = TRUE, upgrade = TRUE)"
+# Install the local iSEEbug package and output installation logs for debugging
+RUN R -e "remotes::install_local('.', dependencies = TRUE, upgrade = TRUE, quiet = FALSE)"
+
+# Verify that the iSEEbug package is installed
 
 # Expose the application port
-EXPOSE 3838
+EXPOSE 8080
 
 # Command to run the Shiny app
-CMD ["R", "-e", "app <- iSEEbug::iSEEbug(); shiny::runApp(app, host = '0.0.0.0', port = 3838)"]
+CMD ["R", "-e", "app <- iSEEbug::iSEEbug(); shiny::runApp(app, host = '0.0.0.0', port = 8080)"]
+
+