Specify base image when writing Dockerfile

Author: bschilder

Dockerfile

@@ -0,0 +1,65 @@
+# ----- R Package Dockerfile -----
+#
+# This Dockerfile is designed for developers of any R package stored on GitHub.
+#
+# It runs several steps:
+#   1. Pulls the official bioconductor Docker container (which includes Rstudio).
+#   2. Runs CRAN checks on the R package.
+#   3. Installs the R package and all of its dependencies (including Depends, Imports, and Suggests).
+#
+# You can then create an image of the Docker container in any command line:
+#   docker pull <DockerHub_repo_name>/<package_name>
+# Once the image has been created, you can launch it with:
+#   docker run -d -e ROOT=true -e PASSWORD=bioc -v ~/Desktop:/Desktop -v /Volumes:/Volumes --rm -p 8788:8787 <DockerHub_repo_name>/<package_name>
+# Finally, launch the containerised Rstudio by entering the following URL in any web browser:
+#   http://localhost:8788/
+#
+# The username will be "rstudio" by default,
+# and you can set the password to whatever you like,
+#
+# This DockerFile was partly adapted from the [scFlow Dockerfile](https://github.com/combiz/scFlow/blob/master/Dockerfile).
+FROM $CONT
+RUN apt-get update && \
+    apt-get install -y \
+    git-core \
+    libcurl4-openssl-dev \
+    libgit2-dev \
+    libicu-dev \
+    libssl-dev \
+    make pandoc \
+    pandoc-citeproc \
+    zlib1g-dev \
+  	xfonts-100dpi \
+  	xfonts-75dpi \
+  	biber \
+  	libsbml5-dev \
+  	qpdf \
+  	cmake \
+  	&& apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+# Create a buildzone folder named after the R package
+# BiocCheck requires the buildzone to have the same name as the R package
+ARG PKG
+RUN echo $PKG
+RUN mkdir -p /$PKG
+ADD . /$PKG
+WORKDIR /$PKG
+# Install dependencies with AnVil (faster)
+RUN Rscript -e 'options(download.file.method="libcurl", crayon.enabled=TRUE, timeout=2000); \
+                if(!require("BiocManager")) install.packages("BiocManager"); \
+                if(!require("AnVIL"))  {BiocManager::install("AnVIL", ask = FALSE)}; \
+                AnVIL::install(c("remotes","devtools")); \
+                try({remotes::install_github("bergant/rapiclient")}); \
+                bioc_ver <- BiocManager::version(); \
+                options(repos = c(AnVIL::repositories(),\
+                                  AnVIL = file.path("https://bioconductordocker.blob.core.windows.net/packages",bioc_ver,"bioc"),\
+                                  CRAN = "https://cran.rstudio.com/"),\
+                                  download.file.method = "libcurl", Ncpus = 2); \
+                deps <- remotes::dev_package_deps(dependencies = TRUE)$package; \
+                AnVIL::install(pkgs = deps,  ask = FALSE); \
+                deps_left <- deps[!deps %in% rownames(installed.packages())]; \
+                if(length(deps_left)>0) devtools::install_dev_deps(dependencies = TRUE, upgrade = "never");' 
+# Install R package from source
+RUN R -e 'options(crayon.enabled = TRUE); \
+          remotes::install_local(upgrade="never")'
+RUN rm -rf /$PKG

R/use_dockerfile.R

@@ -2,6 +2,7 @@
 #' 
 #' Creates a Docker file to be used with the GitHub Actions (GHA) workflows
 #' distributed by \pkg{rworkflows}.
+#' @param base_image Base Docker image to use.
 #' @param save_dir Directory to save the Docker file to.
 #' @param path Path to the Docker file.
 #' @param force_new If a Docker file already exists, overwrite it 
@@ -17,9 +18,11 @@
 #' path <- use_dockerfile(save_dir=tempdir())
 use_dockerfile <- function(save_dir=here::here(),
                            path=file.path(save_dir,"Dockerfile"),
+                           base_image=construct_cont()[[1]],
                            force_new=FALSE,
                            show=FALSE,
                            verbose=TRUE){
+  # devoptera::args2vars(use_dockerfile)
 
   if(file.exists(path) &&
      isFALSE(force_new)){
@@ -31,6 +34,9 @@ use_dockerfile <- function(save_dir=here::here(),
                                  package = "rworkflows"), 
               to = path,  
               overwrite = TRUE)
+    txt <- readLines(path)
+    txt <- gsub("^FROM \\{BASE_IMAGE\\}",paste("FROM",base_image),txt)
+    writeLines(txt,path)
   }
   if(isTRUE(show)){
     messager("Docker file preview:",v=verbose)

action.yml

@@ -486,10 +486,12 @@ runs:
     - name: 🐳✏️ Create Docker file 
       if: |
         (!contains(github.event.head_commit.message, '/nodocker')) && inputs.run_docker == 'true' && runner.os == 'Linux'
+      env:
+        BASE_IMAGE: ${{ matrix.config.cont }}
       run: |
         options(crayon.enabled = TRUE)
         if(!require("rworkflows", quietly=TRUE)) remotes::install_github("neurogenomics/rworkflows")
-        path <- rworkflows::use_dockerfile()
+        path <- rworkflows::use_dockerfile(base_image=Sys.getenv("BASE_IMAGE"))
       shell: Rscript {0} 
 
     - name: 🐳🚀 Build and push to GHCR 

inst/templates/Dockerfile

@@ -18,7 +18,7 @@
 # and you can set the password to whatever you like,
 #
 # This DockerFile was partly adapted from the [scFlow Dockerfile](https://github.com/combiz/scFlow/blob/master/Dockerfile).
-FROM $BASE_IMAGE
+FROM {BASE_IMAGE}
 RUN apt-get update && \
     apt-get install -y \
     git-core \