Merge pull request #548 from jashapiro/jashapiro/542-update-hello-r-d…

…ocker

Set Renv not to activate in docker images

analyses/cell-type-ewings/.Rprofile

@@ -1 +1,4 @@
-source("renv/activate.R")
+# Don't activate renv in an OpenScPCA docker image
+if(Sys.getenv('OPENSCPCA_DOCKER') != 'TRUE'){
+  source('renv/activate.R')
+}

analyses/cell-type-ewings/Dockerfile

@@ -8,6 +8,9 @@ LABEL org.opencontainers.image.description="Docker image for the OpenScPCA analy
 LABEL org.opencontainers.image.authors="OpenScPCA scpca@ccdatalab.org"
 LABEL org.opencontainers.image.source="https://github.com/AlexsLemonade/OpenScPCA-analysis/tree/main/analyses/cell-type-ewings"
 
+# Set an environment variable to allow checking if we are in an OpenScPCA container
+ENV OPENSCPCA_DOCKER TRUE
+
 # Disable the renv cache to install packages directly into the R library
 ENV RENV_CONFIG_CACHE_ENABLED FALSE
 # set a name for the conda environment
@@ -18,11 +21,11 @@ ENV PATH="/opt/conda/bin:${PATH}"
 
 # Install dependencies for renv library
 RUN apt-get -y update &&  \
-    DEBIAN_FRONTEND=noninteractive \
-    apt-get install --no-install-recommends -y \
-    pandoc \
-    wget \
-    && rm -rf /var/lib/apt/lists/*
+  DEBIAN_FRONTEND=noninteractive \
+  apt-get install --no-install-recommends -y \
+  pandoc \
+  wget \
+  && rm -rf /var/lib/apt/lists/*
 
 # Install miniconda
 # adapted from https://github.com/ContinuumIO/docker-images/blob/main/miniconda3/debian/Dockerfile

analyses/doublet-detection/.Rprofile

@@ -1 +1,4 @@
-source("renv/activate.R")
+# Don't activate renv in an OpenScPCA docker image
+if(Sys.getenv('OPENSCPCA_DOCKER') != 'TRUE'){
+  source('renv/activate.R')
+}

analyses/doublet-detection/Dockerfile

@@ -8,6 +8,9 @@ LABEL org.opencontainers.image.source="https://github.com/AlexsLemonade/OpenScPC
 # set a name for the conda environment
 ARG ENV_NAME=openscpca-doublet-detection
 
+# Set an environment variable to allow checking if we are in an OpenScPCA container
+ENV OPENSCPCA_DOCKER TRUE
+
 # set environment variables to install miniconda
 ENV PATH="/opt/conda/bin:${PATH}"
 

analyses/hello-R/.Rprofile

@@ -1 +1,4 @@
-source("renv/activate.R")
+# Don't activate renv in an OpenScPCA docker image
+if(Sys.getenv('OPENSCPCA_DOCKER') != 'TRUE'){
+  source('renv/activate.R')
+}

analyses/hello-R/Dockerfile

@@ -6,6 +6,16 @@ FROM bioconductor/r-ver:3.19
 LABEL org.opencontainers.image.authors="OpenScPCA scpca@ccdatalab.org"
 LABEL org.opencontainers.image.source="https://github.com/AlexsLemonade/OpenScPCA-analysis/tree/main/analyses/hello-R"
 
+# Set an environment variable to allow checking if we are in an OpenScPCA container
+ENV OPENSCPCA_DOCKER TRUE
+
+# Install additional system dependencies
+RUN apt-get -y update &&  \
+    DEBIAN_FRONTEND=noninteractive \
+    apt-get install --no-install-recommends -y \
+    pandoc \
+    && rm -rf /var/lib/apt/lists/*
+
 # Install renv to enable later package installation
 RUN Rscript -e "install.packages('renv')"
 

analyses/hello-python/Dockerfile

@@ -6,6 +6,9 @@ FROM continuumio/miniconda3:24.1.2-0
 LABEL org.opencontainers.image.authors="OpenScPCA scpca@ccdatalab.org"
 LABEL org.opencontainers.image.source="https://github.com/AlexsLemonade/OpenScPCA-analysis/tree/main/analyses/hello-python"
 
+# Set an environment variable to allow checking if we are in an OpenScPCA container
+ENV OPENSCPCA_DOCKER TRUE
+
 # set a name for the conda environment
 ARG ENV_NAME=openscpca-hello-python
 

analyses/simulate-sce/.Rprofile

@@ -1 +1,4 @@
-source("renv/activate.R")
+# Don't activate renv in an OpenScPCA docker image
+if(Sys.getenv('OPENSCPCA_DOCKER') != 'TRUE'){
+  source('renv/activate.R')
+}

analyses/simulate-sce/Dockerfile

@@ -8,6 +8,9 @@ LABEL org.opencontainers.image.description="Docker image for the OpenScPCA analy
 LABEL org.opencontainers.image.authors="OpenScPCA scpca@ccdatalab.org"
 LABEL org.opencontainers.image.source="https://github.com/AlexsLemonade/OpenScPCA-analysis/tree/main/analyses/simulate-sce"
 
+# Set an environment variable to allow checking if we are in an OpenScPCA container
+ENV OPENSCPCA_DOCKER TRUE
+
 ENV RENV_CONFIG_CACHE_ENABLED FALSE
 RUN Rscript -e "install.packages(c('remotes', 'renv'))"
 

create-analysis-module.py

@@ -215,6 +215,15 @@ def main() -> None:
             ["Rscript", "-e", renv_script],
             cwd=module_dir,
         )
+
+        # Set .Rprofile to not activate renv in an OpenScPCA Docker image
+        (module_dir / ".Rprofile").write_text(
+            "# Don't activate renv in an OpenScPCA docker image\n"
+            "if (Sys.getenv('OPENSCPCA_DOCKER') != 'TRUE') {\n"
+            "  source('renv/activate.R')\n"
+            "}\n"
+        )
+
         # make the components directory and add a dependencies.R file
         component_dir = module_dir / "components"
         component_dir.mkdir(exist_ok=True)

templates/analysis-module/Dockerfile

@@ -5,3 +5,6 @@ FROM ubuntu:22.04
 # For more information, see https://specs.opencontainers.org/image-spec/annotations/?v=v1.0.1
 LABEL org.opencontainers.image.authors="OpenScPCA scpca@ccdatalab.org"
 LABEL org.opencontainers.image.source="https://github.com/AlexsLemonade/OpenScPCA-analysis/tree/main/templates/analysis-module"
+
+# Set an environment variable to allow checking if we are in an OpenScPCA container
+ENV OPENSCPCA_DOCKER TRUE