Merge branch 'main' into allyhawkins/cluster-numbers-table

.github/workflows/docker_all-modules.yml

@@ -42,6 +42,7 @@ jobs:
           - cell-type-wilms-tumor-14
           - cell-type-nonETP-ALL-03
           - cell-type-ETP-ALL-03
+          - cell-type-consensus
     uses: ./.github/workflows/build-push-docker-module.yml
     if: github.repository_owner == 'AlexsLemonade'
     with:

.github/workflows/docker_cell-type-consensus.yml

@@ -13,22 +13,22 @@ concurrency:
   cancel-in-progress: true
 
 on:
-  # pull_request:
-  #   branches:
-  #     - main
-  #   paths:
-  #     - "analyses/cell-type-consensus/Dockerfile"
-  #     - "analyses/cell-type-consensus/.dockerignore"
-  #     - "analyses/cell-type-consensus/renv.lock"
-  #     - "analyses/cell-type-consensus/conda-lock.yml"
-  # push:
-  #   branches:
-  #     - main
-  #   paths:
-  #     - "analyses/cell-type-consensus/Dockerfile"
-  #     - "analyses/cell-type-consensus/.dockerignore"
-  #     - "analyses/cell-type-consensus/renv.lock"
-  #     - "analyses/cell-type-consensus/conda-lock.yml"
+  pull_request:
+    branches:
+      - main
+    paths:
+      - "analyses/cell-type-consensus/Dockerfile"
+      - "analyses/cell-type-consensus/.dockerignore"
+      - "analyses/cell-type-consensus/renv.lock"
+      - "analyses/cell-type-consensus/conda-lock.yml"
+  push:
+    branches:
+      - main
+    paths:
+      - "analyses/cell-type-consensus/Dockerfile"
+      - "analyses/cell-type-consensus/.dockerignore"
+      - "analyses/cell-type-consensus/renv.lock"
+      - "analyses/cell-type-consensus/conda-lock.yml"
   workflow_dispatch:
     inputs:
       push-ecr:

analyses/cell-type-consensus/Dockerfile

@@ -1,10 +1,40 @@
-# A template docker file for creating a new analysis
-FROM ubuntu:22.04
+# Dockerfile for cell-type-consensus module
+FROM bioconductor/r-ver:3.20
 
 # Labels following the Open Containers Initiative (OCI) recommendations
 # For more information, see https://specs.opencontainers.org/image-spec/annotations/?v=v1.0.1
+LABEL org.opencontainers.image.title="openscpca/cell-type-consensus"
+LABEL org.opencontainers.image.description="Docker image for the OpenScPCA analysis module 'cell-type-consensus'"
 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"
+LABEL org.opencontainers.image.source="https://github.com/AlexsLemonade/OpenScPCA-analysis/tree/main/analyses/cell-type-consensus"
 
 # 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
+
+# Install dependencies for renv library
+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')"
+
+# Copy the renv.lock file from the host environment to the image
+COPY renv.lock renv.lock
+
+# Temporarily install Rhtslib separately
+RUN Rscript -e 'BiocManager::install("Rhtslib")'
+
+# restore from renv.lock file and clean up to reduce image size
+RUN Rscript -e 'renv::restore()' && \
+  rm -rf ~/.cache/R/renv && \
+  rm -rf /tmp/downloaded_packages && \
+  rm -rf /tmp/Rtmp*
+
+# Set CMD to bash to activate the environment for any commands
+CMD ["/bin/bash"]