replace dockerfile with contents of dockerfile.new, build with docker…

…file (#250)

.github/workflows/build.yml

@@ -39,7 +39,7 @@ jobs:
           push: true
           output: true
           tags: ghcr.io/r-odaf/r-odaf_health_canada:r-pkg-test
-          file: ./Dockerfile.new
+          file: ./Dockerfile
           cache-from: type=registry,ref=ghcr.io/r-odaf/r-odaf_health_canada:cache
           cache-to: type=inline
       - name: Disk space after build

Dockerfile

@@ -2,93 +2,54 @@
 ## Build R-ODAF container for transcriptomic analysis ##
 ########################################################
 # Mamba base image
-FROM condaforge/mambaforge:23.3.1-1 as base
-#continuumio/miniconda3 - difficult to install mamba, so switched away from this base 
+# snakemake image is based on mambaorg/micromamba
+# mambaorg/micromamba in turn is based on debian:bookworm-slim
+FROM snakemake/snakemake:stable
+# v
+# v8.4.8
+
 
 # Required to avoid interactive prompts
-ARG DEBIAN_FRONTEND=noninteractive
+#ARG DEBIAN_FRONTEND=noninteractive
 ARG PLATFORM=temposeq
 ARG BUILD_CORES=8
-
-# Set up a user for running; -m creates home directory, -s sets default shell
 RUN useradd -ms /bin/bash R-ODAF
-
-# Install dependencies for running pipeline
-RUN apt-get update && apt-get -y install \
-	build-essential \
-	wget \
-	curl \
-	git \
-	libcairo2-dev \
-	libxt-dev \
-	tree \
-      gosu \
-	vim && \
-      mamba install -y -c conda-forge -c bioconda -n base snakemake && \
-      rm -rf /var/lib/apt/lists/* && \
-      gosu nobody true  && \
-      df -h && \
-      apt-get clean && \
-      df -h
-      # verify that gosu works
-      # free up disk space on runner
+# Install runtime dependencies that are necessary for your application
+# Why /var/lib/dpkg/lock-frontend doesn't exist... I have no idea
+RUN mkdir -p /var/lib/dpkg && touch /var/lib/dpkg/lock-frontend \
+      &&apt-get update \
+      && apt-get install --no-install-recommends gosu  \
+      && gosu nobody true \
+      && rm -rf /var/lib/apt/lists/* \
+      && apt-get clean \
+      && df -h
 
 RUN mkdir -p /home/R-ODAF/R-ODAF_Health_Canada
 WORKDIR "/home/R-ODAF/R-ODAF_Health_Canada"
 COPY . .
-RUN chown -R R-ODAF:R-ODAF /home/R-ODAF
+RUN mv inputs inputs.bak \
+      && wget https://github.com/EHSRB-BSRSE-Bioinformatics/test-data/archive/master.tar.gz \
+      && tar -zxvf master.tar.gz \
+      && mv -f test-data-main/dev/${PLATFORM}/* ./ \
+      && wget https://github.com/EHSRB-BSRSE-Bioinformatics/unify_temposeq_manifests/raw/main/output_manifests/Human_S1500_1.2_standardized.csv \
+      && rm master.tar.gz
+
+RUN chown -R R-ODAF:R-ODAF /home/R-ODAF && df -h
 USER R-ODAF
-RUN mv inputs inputs.bak
-
-RUN git clone https://github.com/EHSRB-BSRSE-Bioinformatics/test-data \
-&& mv test-data/${PLATFORM}/* ./ \
-&& wget https://github.com/EHSRB-BSRSE-Bioinformatics/unify_temposeq_manifests/raw/main/output_manifests/Human_S1500_1.2_standardized.csv \
-&& df -h
 
 # Build environments with Snakemake
-RUN /bin/bash -c "snakemake --cores ${BUILD_CORES} --use-conda --conda-create-envs-only && conda clean -y -a && df -h"
+RUN snakemake --cores ${BUILD_CORES} --software-deployment-method conda --conda-create-envs-only 
 
 # Install extra dependency for reports
-RUN /bin/bash -c "conda run -p $(grep -rl "R-ODAF_reports" .snakemake/conda/*.yaml | sed s/\.yaml//) Rscript install.R"
-
-# Change ownership of files
-USER root
-RUN chown -R R-ODAF:R-ODAF /home/R-ODAF
-USER R-ODAF
-
-########################################################
-## Build R-ODAF container for transcriptomic analysis ##
-########################################################
-# R-ODAF base image
-# Run tests using base dependencies, but updated code
-# Note that if you alter any dependencies, the base container must be rebuilt
-FROM base as tests
-
-# Run tests
-RUN /bin/bash -c "df -h && snakemake --cores 8 --use-conda"
+RUN mamba run -p $(grep -rl "R-ODAF_reports" .snakemake/conda/*.yaml | sed s/\.yaml//) Rscript install.R 
 
-# Clean up files
-FROM tests as cleanup
+RUN snakemake --cores ${BUILD_CORES} --software-deployment-method conda \
+      && df -h \
+      && mkdir ./tests \
+      && mv output test-data-main truth_checksums wikipathways-20210810-gmt-Homo_sapiens.gmt Human_S1500_1.2_standardized.csv inputs ./tests/ \
+      && mv inputs.bak inputs \
+      && rm -rf ./tests
 
-# Clean up directories
-RUN df -h &&\
-      mkdir ./tests && \
-      mv output \
-      test-data \
-      truth_checksums \
-      wikipathways-20210810-gmt-Homo_sapiens.gmt \
-      Human_S1500_1.2_standardized.csv \
-      inputs \
-      ./tests/
-RUN /bin/bash -c "tree inputs.bak && \
-                  mv inputs.bak inputs"
-# Move test files
 USER root
-RUN rm -r ./tests
-
-########################################################
-## Build R-ODAF container for transcriptomic analysis ##
-########################################################
-# From tested container with updated code
-FROM cleanup
+# Set the entrypoint for the container
 ENTRYPOINT ["/home/R-ODAF/R-ODAF_Health_Canada/entrypoint.sh"]