From 13a56743f2ed672a2400e70953585ff328744b3a Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Tue, 17 Dec 2024 12:52:56 -0600 Subject: [PATCH 1/5] use renv in dockerfile --- analyses/cell-type-consensus/Dockerfile | 36 ++++++++++++++++++++++--- 1 file changed, 33 insertions(+), 3 deletions(-) diff --git a/analyses/cell-type-consensus/Dockerfile b/analyses/cell-type-consensus/Dockerfile index 80010ba65..685a3bb72 100644 --- a/analyses/cell-type-consensus/Dockerfile +++ b/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"] From c3f41266f9674ebd92849434e89666674d406210 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Tue, 17 Dec 2024 12:57:47 -0600 Subject: [PATCH 2/5] uncomment docker gha --- .../workflows/docker_cell-type-consensus.yml | 32 +++++++++---------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/.github/workflows/docker_cell-type-consensus.yml b/.github/workflows/docker_cell-type-consensus.yml index 8a7435aa5..05eab341a 100644 --- a/.github/workflows/docker_cell-type-consensus.yml +++ b/.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: From 5c781d486322e55ca7edc7d63f916ca2eba5420a Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Tue, 17 Dec 2024 12:58:34 -0600 Subject: [PATCH 3/5] add consensus to docker gha --- .github/workflows/docker_all-modules.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/docker_all-modules.yml b/.github/workflows/docker_all-modules.yml index a2285a0e0..b383b5624 100644 --- a/.github/workflows/docker_all-modules.yml +++ b/.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: From 22e399ce96f26b5b601b0b1d8a0455c249a8f4f1 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 12 Dec 2024 13:00:27 -0600 Subject: [PATCH 4/5] update lockfile --- analyses/cell-type-consensus/renv.lock | 1815 ++++++++++++++++++++++-- 1 file changed, 1693 insertions(+), 122 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"Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "stats", + "utils" + ], + "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2" + }, + "yaml": { + "Package": "yaml", + "Version": "2.3.10", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "51dab85c6c98e50a18d7551e9d49f76c" + }, + "zlibbioc": { + "Package": "zlibbioc", + "Version": "1.52.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.20", + "Hash": "89bfb698d6eb2fdf03c923ffd32e0c3f" } } } From edb814cb2f659d3b184d743db70ec1cf146d4c20 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Tue, 17 Dec 2024 10:53:43 -0600 Subject: [PATCH 5/5] test updating lock file --- analyses/cell-type-consensus/renv.lock | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/analyses/cell-type-consensus/renv.lock b/analyses/cell-type-consensus/renv.lock index e189ec681..0e6a57bb8 100644 --- a/analyses/cell-type-consensus/renv.lock +++ b/analyses/cell-type-consensus/renv.lock @@ -1,26 +1,26 @@ { "R": { - "Version": "4.4.0", + "Version": "4.4.2", "Repositories": [ { "Name": "BioCsoft", - "URL": "https://bioconductor.org/packages/3.19/bioc" + "URL": "https://bioconductor.org/packages/3.20/bioc" }, { "Name": "BioCann", - "URL": "https://bioconductor.org/packages/3.19/data/annotation" + "URL": "https://bioconductor.org/packages/3.20/data/annotation" }, { "Name": "BioCexp", - "URL": "https://bioconductor.org/packages/3.19/data/experiment" + "URL": "https://bioconductor.org/packages/3.20/data/experiment" }, { "Name": "BioCworkflows", - "URL": "https://bioconductor.org/packages/3.19/workflows" + "URL": "https://bioconductor.org/packages/3.20/workflows" }, { "Name": "BioCbooks", - "URL": "https://bioconductor.org/packages/3.19/books" + "URL": "https://bioconductor.org/packages/3.20/books" }, { "Name": "CRAN", @@ -29,7 +29,7 @@ ] }, "Bioconductor": { - "Version": "3.19" + "Version": "3.20" }, "Packages": { "AnnotationDbi": {