From 0c6049ff0eee708b27cea0f7b90720d4eb61a050 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Tue, 3 Sep 2024 15:50:15 -0400 Subject: [PATCH 1/4] remove complaints about ENV --- analyses/hello-R/Dockerfile | 12 ++++++------ docs/ensuring-repro/docker/docker-images.md | 4 ++-- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/analyses/hello-R/Dockerfile b/analyses/hello-R/Dockerfile index 4bbd899f6..0cd79c611 100644 --- a/analyses/hello-R/Dockerfile +++ b/analyses/hello-R/Dockerfile @@ -7,20 +7,20 @@ 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 +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/* + 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')" # Disable the renv cache to install packages directly into the R library -ENV RENV_CONFIG_CACHE_ENABLED FALSE +ENV RENV_CONFIG_CACHE_ENABLED=FALSE # Copy the renv.lock file from the host environment to the image COPY renv.lock renv.lock diff --git a/docs/ensuring-repro/docker/docker-images.md b/docs/ensuring-repro/docker/docker-images.md index fd21343b9..b50db311a 100644 --- a/docs/ensuring-repro/docker/docker-images.md +++ b/docs/ensuring-repro/docker/docker-images.md @@ -80,7 +80,7 @@ FROM bioconductor/r-ver:3.19 RUN Rscript -e "install.packages('renv')" # Disable the renv cache to install packages directly into the R library -ENV RENV_CONFIG_CACHE_ENABLED FALSE +ENV RENV_CONFIG_CACHE_ENABLED=FALSE # Copy the renv.lock file from the host environment to the image COPY renv.lock renv.lock @@ -173,7 +173,7 @@ RUN conda install --channel=conda-forge --name=base conda-lock \ RUN Rscript -e "install.packages('renv')" # Disable the renv cache to install packages directly into the R library -ENV RENV_CONFIG_CACHE_ENABLED FALSE +ENV RENV_CONFIG_CACHE_ENABLED=FALSE # Copy conda lock file to image COPY conda-lock.yml conda-lock.yml From 0414e844a5cf822849cab67cc40e763ab526a0ba Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Tue, 3 Sep 2024 15:58:47 -0400 Subject: [PATCH 2/4] Add workflow triggers to all existing --- .github/workflows/run_cell-type-ewings.yml | 1 + .github/workflows/run_cell-type-wilms-tumor-06.yml | 1 + .github/workflows/run_doublet-detection.yml | 2 +- .github/workflows/run_hello-R.yml | 3 +++ .github/workflows/run_hello-python.yml | 3 +++ 5 files changed, 9 insertions(+), 1 deletion(-) diff --git a/.github/workflows/run_cell-type-ewings.yml b/.github/workflows/run_cell-type-ewings.yml index 5e06262a8..54efbfa02 100644 --- a/.github/workflows/run_cell-type-ewings.yml +++ b/.github/workflows/run_cell-type-ewings.yml @@ -24,6 +24,7 @@ on: - analyses/cell-type-ewings/** - "!analyses/cell-type-ewings/Dockerfile" - "!analyses/cell-type-ewings/.dockerignore" + - .github/workflows/run_cell-type-ewings.yml jobs: run-module: if: github.repository_owner == 'AlexsLemonade' diff --git a/.github/workflows/run_cell-type-wilms-tumor-06.yml b/.github/workflows/run_cell-type-wilms-tumor-06.yml index 030a04b0c..eac8da395 100644 --- a/.github/workflows/run_cell-type-wilms-tumor-06.yml +++ b/.github/workflows/run_cell-type-wilms-tumor-06.yml @@ -27,6 +27,7 @@ on: - "analyses/cell-type-wilms-tumor-06/**" - "!analyses/cell-type-wilms-tumor-06/Dockerfile" - "!analyses/cell-type-wilms-tumor-06/.dockerignore" + - ".github/workflows/run_cell-type-wilms-tumor-06.yml" jobs: run-module: diff --git a/.github/workflows/run_doublet-detection.yml b/.github/workflows/run_doublet-detection.yml index 37e514e71..930ac79f3 100644 --- a/.github/workflows/run_doublet-detection.yml +++ b/.github/workflows/run_doublet-detection.yml @@ -26,7 +26,7 @@ on: - analyses/doublet-detection/** - "!analyses/doublet-detection/Dockerfile" - "!analyses/doublet-detection/.dockerignore" - # - .github/workflows/run_doublet-detection.yml + - .github/workflows/run_doublet-detection.yml jobs: run-module: diff --git a/.github/workflows/run_hello-R.yml b/.github/workflows/run_hello-R.yml index edf136311..f34598a7b 100644 --- a/.github/workflows/run_hello-R.yml +++ b/.github/workflows/run_hello-R.yml @@ -22,6 +22,9 @@ on: - main paths: - analyses/hello-R/** + - "!analyses/hello-R/Dockerfile" + - "!analyses/hello-R/.dockerignore" + - .github/workflows/run_hello-R.yml jobs: run-module: if: github.repository_owner == 'AlexsLemonade' diff --git a/.github/workflows/run_hello-python.yml b/.github/workflows/run_hello-python.yml index 57fbf50e3..20043b146 100644 --- a/.github/workflows/run_hello-python.yml +++ b/.github/workflows/run_hello-python.yml @@ -22,6 +22,9 @@ on: - main paths: - analyses/hello-python/** + - "!analyses/hello-python/Dockerfile" + - "!analyses/hello-python/.dockerignore" + - .github/workflows/run_hello-python.yml jobs: run-module: From daf1b171fb6e96d3106932015c16b1f87a8673f9 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Tue, 3 Sep 2024 16:02:55 -0400 Subject: [PATCH 3/4] update paths in templates --- templates/workflows/run_conda-module.yml | 5 ++++- templates/workflows/run_conda-renv-module.yml | 5 ++++- templates/workflows/run_renv-module.yml | 5 ++++- 3 files changed, 12 insertions(+), 3 deletions(-) diff --git a/templates/workflows/run_conda-module.yml b/templates/workflows/run_conda-module.yml index 60b539531..713aed78e 100644 --- a/templates/workflows/run_conda-module.yml +++ b/templates/workflows/run_conda-module.yml @@ -24,7 +24,10 @@ on: # branches: # - main # paths: - # - "analyses/{{ openscpca_module }}/**" + # - analyses/{{ openscpca_module }}/** + # - "!analyses/{{ openscpca_module }}/Dockerfile" + # - "!analyses/{{ openscpca_module }}/.dockerignore" + # - .github/workflows/run_{{ openscpca_module }}.yml jobs: run-module: diff --git a/templates/workflows/run_conda-renv-module.yml b/templates/workflows/run_conda-renv-module.yml index 21da5714e..25a5f1f73 100644 --- a/templates/workflows/run_conda-renv-module.yml +++ b/templates/workflows/run_conda-renv-module.yml @@ -24,7 +24,10 @@ on: # branches: # - main # paths: - # - "analyses/{{ openscpca_module }}/**" + # - analyses/{{ openscpca_module }}/** + # - "!analyses/{{ openscpca_module }}/Dockerfile" + # - "!analyses/{{ openscpca_module }}/.dockerignore" + # - .github/workflows/run_{{ openscpca_module }}.yml jobs: run-module: diff --git a/templates/workflows/run_renv-module.yml b/templates/workflows/run_renv-module.yml index d839c230d..30438e523 100644 --- a/templates/workflows/run_renv-module.yml +++ b/templates/workflows/run_renv-module.yml @@ -24,7 +24,10 @@ on: # branches: # - main # paths: - # - "analyses/{{ openscpca_module }}/**" + # - analyses/{{ openscpca_module }}/** + # - "!analyses/{{ openscpca_module }}/Dockerfile" + # - "!analyses/{{ openscpca_module }}/.dockerignore" + # - .github/workflows/run_{{ openscpca_module }}.yml jobs: run-module: From f48d292ed1faffb566ea81df0365465d60258e4c Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Tue, 3 Sep 2024 17:01:31 -0400 Subject: [PATCH 4/4] missed a couple --- .github/workflows/run_cell-type-wilms-tumor-06.yml | 4 ++-- .github/workflows/run_metacells.yml | 5 ++++- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/.github/workflows/run_cell-type-wilms-tumor-06.yml b/.github/workflows/run_cell-type-wilms-tumor-06.yml index eac8da395..5547c9882 100644 --- a/.github/workflows/run_cell-type-wilms-tumor-06.yml +++ b/.github/workflows/run_cell-type-wilms-tumor-06.yml @@ -24,10 +24,10 @@ on: branches: - main paths: - - "analyses/cell-type-wilms-tumor-06/**" + - analyses/cell-type-wilms-tumor-06/** - "!analyses/cell-type-wilms-tumor-06/Dockerfile" - "!analyses/cell-type-wilms-tumor-06/.dockerignore" - - ".github/workflows/run_cell-type-wilms-tumor-06.yml" + - .github/workflows/run_cell-type-wilms-tumor-06.yml jobs: run-module: diff --git a/.github/workflows/run_metacells.yml b/.github/workflows/run_metacells.yml index 7b54b3f90..cc5384f83 100644 --- a/.github/workflows/run_metacells.yml +++ b/.github/workflows/run_metacells.yml @@ -24,7 +24,10 @@ on: branches: - main paths: - - "analyses/metacells/**" + - analyses/metacells/** + - "!analyses/metacells/Dockerfile" + - "!analyses/metacells/.dockerignore" + - .github/workflows/run_metacells.yml jobs: run-module: