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Make GHA trigger & Dockerfiles consistent #748

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merged 5 commits into from
Sep 4, 2024
Merged

Make GHA trigger & Dockerfiles consistent #748

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0c6049f
remove complaints about ENV
jashapiro Sep 3, 2024
0414e84
Add workflow triggers to all existing
jashapiro Sep 3, 2024
daf1b17
update paths in templates
jashapiro Sep 3, 2024
7e0f0c5
Merge remote-tracking branch 'upstream/main' into 676-trigger-consist…
jashapiro Sep 3, 2024
f48d292
missed a couple
jashapiro Sep 3, 2024
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1 change: 1 addition & 0 deletions .github/workflows/run_cell-type-ewings.yml
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Expand Up @@ -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'
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3 changes: 2 additions & 1 deletion .github/workflows/run_cell-type-wilms-tumor-06.yml
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Expand Up @@ -24,9 +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

jobs:
run-module:
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2 changes: 1 addition & 1 deletion .github/workflows/run_doublet-detection.yml
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Expand Up @@ -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:
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3 changes: 3 additions & 0 deletions .github/workflows/run_hello-R.yml
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Expand Up @@ -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'
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3 changes: 3 additions & 0 deletions .github/workflows/run_hello-python.yml
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Expand Up @@ -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:
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5 changes: 4 additions & 1 deletion .github/workflows/run_metacells.yml
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Expand Up @@ -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:
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12 changes: 6 additions & 6 deletions analyses/hello-R/Dockerfile
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Expand Up @@ -7,20 +7,20 @@ LABEL org.opencontainers.image.authors="OpenScPCA [email protected]"
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
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4 changes: 2 additions & 2 deletions docs/ensuring-repro/docker/docker-images.md
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Expand Up @@ -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
Expand Down Expand Up @@ -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
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5 changes: 4 additions & 1 deletion templates/workflows/run_conda-module.yml
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Expand Up @@ -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:
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5 changes: 4 additions & 1 deletion templates/workflows/run_conda-renv-module.yml
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Expand Up @@ -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:
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5 changes: 4 additions & 1 deletion templates/workflows/run_renv-module.yml
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Expand Up @@ -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:
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