Added docs for bioconductor submission -- related to #96 #11
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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | |
# Additional help taken from https://fromthebottomoftheheap.net/2020/04/30/rendering-your-readme-with-github-actions/ | |
on: | |
push: | |
branches: dev | |
paths: [README.Rmd, render-README.yaml] | |
name: render-README | |
jobs: | |
render: | |
runs-on: macos-latest | |
env: | |
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
steps: | |
- uses: actions/checkout@v3 | |
- uses: r-lib/actions/setup-r@v2 | |
with: | |
use-public-rspm: true | |
- uses: r-lib/actions/setup-r-dependencies@v2 | |
- uses: r-lib/actions/setup-pandoc@v2 | |
- name: install CRAN packages | |
run: Rscript -e 'install.packages(c("rmarkdown","ggplot2", "dplyr", "purrr", "remotes", "devtools", "BiocManager", "Seurat"), force = TRUE)' | |
- name: install BioConductor packages | |
run: Rscript -e 'BiocManager::install(c("SingleCellExperiment", "scater", "scran", "scuttle", "bluster"), force = TRUE)' | |
- name: install GitHub packages | |
run: Rscript -e 'remotes::install_github("jr-leary7/scLANE")' | |
- name: render README | |
run: Rscript -e 'rmarkdown::render("README.Rmd", output_format = "github_document", output_file = "README.md")' | |
- name: commit rendered README | |
run: | | |
git config --local user.name "jr-leary7" | |
git config --local user.email "jrleary@live.unc.edu" | |
git add README.md man/figures/README-* | |
git commit -m "Recompiled README.Rmd" || echo "No changes to commit" | |
git push origin || echo "No changes to commit" |