add metaphlan tree with taxids instead of genome ids, and taxa data a… #122
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| ## Copied this workflow from: https://github.com/waldronlab/bugphyzz/blob/main/.github/workflows/pkgdown.yaml | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - master | |
| pull_request: | |
| branches: | |
| - main | |
| - master | |
| name: pkgdown | |
| jobs: | |
| pkgdown: | |
| runs-on: ubuntu-latest | |
| container: bioconductor/bioconductor_docker:devel | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Install apt dependencies | |
| run: | | |
| sudo apt-get update && sudo apt-get install -y rsync | |
| - name: Install R dependencies | |
| run: | | |
| install.packages("pkgdown", dependencies = TRUE) | |
| remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories()) | |
| shell: Rscript {0} | |
| - name: Install package | |
| run: R CMD INSTALL . | |
| - name: Build site | |
| run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) | |
| shell: Rscript {0} | |
| - name: Deploy to GitHub pages 🚀 | |
| uses: JamesIves/github-pages-deploy-action@v4 | |
| with: | |
| branch: gh-pages | |
| clean: false | |
| folder: docs |