Update deploy.yml #204
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| name: deploy | |
| on: | |
| workflow_dispatch: | |
| pull_request: | |
| types: | |
| - closed | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| permissions: | |
| contents: read | |
| pages: write | |
| id-token: write | |
| concurrency: | |
| group: "pages" | |
| cancel-in-progress: false | |
| jobs: | |
| build: | |
| if: github.event.pull_request.merged == true | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: CheckoutRepo | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: MicromambaCreateEnv | |
| uses: mamba-org/setup-micromamba@main | |
| with: | |
| environment-name: Rseurat | |
| environment-file: configs/conda.yml | |
| #cache-env: true | |
| - name: MicromambaActivateEnv | |
| run: micromamba activate Rseurat | |
| - name: TidyverseDependencies | |
| run: | | |
| sudo apt update && sudo apt install -y libicu-dev make libcurl4-openssl-dev libssl-dev zlib1g-dev libfontconfig1-dev libfreetype6-dev libfribidi-dev libharfbuzz-dev libjpeg-dev libpng-dev libtiff-dev pandoc libxml2-dev | |
| - name: InstallSeuratDatasets | |
| run: | | |
| Rscript -e "install.packages(pkgs='ifnb.SeuratData', repos='https://seurat.nygenome.org/', type='source')" | |
| Rscript -e "install.packages(pkgs='pbmc3k.SeuratData', repos='https://seurat.nygenome.org/', type='source')" | |
| - name: DownloadZenodo | |
| working-directory: ./rmd | |
| run: | | |
| Rscript -e "utils::download.file('https://zenodo.org/record/7891484/files/panc_sub_processed.RDS?download=1',destfile='datasets/preprocessed_rds/panc_sub_processed.RDS',method='wget')" | |
| - name: RmarkdownRenderSite | |
| run: Rscript -e "rmarkdown::render_site('rmd')" | |
| - name: Upload artifact | |
| uses: actions/upload-pages-artifact@v1 | |
| with: | |
| path: ./rmd/site | |
| deploy: | |
| needs: build | |
| environment: | |
| name: github-pages | |
| url: ${{ steps.deployment.outputs.page_url }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Deploy to GitHub Pages | |
| id: deployment | |
| uses: actions/deploy-pages@v2 |