pull DP from VCF and show #69
Workflow file for this run
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| name: mambabuild | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - bundle_update_2023 | |
| env: | |
| atoken: ${{ secrets.ANACONDA_UPLOAD_TOKEN }} | |
| recipe_path: conda/recipe | |
| env_yml_path: conda/env/yml | |
| VERSION: '1.0.1.9003' # versioned by bump2version | |
| jobs: | |
| build_conda_pkgs: | |
| # When merging to one of the branches above and the commit message matches | |
| if: "startsWith(github.event.head_commit.message, 'Bump version:')" | |
| name: Build conda package | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| matrix: | |
| r_version: ["4.2"] | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Micromamba setup | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: ${{ env.env_yml_path }}/condabuild_env.yml | |
| - name: Build + upload cpsr conda pkg | |
| run: | | |
| conda mambabuild ${recipe_path}/cpsr --R=${{ matrix.r_version }} -c pcgr -c conda-forge -c bioconda --token ${atoken} | |
| pkgdown_site: | |
| name: Deploy pkgdown website | |
| runs-on: ubuntu-latest | |
| needs: build_conda_pkgs | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Micromamba setup | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: ${{ env.env_yml_path }}/pkgdown.yml | |
| - name: Publish pkgdown website | |
| run: | | |
| git config --local user.email "[email protected]" | |
| git config --local user.name "GitHub Actions" | |
| micromamba activate pkgdown | |
| printf "cpsr version:\n" | |
| Rscript -e "packageVersion('cpsr')" | |
| Rscript -e "pkgdown::deploy_to_branch(pkg = '.', commit_message = paste(pkgdown:::construct_commit_message('.'), '- see https://sigven.github.io/cpsr/'), branch = 'gh-pages', new_process = FALSE)" | |
| - name: Create tag | |
| uses: actions/github-script@v7 | |
| with: | |
| script: | | |
| const the_tag_name = 'refs/tags/v' + process.env.VERSION | |
| github.rest.git.createRef({ | |
| owner: context.repo.owner, | |
| repo: context.repo.repo, | |
| ref: the_tag_name, | |
| sha: context.sha | |
| }) |