conda recipe #768
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| name: conda recipe | |
| # Controls when the workflow will run | |
| on: | |
| # Triggers the workflow on schedule but only for the default branch (which is master) | |
| schedule: | |
| - cron: '0 7 * * 1-5' | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| # A workflow run is made up of one or more jobs that can run sequentially or in parallel | |
| jobs: | |
| # This workflow contains a single job called "check_recipe" | |
| check_recipe: | |
| name: test bioconda recipes on ${{ matrix.os }} with python ${{ matrix.python-version }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: ['ubuntu-latest','macos-13'] | |
| python-version: ['3.8','3.9','3.10'] | |
| # Steps represent a sequence of tasks that will be executed as part of the job | |
| steps: | |
| # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it | |
| - uses: actions/checkout@v4 | |
| # Setting up miniconda | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| channels: bioconda,conda-forge,anaconda,defaults | |
| activate-environment: test | |
| - name: Set up test environment | |
| shell: bash -l {0} | |
| run: | | |
| conda install -y ppanggolin | |
| - name: check installation | |
| shell: bash -l {0} | |
| run: | | |
| python --version | |
| ppanggolin --version | |
| - name: all workflow run | |
| shell: bash -l {0} | |
| run: | | |
| cd testingDataset/ | |
| ppanggolin all --cpu 1 --anno genomes.gbff.list -o pango | |
| ppanggolin info -p pango/pangenome.h5 --content --parameters --status |