Fix --setupdb #4
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| name: CI | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - name: Pull Prokka | |
| uses: actions/checkout@v5 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: prokka | |
| environment-file: environment.yml | |
| miniforge-version: latest | |
| channels: conda-forge,bioconda | |
| channel-priority: strict | |
| auto-update-conda: true | |
| - name: Add Prokka to PATH | |
| run: | | |
| echo "${{ github.workspace }}/bin" >> $GITHUB_PATH | |
| - name: Test Prokka | |
| run: | | |
| prokka --version | |
| prokka --help | |
| ! prokka --doesnotexist | |
| prokka --depends | |
| prokka --setupdb | |
| prokka --listdb | |
| prokka --cpus 2 --outdir asm --prefix asm test/plasmid.fna | |
| grep '>' asm/asm.fna | |
| prokka --cleandb |