Apptainer Run #49
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| name: Apptainer Run | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - dev | |
| pull_request: | |
| branches-ignore: [] | |
| schedule: | |
| - cron: '0 0 * * SUN' | |
| jobs: | |
| build-linux: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 5 | |
| matrix: | |
| python: [3.8, '3.10'] | |
| fail-fast: false | |
| steps: | |
| - name: precleanup | |
| run: | | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| - name: install graphviz | |
| run: | | |
| sudo apt update | |
| sudo apt-get install -y graphviz software-properties-common | |
| sudo add-apt-repository -y ppa:apptainer/ppa | |
| sudo apt update | |
| sudo apt install -y apptainer | |
| - name: checkout git repo | |
| uses: actions/checkout@v3 | |
| - name: Set up Python 3.X | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: Install dependencies | |
| run: | | |
| pip install .[testing] | |
| - name: install package itself | |
| run: | | |
| pip install . | |
| - name: testing | |
| run: | | |
| sequana_ribofinder --input-directory test/data --reference-file test/data/Lepto.fa --gff-file test/data/Lepto.gff --use-apptainer && cd ribofinder && sh ribofinder.sh | |