Switch to ubuntu in Singularity setup #129
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| # This workflow will install Python dependencies, run tests and lint with a single version of Python | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Python application | |
| on: push | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - name: Install minimap2 | |
| run: | | |
| cd /opt | |
| wget https://github.com/lh3/minimap2/releases/download/v2.17/minimap2-2.17_x64-linux.tar.bz2 | |
| tar -jxvf ./minimap2-2.17_x64-linux.tar.bz2 | |
| echo /opt/minimap2-2.17_x64-linux >> $GITHUB_PATH | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip pipenv | |
| pipenv install --dev | |
| - name: Test with pytest | |
| run: | | |
| pipenv run python -m pytest |