tracs-CI #13
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| name: tracs-CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - dev | |
| pull_request: | |
| branches: | |
| - main | |
| - dev | |
| schedule: | |
| - cron: '1 1 1 * *' | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.9, '3.10'] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update && sudo apt-get install -y build-essential wget zlib1g-dev libncurses5-dev libbz2-dev liblzma-dev | |
| sudo apt-get install -y libboost-all-dev | |
| sudo apt-get install -y python3-pybind11 | |
| python --version | |
| python -m pip install --upgrade pip setuptools | |
| python -m pip install pybind11 pytest | |
| # Check if pybind11 was installed correctly | |
| python -m pip list | grep pybind11 | |
| - name: Install python dependencies | |
| run: | | |
| pip install scipy --prefer-binary | |
| pip install sourmash | |
| - name: Install Minimap2 | |
| run: | | |
| wget https://github.com/lh3/minimap2/releases/download/v2.26/minimap2-2.26_x64-linux.tar.bz2 | |
| tar -xvf minimap2-2.26_x64-linux.tar.bz2 | |
| sudo cp minimap2-2.26_x64-linux/minimap2 /usr/local/bin/ | |
| - name: Install Samtools | |
| run: | | |
| wget https://github.com/samtools/samtools/releases/download/1.18/samtools-1.18.tar.bz2 | |
| tar -xjf samtools-1.18.tar.bz2 | |
| cd samtools-1.18 | |
| ./configure --prefix=/usr/local/ | |
| make | |
| sudo make install | |
| - name: Install Htsbox | |
| run: | | |
| git clone https://github.com/lh3/htsbox | |
| cd htsbox | |
| make | |
| sudo cp htsbox /usr/local/bin/ | |
| - name: Download test data | |
| run: | | |
| wget https://github.com/gtonkinhill/tracm-test-data/archive/refs/tags/v0.0.2.zip | |
| unzip v0.0.2.zip | |
| - name: Install | |
| run: python setup.py install | |
| - name: Validation Tests | |
| run: pytest -W ignore -q --datafolder="${{ github.workspace }}/tracm-test-data-0.0.2/" | |