Debug of env #3
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| name: E2E test for Stx2 deletion | |
| on: | |
| push: | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| max-parallel: 2 | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| python-version: ["3.13"] | |
| name: Python ${{ matrix.python-version }} on ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| miniconda-version: "latest" | |
| activate-environment: test-env | |
| channels: bioconda, conda-forge, defaults | |
| - name: Create and activate conda environment | |
| run: | | |
| conda create -y -n env-dajin2 python=${{ matrix.python-version }} pip pytest | |
| conda activate env-dajin2 | |
| - name: Install DAJIN2 and dependencies | |
| run: | | |
| pip install -e . # Install DAJIN2 in editable mode | |
| - name: Download example dataset | |
| run: | | |
| if [ ! -d example_single ]; then | |
| curl -LJO https://github.com/akikuno/DAJIN2/raw/main/examples/example_single.tar.gz | |
| tar -xf example_single.tar.gz | |
| fi | |
| - name: Run DAJIN2 with parameters | |
| env: | |
| PYTHONPATH: src | |
| run: | | |
| time DAJIN2 \ | |
| --control example_single/control \ | |
| --sample example_single/sample \ | |
| --allele example_single/stx2_deletion.fa \ | |
| --name stx2_deletion \ | |
| --genome mm39 \ | |
| --threads 4 \ | |
| --debug || exit 1 |