Add gffutils arguments & customize LiftOn to take GTF file as input #5
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| name: Run tests | |
| on: | |
| push: | |
| branches: [ "*" ] | |
| pull_request: | |
| branches: [ "*" ] | |
| permissions: | |
| contents: read | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python 3.12 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: "3.12" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip flake8 | |
| sudo apt install wget | |
| wget https://github.com/lh3/miniprot/releases/download/v0.13/miniprot-0.13_x64-linux.tar.bz2 | |
| tar xvf miniprot-0.13_x64-linux.tar.bz2 | |
| cp miniprot-0.13_x64-linux/miniprot /usr/local/bin | |
| rm -rf miniprot-0.13_x64-linux* | |
| wget https://github.com/lh3/minimap2/releases/download/v2.28/minimap2-2.28_x64-linux.tar.bz2 | |
| tar xvf minimap2-2.28_x64-linux.tar.bz2 | |
| mv minimap2-2.28_x64-linux/k8 minimap2-2.28_x64-linux/paftools.js minimap2-2.28_x64-linux/minimap2 /usr/local/bin | |
| rm -rf minimap2-2.28_x64-linux* | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Install lifton | |
| run: | | |
| python -m pip install -e . | |
| - name: Test using example from test dir | |
| run: | | |
| cd test && bash -xeu lifton_chr22_example.sh | |