ML predictor integration into pvacseq #197
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| name: pVACtools tests | |
| on: | |
| push: | |
| branches: [ master, staging, hotfix ] | |
| pull_request: | |
| types: [opened, synchronize, edited, reopened] | |
| branches: | |
| - '**' | |
| jobs: | |
| run_tests: | |
| name: "Test prediction algorithms used by pVACtools in various Python versions" | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| matrix: | |
| python-version: ['3.9', '3.10', '3.11'] | |
| steps: | |
| - name: Maximize build space | |
| uses: AdityaGarg8/remove-unwanted-software@v2 | |
| with: | |
| remove-android: 'true' | |
| remove-dotnet: 'true' | |
| remove-haskell: 'true' | |
| remove-codeql: 'true' | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get -qq update | |
| sudo apt-get install -y ghostscript | |
| sudo apt-get install -y gcc | |
| sudo apt-get install -y pandoc | |
| sudo apt-get install -y mafft | |
| sudo apt-get install -y build-essential | |
| pip install pypandoc==1.7.2 | |
| pip install coverage | |
| pip install coveralls | |
| - name: Install Python dependencies | |
| run: | | |
| pip install polars==0.16.18 | |
| pip install pypandoc==1.7.2 | |
| pip install "tensorflow<2.16" | |
| pip install git+https://github.com/griffithlab/bigmhc.git#egg=bigmhc | |
| pip install git+https://github.com/griffithlab/deepimmuno.git#egg=deepimmuno | |
| pip install -e . | |
| mhcflurry-downloads fetch | |
| - name: Install MixMHCpred | |
| uses: actions/checkout@master | |
| with: | |
| repository: GfellerLab/MixMHCpred | |
| path: ./MixMHCpred | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Set up MixMHCpred | |
| run: | | |
| cd MixMHCpred | |
| pip install -r code/setup_pythonLibrary.txt | |
| chmod +x MixMHCpred | |
| echo "$(pwd -P)" >> $GITHUB_PATH | |
| cd .. | |
| - name: Install PRIME | |
| uses: actions/checkout@master | |
| with: | |
| repository: GfellerLab/PRIME | |
| path: ./PRIME | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Set up PRIME | |
| run: | | |
| cd PRIME | |
| echo "$(pwd -P)" >> $GITHUB_PATH | |
| cd lib | |
| g++ -O3 PRIME.cc -o PRIME.x | |
| cd ../.. | |
| - name: List installed packages | |
| run: | | |
| pip list | |
| - name: Run tests | |
| env: | |
| TEST_FLAG: 1 | |
| run: python -m unittest predictor_tests/test_call_iedb.py |