bin/GSvar_filters.ini: added short-read low mappability filter for lrGS #4634
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| name: MacOS build | |
| on: [push, pull_request] | |
| jobs: | |
| mac-build-and-test: | |
| runs-on: macos-13 | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Update submodules | |
| run: git submodule update --recursive --init | |
| - name: Update Homebrew | |
| run: brew update | |
| - name: Remove existing Python symlinks | |
| run: rm /usr/local/bin/2to3 /usr/local/bin/idle3 /usr/local/bin/pydoc3 /usr/local/bin/python3 /usr/local/bin/python3-config /usr/local/bin/2to3-3.11 /usr/local/bin/idle3.11 /usr/local/bin/pydoc3.11 /usr/local/bin/python3.11 /usr/local/bin/python3.11-config /usr/local/bin/2to3-3.12 /usr/local/bin/idle3.12 /usr/local/bin/pydoc3.12 /usr/local/bin/python3.12 /usr/local/bin/python3.12-config | |
| - name: Install Python 3 | |
| run: brew install python@3.10 | |
| - name: Setup other dependencies | |
| run: brew install lzlib | |
| - name: Install Qt 5 | |
| run: brew install qt@5 | |
| - name: Link Qt installation | |
| run: brew link qt@5 --force | |
| - name: Install matplotlib and numpy for Python 2 | |
| run: sudo pip install matplotlib numpy | |
| - name: Install matplotlib and numpy for Python 3 | |
| run: python3 -m pip install matplotlib numpy --break-system-packages | |
| - name: Build project dependencies | |
| run: make build_3rdparty build_libs_release build_tools_release build_gui_release build_server_release | |
| - name: Create a folder for SSL | |
| run: mkdir -p $HOME/ssl | |
| shell: bash | |
| - name: Generate SSL certificate-key pair | |
| run: openssl req -new -newkey rsa:4096 -days 365 -nodes -x509 -subj "/C=DE/ST=BW/L=Tuebingen/O=test-certificate/CN=localhost" -keyout $HOME/ssl/test-key.key -out $HOME/ssl/test-cert.crt | |
| - name: Create a settings.ini file for tests | |
| run: .github/workflows/settings_win_mac.sh | |
| shell: bash | |
| - name: Download test files | |
| run: make download_test_files | |
| - name: Start GSvar server and run tests | |
| run: | | |
| bin/GSvarServer & | |
| make -k test_lib test_server test_tools |