pggb low mem consumption args added #39
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| name: ci | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - capnp | |
| permissions: | |
| contents: write | |
| jobs: | |
| Run-panmanUtils: | |
| name: Deploy Job on ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-22.04, ubuntu-24.04, macos-13] | |
| steps: | |
| - name: Checkout Code | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.11 | |
| - name: Cache dependencies | |
| uses: actions/cache@v4 | |
| with: | |
| key: ${{ runner.os }}-${{ github.ref }} | |
| path: .cache | |
| - name: Install mkdocs | |
| if: runner.os == 'Linux' | |
| run: | | |
| pip install mkdocs-material | |
| pip install "mkdocs-material[imaging]" | |
| mkdocs gh-deploy --force | |
| - name: Linux-specific steps | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt update | |
| sudo apt install -y gcc-10 g++-10 | |
| sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-10 100 --slave /usr/bin/g++ g++ /usr/bin/g++-10 --slave /usr/bin/gcov gcov /usr/bin/gcov-10 | |
| sudo update-alternatives --set gcc /usr/bin/gcc-10 | |
| chmod +x install/installationUbuntu.sh | |
| sudo ./install/installationUbuntu.sh | |
| cd build | |
| ./panmanUtils --help | |
| # - name: macOS-specific steps | |
| # if: runner.os == 'macOS' | |
| # run: | | |
| # brew update | |
| # brew install cairo pango gdk-pixbuf libffi | |
| # chmod +x install/installationMacOS.sh | |
| # ./install/installationMacOS.sh | |
| - name: Install Conda | |
| if: runner.os == 'macOS' | |
| run: | | |
| curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh | |
| chmod +x Miniconda3-latest-MacOSX-x86_64.sh | |
| ./Miniconda3-latest-MacOSX-x86_64.sh -b -p $HOME/miniconda | |
| echo "::append-path::$HOME/miniconda/bin" >> $GITHUB_PATH | |
| - name: Setup Conda Environment and Install PanMan | |
| if: runner.os == 'macOS' | |
| run: | | |
| conda config --add channels defaults | |
| conda config --add channels bioconda | |
| conda config --add channels conda-forge | |
| # conda install bioconda::panman -y | |
| conda create -n panenv python=3.11 panman -y | |
| source activate panenv | |
| panmanUtils --help |