Introduce frugal mode #266
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| name: SPAdes GCC & Python versions | |
| on: | |
| workflow_dispatch: | |
| pull_request: | |
| paths-ignore: | |
| - 'docs/**' | |
| - 'mkdocs.yml' | |
| push: | |
| tags: | |
| - '*' | |
| schedule: | |
| - cron: '30 23 6,12,18,24,30 * *' | |
| env: | |
| BUILD_TYPE: Release | |
| BUILD_DIR: ${{github.workspace}}/build | |
| INSTALL_DIR: ${{github.workspace}}/spades | |
| SRC_DIR: ${{github.workspace}}/src | |
| PKG: SPAdes-*-Linux | |
| jobs: | |
| build-gcc9: | |
| runs-on: | |
| labels: [self-hosted, worker-1] | |
| name: '🚧 Build SPAdes with GCC9' | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '🧰 Checkout' | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: '⚙️ Install ccache' | |
| uses: hendrikmuhs/ccache-action@v1.2 | |
| with: | |
| variant: sccache | |
| key: sccache-${{env.BUILD_TYPE}}-gcc9 | |
| - name: '⚙️ Configure CMake' | |
| run: > | |
| cmake | |
| -B ${{env.BUILD_DIR}} | |
| -S ${{env.SRC_DIR}} | |
| -DCMAKE_C_COMPILER=gcc-9 -DCMAKE_CXX_COMPILER=g++-9 | |
| -DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache | |
| -DCMAKE_INSTALL_PREFIX=${{env.INSTALL_DIR}} | |
| -DCPACK_PACKAGE_FILE_NAME=SPAdes-GCC9-Linux | |
| - name: '🚧 Build' | |
| run: > | |
| cmake | |
| --build ${{env.BUILD_DIR}} | |
| -j16 | |
| -t package | |
| - name: '📦 Package' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: build-artifacts-gcc9 | |
| path: | | |
| ${{env.BUILD_DIR}}/${{env.PKG}}.tar.gz | |
| spades-test-python38: | |
| name: 'E. coli 1k run with Python3.8' | |
| runs-on: | |
| labels: [self-hosted, worker-1] | |
| needs: build-gcc9 | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '📦 Download package' | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: build-artifacts-gcc9 | |
| path: ${{env.INSTALL_DIR}} | |
| - name: '📦 Unpack package' | |
| working-directory: ${{env.INSTALL_DIR}} | |
| run: > | |
| tar -zxf ${{env.PKG}}.tar.gz | |
| - name: 'E.coli 1K with Python 3.8' | |
| run: > | |
| python3.8 ${{env.INSTALL_DIR}}/${{env.PKG}}/bin/spades.py --test | |
| build-gcc10: | |
| runs-on: | |
| labels: [self-hosted, worker-1] | |
| name: '🚧 Build SPAdes with GCC10' | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '🧰 Checkout' | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: '⚙️ Install ccache' | |
| uses: hendrikmuhs/ccache-action@v1.2 | |
| with: | |
| variant: sccache | |
| key: sccache-${{env.BUILD_TYPE}}-gcc10 | |
| - name: '⚙️ Configure CMake' | |
| run: > | |
| cmake | |
| -B ${{env.BUILD_DIR}} | |
| -S ${{env.SRC_DIR}} | |
| -DCMAKE_C_COMPILER=gcc-10 -DCMAKE_CXX_COMPILER=g++-10 | |
| -DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache | |
| -DCMAKE_INSTALL_PREFIX=${{env.INSTALL_DIR}} | |
| -DCPACK_PACKAGE_FILE_NAME=SPAdes-GCC10-Linux | |
| - name: '🚧 Build' | |
| run: > | |
| cmake | |
| --build ${{env.BUILD_DIR}} | |
| -j16 | |
| -t package | |
| - name: '📦 Package' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: build-artifacts-gcc10 | |
| path: | | |
| ${{env.BUILD_DIR}}/${{env.PKG}}.tar.gz | |
| spades-test-python39: | |
| name: 'E. coli 1k run with Python3.9' | |
| runs-on: | |
| labels: [self-hosted, worker-1] | |
| needs: build-gcc10 | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '📦 Download package' | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: build-artifacts-gcc10 | |
| path: ${{env.INSTALL_DIR}} | |
| - name: '📦 Unpack package' | |
| working-directory: ${{env.INSTALL_DIR}} | |
| run: > | |
| tar -zxf ${{env.PKG}}.tar.gz | |
| - name: 'E.coli 1K SC with Python 3.9' | |
| run: > | |
| python3.9 ${{env.INSTALL_DIR}}/${{env.PKG}}/bin/spades.py --test --sc | |
| build-gcc11: | |
| runs-on: | |
| labels: [self-hosted, worker-1] | |
| name: '🚧 Build SPAdes with GCC11' | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '🧰 Checkout' | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: '⚙️ Install ccache' | |
| uses: hendrikmuhs/ccache-action@v1.2 | |
| with: | |
| variant: sccache | |
| key: sccache-${{env.BUILD_TYPE}}-gcc11 | |
| - name: '⚙️ Configure CMake' | |
| run: > | |
| cmake | |
| -B ${{env.BUILD_DIR}} | |
| -S ${{env.SRC_DIR}} | |
| -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ | |
| -DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache | |
| -DCMAKE_INSTALL_PREFIX=${{env.INSTALL_DIR}} | |
| -DCPACK_PACKAGE_FILE_NAME=SPAdes-GCC11-Linux | |
| - name: '🚧 Build' | |
| run: > | |
| cmake | |
| --build ${{env.BUILD_DIR}} | |
| -j16 | |
| -t package | |
| - name: '📦 Package' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: build-artifacts-gcc11 | |
| path: | | |
| ${{env.BUILD_DIR}}/${{env.PKG}}.tar.gz | |
| spades-test-python310: | |
| name: 'E. coli 1k run with Python3.10' | |
| runs-on: | |
| labels: [self-hosted, worker-1] | |
| needs: build-gcc11 | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '📦 Download package' | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: build-artifacts-gcc11 | |
| path: ${{env.INSTALL_DIR}} | |
| - name: '📦 Unpack package' | |
| working-directory: ${{env.INSTALL_DIR}} | |
| run: > | |
| tar -zxf ${{env.PKG}}.tar.gz | |
| - name: 'E.coli 1K meta with Python 3.10' | |
| run: > | |
| python3.10 ${{env.INSTALL_DIR}}/${{env.PKG}}/bin/spades.py --test --meta | |
| build-gcc12: | |
| runs-on: | |
| labels: [self-hosted, worker-1] | |
| name: '🚧 Build SPAdes with GCC12' | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '🧰 Checkout' | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: '⚙️ Install ccache' | |
| uses: hendrikmuhs/ccache-action@v1.2 | |
| with: | |
| variant: sccache | |
| key: sccache-${{env.BUILD_TYPE}}-gcc12 | |
| - name: '⚙️ Configure CMake' | |
| run: > | |
| cmake | |
| -B ${{env.BUILD_DIR}} | |
| -S ${{env.SRC_DIR}} | |
| -DCMAKE_C_COMPILER=/home/ubuntu/bin/gcc12/bin/gcc -DCMAKE_CXX_COMPILER=/home/ubuntu/bin/gcc12/bin/g++ | |
| -DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache | |
| -DCMAKE_INSTALL_PREFIX=${{env.INSTALL_DIR}} | |
| -DCPACK_PACKAGE_FILE_NAME=SPAdes-GCC12-Linux | |
| - name: '🚧 Build' | |
| run: > | |
| cmake | |
| --build ${{env.BUILD_DIR}} | |
| -j16 | |
| -t package | |
| - name: '📦 Package' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: build-artifacts-gcc12 | |
| path: | | |
| ${{env.BUILD_DIR}}/${{env.PKG}}.tar.gz | |
| spades-test-python311: | |
| name: 'E. coli 1k run with Python3.11' | |
| runs-on: | |
| labels: [self-hosted, worker-1] | |
| needs: build-gcc12 | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '📦 Download package' | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: build-artifacts-gcc12 | |
| path: ${{env.INSTALL_DIR}} | |
| - name: '📦 Unpack package' | |
| working-directory: ${{env.INSTALL_DIR}} | |
| run: > | |
| tar -zxf ${{env.PKG}}.tar.gz | |
| - name: 'E.coli 1K RNA with Python 3.11' | |
| run: > | |
| python3.11 ${{env.INSTALL_DIR}}/${{env.PKG}}/bin/spades.py --test --rna | |
| build-gcc13: | |
| runs-on: | |
| labels: [self-hosted, worker-1] | |
| name: '🚧 Build SPAdes with GCC13' | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '🧰 Checkout' | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: '⚙️ Install ccache' | |
| uses: hendrikmuhs/ccache-action@v1.2 | |
| with: | |
| variant: sccache | |
| key: sccache-${{env.BUILD_TYPE}}-gcc13 | |
| - name: '⚙️ Configure CMake' | |
| run: > | |
| cmake | |
| -B ${{env.BUILD_DIR}} | |
| -S ${{env.SRC_DIR}} | |
| -DCMAKE_C_COMPILER=/home/ubuntu/bin/gcc13/bin/gcc -DCMAKE_CXX_COMPILER=/home/ubuntu/bin/gcc13/bin/g++ | |
| -DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache | |
| -DCMAKE_INSTALL_PREFIX=${{env.INSTALL_DIR}} | |
| -DCPACK_PACKAGE_FILE_NAME=SPAdes-GCC13-Linux | |
| - name: '🚧 Build' | |
| run: > | |
| cmake | |
| --build ${{env.BUILD_DIR}} | |
| -j16 | |
| -t package | |
| - name: '📦 Package' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: build-artifacts-gcc13 | |
| path: | | |
| ${{env.BUILD_DIR}}/${{env.PKG}}.tar.gz | |
| spades-test-python312: | |
| name: 'E. coli 1k run with Python3.12' | |
| runs-on: | |
| labels: [self-hosted, worker-1] | |
| needs: build-gcc13 | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '📦 Download package' | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: build-artifacts-gcc13 | |
| path: ${{env.INSTALL_DIR}} | |
| - name: '📦 Unpack package' | |
| working-directory: ${{env.INSTALL_DIR}} | |
| run: > | |
| tar -zxf ${{env.PKG}}.tar.gz | |
| - name: 'E.coli 1K Isolate with Python 3.13' | |
| run: > | |
| python3.12 ${{env.INSTALL_DIR}}/${{env.PKG}}/bin/spades.py --test --isolate |