Quick fix to process conjugate overlaps #130
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| name: SPAdes basic tests | |
| on: | |
| workflow_dispatch: | |
| push: | |
| branches: | |
| - master | |
| - main | |
| - next | |
| tags: | |
| - '*' | |
| paths-ignore: | |
| - 'docs/**' | |
| - 'mkdocs.yml' | |
| pull_request: | |
| paths-ignore: | |
| - 'docs/**' | |
| - 'mkdocs.yml' | |
| env: | |
| BUILD_TYPE: Release | |
| BUILD_DIR: './build' | |
| SRC_DIR: './src' | |
| INSTALL_DIR: ${{github.workspace}}/spades | |
| PKG_LINUX: SPAdes-*-Linux | |
| PKG_MAC: SPAdes-*-Darwin | |
| jobs: | |
| build-linux: | |
| runs-on: self-hosted | |
| name: '🐧 Build SPAdes for Linux' | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '🧰 Checkout' | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: '⚙️ Install ccache' | |
| uses: hendrikmuhs/[email protected] | |
| with: | |
| variant: sccache | |
| key: sccache-${{env.BUILD_TYPE}}-linux | |
| - name: '⚙️ Configure CMake' | |
| run: > | |
| cmake | |
| -B $BUILD_DIR | |
| -S $SRC_DIR | |
| -DSPADES_USE_NCBISDK=ON -DSPADES_ENABLE_PROJECTS=all | |
| -DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache | |
| - name: '🚧 Build' | |
| run: > | |
| cmake | |
| --build ${{env.BUILD_DIR}} | |
| -j16 | |
| -t package include_test debruijn_test | |
| - name: '📦 Package' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: build-artifacts-linux | |
| path: | | |
| ${{env.BUILD_DIR}}/${{env.PKG_LINUX}}.tar.gz | |
| ${{env.BUILD_DIR}}/bin/debruijn_test | |
| ${{env.BUILD_DIR}}/bin/include_test | |
| spades-1k-checks-linux: | |
| name: '🚬 E. coli 1k smoke checks' | |
| runs-on: self-hosted | |
| needs: build-linux | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '📦 Download package' | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: build-artifacts-linux | |
| path: ${{env.INSTALL_DIR}} | |
| - name: '📦 Unpack package' | |
| working-directory: ${{env.INSTALL_DIR}} | |
| run: > | |
| tar -zxf $PKG_LINUX.tar.gz | |
| - name: '1k multi-cell' | |
| run: > | |
| $INSTALL_DIR/$PKG_LINUX/bin/spades.py --test | |
| - name: '1k single-cell' | |
| run: > | |
| $INSTALL_DIR/$PKG_LINUX/bin/spades.py --sc --test | |
| - name: '1k meta' | |
| run: > | |
| $INSTALL_DIR/$PKG_LINUX/bin/metaspades.py --test | |
| - name: '1k plasmid' | |
| run: > | |
| $INSTALL_DIR/$PKG_LINUX/bin/plasmidspades.py --test | |
| - name: '1k rna' | |
| run: > | |
| $INSTALL_DIR/$PKG_LINUX/bin/rnaspades.py --test | |
| - name: '1k corona' | |
| run: > | |
| $INSTALL_DIR/$PKG_LINUX/bin/coronaspades.py --test | |
| spades-unittests-linux: | |
| name: 'SPAdes unittests' | |
| runs-on: self-hosted | |
| needs: build-linux | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '🧰 Checkout' | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: '📦 Download package' | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: build-artifacts-linux | |
| path: ${{env.BUILD_DIR}} | |
| - name: '🔎 Include tests' | |
| working-directory: ${{github.workspace}} | |
| run: > | |
| chmod +x $BUILD_DIR/bin/include_test && | |
| $BUILD_DIR/bin/include_test | |
| - name: '🔎 De-Bruijn tests' | |
| working-directory: ${{github.workspace}} | |
| run: > | |
| chmod +x $BUILD_DIR/bin/debruijn_test && | |
| $BUILD_DIR/bin/debruijn_test | |
| build-mac: | |
| strategy: | |
| matrix: | |
| include: | |
| - os: macos-13 | |
| arch: x86_64 | |
| - os: macos-14 | |
| arch: arm64 | |
| name: '🍎 Build SPAdes for macOS' | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '🧰 Checkout' | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: '⚙️ Install dependencies' | |
| run: > | |
| brew install llvm libomp bzip2 | |
| - name: '⚙️ Install ccache' | |
| uses: hendrikmuhs/[email protected] | |
| with: | |
| variant: sccache | |
| key: sccache-${{env.BUILD_TYPE}}-${{ matrix.os }} | |
| - name: '⚙️ Configure CMake' | |
| run: > | |
| cmake | |
| -B $BUILD_DIR | |
| -S $SRC_DIR | |
| -DSPADES_USE_NCBISDK=ON -DSPADES_ENABLE_PROJECTS=all | |
| -DCMAKE_C_COMPILER=$(brew --prefix llvm)/bin/clang | |
| -DCMAKE_CXX_COMPILER=$(brew --prefix llvm)/bin/clang++ | |
| -DCMAKE_EXE_LINKER_FLAGS=-L$(brew --prefix llvm)/lib/c++ | |
| -DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache | |
| - name: '🚧 Build' | |
| run: > | |
| cmake | |
| --build $BUILD_DIR | |
| -j16 | |
| -t package include_test debruijn_test | |
| - name: '📦 Package' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: build-artifacts-mac-${{ matrix.arch }} | |
| path: | | |
| ${{env.BUILD_DIR}}/${{env.PKG_MAC}}.tar.gz | |
| ${{env.BUILD_DIR}}/bin/debruijn_test | |
| ${{env.BUILD_DIR}}/bin/include_test | |
| spades-1k-checks-mac: | |
| name: '🚬 E. coli 1k smoke checks' | |
| strategy: | |
| matrix: | |
| include: | |
| - os: macos-13 | |
| arch: x86_64 | |
| - os: macos-14 | |
| arch: arm64 | |
| runs-on: ${{ matrix.os }} | |
| needs: build-mac | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '⚙️ Install dependencies' | |
| run: > | |
| brew install llvm libomp bzip2 | |
| - name: '📦 Download package' | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: build-artifacts-mac-${{ matrix.arch }} | |
| path: ${{env.INSTALL_DIR}} | |
| - name: '📦 Unpack package' | |
| working-directory: ${{env.INSTALL_DIR}} | |
| run: > | |
| tar -zxf ${{env.PKG_MAC}}.tar.gz | |
| - name: '1k multi-cell' | |
| run: > | |
| $INSTALL_DIR/$PKG_MAC/bin/spades.py --test | |
| - name: '1k single-cell' | |
| run: > | |
| $INSTALL_DIR/$PKG_MAC/bin/spades.py --sc --test | |
| - name: '1k meta' | |
| run: > | |
| $INSTALL_DIR/$PKG_MAC/bin/metaspades.py --test | |
| - name: '1k plasmid' | |
| run: > | |
| $INSTALL_DIR/$PKG_MAC/bin/plasmidspades.py --test | |
| - name: '1k rna' | |
| run: > | |
| $INSTALL_DIR/$PKG_MAC/bin/rnaspades.py --test | |
| - name: '1k corona' | |
| run: > | |
| $INSTALL_DIR/$PKG_MAC/bin/coronaspades.py --test | |
| spades-unittests-mac: | |
| name: 'SPAdes unittests' | |
| strategy: | |
| matrix: | |
| include: | |
| - os: macos-13 | |
| arch: x86_64 | |
| - os: macos-14 | |
| arch: arm64 | |
| runs-on: ${{ matrix.os }} | |
| needs: build-mac | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '🧰 Checkout' | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: '📦 Download package' | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: build-artifacts-mac-${{ matrix.arch }} | |
| path: ${{env.BUILD_DIR}} | |
| - name: '⚙️ Install dependencies' | |
| run: > | |
| brew install llvm libomp bzip2 | |
| - name: '🔎 Include tests' | |
| working-directory: ${{github.workspace}} | |
| run: > | |
| chmod +x $BUILD_DIR/bin/include_test && | |
| $BUILD_DIR/bin/include_test | |
| - name: '🔎 De-Bruijn tests' | |
| working-directory: ${{github.workspace}} | |
| run: > | |
| chmod +x $BUILD_DIR/bin/debruijn_test && | |
| $BUILD_DIR/bin/debruijn_test |