[DO NOT MERGE] hpcSPAdes rebase, cleanup & implementation #76
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| name: rnaSPAdes tests | |
| on: | |
| workflow_dispatch: | |
| pull_request: | |
| paths-ignore: | |
| - 'docs/**' | |
| - 'mkdocs.yml' | |
| push: | |
| tags: | |
| - '*' | |
| schedule: | |
| - cron: '0 7 * * 3' | |
| env: | |
| BUILD_TYPE: Release | |
| BUILD_DIR: ${{github.workspace}}/build | |
| INSTALL_DIR: ${{github.workspace}}/spades | |
| SRC_DIR: ${{github.workspace}}/src | |
| PKG: SPAdes-*-Linux | |
| jobs: | |
| build: | |
| runs-on: self-hosted | |
| name: '🚧 Build SPAdes' | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '🧰 Checkout' | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: '⚙️ Install ccache' | |
| uses: hendrikmuhs/[email protected] | |
| with: | |
| variant: sccache | |
| key: sccache-${{env.BUILD_TYPE}} | |
| - name: '⚙️ Configure CMake' | |
| run: > | |
| cmake | |
| -B ${{env.BUILD_DIR}} | |
| -S ${{env.SRC_DIR}} | |
| -DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache | |
| -DCMAKE_INSTALL_PREFIX=${{env.INSTALL_DIR}} | |
| - name: '🚧 Build' | |
| run: > | |
| cmake | |
| --build ${{env.BUILD_DIR}} | |
| -j16 | |
| -t package | |
| - name: '📦 Package' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: build-artifacts | |
| path: | | |
| ${{env.BUILD_DIR}}/${{env.PKG}}.tar.gz | |
| rna-zmays: | |
| name: 'Z.mays' | |
| runs-on: self-hosted | |
| needs: build | |
| 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 | |
| path: ${{env.INSTALL_DIR}} | |
| - name: '📦 Unpack package' | |
| working-directory: ${{env.INSTALL_DIR}} | |
| run: > | |
| tar -zxf ${{env.PKG}}.tar.gz | |
| - name: 'Assembly' | |
| run: > | |
| ${{env.SRC_DIR}}/test/teamcity/github_runner.py | |
| --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin | |
| --no_contig_archive | |
| /data/rna_tests/ZMAYS_RNA.info | |
| rna-zmays-ss: | |
| name: 'Z.mays strand specific' | |
| runs-on: self-hosted | |
| needs: build | |
| 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 | |
| path: ${{env.INSTALL_DIR}} | |
| - name: '📦 Unpack package' | |
| working-directory: ${{env.INSTALL_DIR}} | |
| run: > | |
| tar -zxf ${{env.PKG}}.tar.gz | |
| - name: 'Assembly' | |
| run: > | |
| ${{env.SRC_DIR}}/test/teamcity/github_runner.py | |
| --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin | |
| --no_contig_archive | |
| /data/rna_tests/ZMAYS_SS_RNA.info | |
| rna-celegans: | |
| name: 'C.elegans' | |
| runs-on: self-hosted | |
| needs: build | |
| 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 | |
| path: ${{env.INSTALL_DIR}} | |
| - name: '📦 Unpack package' | |
| working-directory: ${{env.INSTALL_DIR}} | |
| run: > | |
| tar -zxf ${{env.PKG}}.tar.gz | |
| - name: 'Assembly' | |
| run: > | |
| ${{env.SRC_DIR}}/test/teamcity/github_runner.py | |
| --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin | |
| --no_contig_archive | |
| /data/rna_tests/CELEGANS_RNA.info | |
| rna-celegans-hybrid: | |
| name: 'C.elegans hybrid mode' | |
| runs-on: self-hosted | |
| needs: build | |
| 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 | |
| path: ${{env.INSTALL_DIR}} | |
| - name: '📦 Unpack package' | |
| working-directory: ${{env.INSTALL_DIR}} | |
| run: > | |
| tar -zxf ${{env.PKG}}.tar.gz | |
| - name: 'Assembly' | |
| run: > | |
| ${{env.SRC_DIR}}/test/teamcity/github_runner.py | |
| --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin | |
| --no_contig_archive | |
| /data/rna_tests/CELEGANS_RNA_HYBRID.info | |
| rna-celegans-fl: | |
| name: 'C.elegans full-length reads' | |
| runs-on: self-hosted | |
| needs: build | |
| 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 | |
| path: ${{env.INSTALL_DIR}} | |
| - name: '📦 Unpack package' | |
| working-directory: ${{env.INSTALL_DIR}} | |
| run: > | |
| tar -zxf ${{env.PKG}}.tar.gz | |
| - name: 'Assembly' | |
| run: > | |
| ${{env.SRC_DIR}}/test/teamcity/github_runner.py | |
| --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin | |
| --no_contig_archive | |
| /data/rna_tests/CELEGANS_RNA_FL.info |