Update all SPAdes saves #1
Workflow file for this run
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| name: Update all SPAdes saves | |
| on: | |
| workflow_dispatch: | |
| 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@v3 | |
| with: | |
| fetch-depth: 1 | |
| - name: '⚙️ Install ccache' | |
| uses: hendrikmuhs/ccache-action@v1.2 | |
| with: | |
| variant: sccache | |
| - 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}} | |
| key: sccache-${{env.BUILD_TYPE}} | |
| - name: '🚧 Build' | |
| run: > | |
| cmake | |
| --build ${{env.BUILD_DIR}} | |
| -j16 | |
| -t package | |
| - name: '📦 Package' | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: build-artifacts | |
| path: | | |
| ${{env.BUILD_DIR}}/${{env.PKG}}.tar.gz | |
| run-saves-ecoli-100k: | |
| name: 'Run saves E.coli 100K' | |
| runs-on: | |
| labels: [self-hosted, worker-1] | |
| needs: build | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '🧰 Checkout' | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| - name: '📦 Download package' | |
| uses: actions/download-artifact@v3 | |
| 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 --no_cleanup --ignore_checks | |
| /data/pipeline_tests/Saves_E.coli_100K.info | |
| run-saves-ecoli-ucsd-lane1: | |
| name: 'Run saves E.coli UCSD lane 1' | |
| runs-on: | |
| labels: [self-hosted, worker-1] | |
| needs: build | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '🧰 Checkout' | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| - name: '📦 Download package' | |
| uses: actions/download-artifact@v3 | |
| 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 --no_cleanup --ignore_checks | |
| /data/pipeline_tests/Saves_E.coli_UCSD_lane1.info | |
| run-meta-ecoli-mix-saves: | |
| name: 'Run E.coli mix saves' | |
| runs-on: | |
| labels: [self-hosted, worker-1] | |
| needs: build | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '🧰 Checkout' | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| - name: '📦 Download package' | |
| uses: actions/download-artifact@v3 | |
| 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 --no_cleanup --ignore_checks | |
| /data/meta_tests/ECOLI_MIX_SAVES.info | |
| copy-saves: | |
| runs-on: | |
| labels: [self-hosted, worker-1] | |
| name: '💾️ Copy saves' | |
| needs: [run-saves-ecoli-100k, run-saves-ecoli-ucsd-lane1, run-meta-ecoli-mix-saves] | |
| steps: | |
| - name: 'E.coli 100K' | |
| run: > | |
| python3 ${{env.SRC_DIR}}/test/teamcity/update_saves.py | |
| --saves_dir /data/pipeline_tests/etalon/ECOLI_IS220_100K | |
| --output_dir /scratch/spades_output/ECOLI_100K/ | |
| - name: 'E.coli UCSD lane 1' | |
| run: > | |
| python3 ${{env.SRC_DIR}}/test/teamcity/update_saves.py | |
| --saves_dir /data/pipeline_tests/etalon/SAVES_ECOLI_UCSD_L1 | |
| --output_dir /scratch/spades_output/SAVES_ECOLI_UCSD_L1/ | |
| - name: 'Meta E.coli UCSD lane 1' | |
| run: > | |
| python3 ${{env.SRC_DIR}}/test/teamcity/update_saves.py | |
| --saves_dir /data/meta_tests/etalon/ECOLI_MIX_SAVES | |
| --output_dir /scratch/meta_output/ECOLI_MIX_SAVES/ | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| rm -rf /scratch/spades_output/ECOLI_100K/K* && | |
| rm -rf /scratch/spades_output/SAVES_ECOLI_UCSD_L1/K* && | |
| rm -rf /scratch/meta_output/ECOLI_MIX_SAVES/K* | |
| check-saves-ecoli-100k: | |
| name: 'Check saves E.coli 100K' | |
| runs-on: self-hosted | |
| needs: [build, copy-saves] | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '🧰 Checkout' | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| - name: '📦 Download package' | |
| uses: actions/download-artifact@v3 | |
| 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/pipeline_tests/Saves_E.coli_100K.info | |
| check-saves-ecoli-ucsd-lane1: | |
| name: 'Check saves E.coli UCSD lane 1' | |
| runs-on: self-hosted | |
| needs: [build, copy-saves] | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '🧰 Checkout' | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| - name: '📦 Download package' | |
| uses: actions/download-artifact@v3 | |
| 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/pipeline_tests/Saves_E.coli_UCSD_lane1.info | |
| check-meta-ecoli-mix-saves: | |
| name: 'Check E.coli mix saves' | |
| runs-on: self-hosted | |
| needs: [build, copy-saves] | |
| steps: | |
| - name: '🧹 Cleanup' | |
| run: > | |
| set -e && | |
| shopt -s dotglob && | |
| rm -rf * | |
| - name: '🧰 Checkout' | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| - name: '📦 Download package' | |
| uses: actions/download-artifact@v3 | |
| 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/meta_tests/ECOLI_MIX_SAVES.info | |