Compilation and code reuse improvements. #4
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| name: Self-hosted CI | |
| on: | |
| pull_request: | |
| branches: [ master ] | |
| paths-ignore: | |
| - '**.md' | |
| workflow_dispatch: | |
| jobs: | |
| check-prerequisites: | |
| name: Check prerequisites | |
| runs-on: [self-hosted, kmc] | |
| env: | |
| DATA_DIR: ../../../../data | |
| SCRIPT: tests/kmc_CLI/check-prerequisites.py | |
| steps: | |
| - name: Check prerequisites | |
| run: | | |
| chmod +x $SCRIPT | |
| /usr/bin/time -v $SCRIPT $DATA_DIR | |
| prepare-small-fastq-tests: | |
| name: Prepare small fastq tests | |
| runs-on: [self-hosted, kmc] | |
| env: | |
| TRIVIAL_COUNTER: tests/kmc_CLI/trivial-k-mer-counter/bin/counter | |
| DATA_DIR: ../../../../data | |
| SCRIPT: tests/kmc_CLI/prepare_small_fastq_tests.py | |
| FILE_TO_GET_PART_FROM: F.vesca/SRR072005.fastq.gz | |
| steps: | |
| - name: Compile trivial counter | |
| run: | | |
| (cd tests/kmc_CLI/trivial-k-mer-counter; /usr/bin/time -v make) | |
| - name: Prepare pattern data | |
| run: | | |
| chmod +x $SCRIPT | |
| /usr/bin/time -v $SCRIPT $DATA_DIR $TRIVIAL_COUNTER $FILE_TO_GET_PART_FROM 400000 | |
| make-tests: | |
| name: Make tests | |
| runs-on: [self-hosted, kmc] | |
| needs: check-prerequisites | |
| env: | |
| KMC_EXE: ./bin/kmc | |
| KMC_DUMP_EXE: ./bin/kmc_dump | |
| KMC_TOOLS: ./bin/kmc_tools | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| submodules: recursive | |
| - name: make (default) | |
| run: | | |
| /usr/bin/time -v make -j32 | |
| small-fastq-tests: | |
| name: Small fastq tests | |
| runs-on: [self-hosted, kmc] | |
| needs: [make-tests, prepare-small-fastq-tests] | |
| env: | |
| DATA_DIR: ../../../../data | |
| SCRIPT: tests/kmc_CLI/run_small_fastq_tests.py | |
| KMC_EXE: ./bin/kmc | |
| KMC_DUMP_EXE: ./bin/kmc_dump | |
| KMC_TOOLS: ./bin/kmc_tools | |
| steps: | |
| - name: Run all small fastq tests | |
| run: | | |
| chmod +x $SCRIPT | |
| /usr/bin/time -v $SCRIPT $DATA_DIR $KMC_EXE $KMC_TOOLS $KMC_DUMP_EXE |