Bump mongodb from 4.3.1 to 4.17.0 #51
Workflow file for this run
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| name: Unit tests | |
| on: [push, pull_request] | |
| env: | |
| MONGODB_VERSION: 3.6.14 | |
| MINICONDA_VERSION: "4.10.3" | |
| CONDA_GENERIC_CHANNEL: "https://dnap.cog.sanger.ac.uk/npg/conda/prod/generic/linux-64/" | |
| CONDA_GENERIC_DEVEL_CHANNEL: "https://dnap.cog.sanger.ac.uk/npg/conda/devel/generic/linux-64/" | |
| MINICONDA_HOME: "/tmp/miniconda" | |
| SOFTWARE_HOME: "/tmp/software" | |
| FREEBAYES_VERSION: "1.2.0" | |
| BIOBAMBAM_VERSION: "2.0.79" | |
| SAMTOOLS1_VERSION: "1.14.0" | |
| jobs: | |
| test: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| node-version: ["12.14.1", "14", "16"] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v3 | |
| - uses: actions/setup-node@v3 | |
| with: | |
| node-version: ${{ matrix.node-version }} | |
| - name: Cache node modules | |
| uses: actions/cache@v3 | |
| env: | |
| cache-name: cache-node-modules | |
| with: | |
| path: ~/.npm | |
| key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ hashFiles('**/package-lock.json') }} | |
| restore-keys: | | |
| ${{ runner.os }}-build-${{ env.cache-name }}- | |
| - name: Cache conda modules | |
| uses: actions/cache@v3 | |
| env: | |
| cache-name: cache-conda-modules | |
| with: | |
| path: /tmp/software | |
| key: ${{ runner.os }}-build-${{ env.cache-name }}-${{env.MONGODB_VERSION}}-${{env.MINICONDA_VERSION}}-${{env.FREEBAYES_VERSION}}-${{env.BIOBAMBAM_VERSION}}-${{env.SAMTOOLS1_VERSION}} | |
| restore-keys: | | |
| ${{ runner.os }}-build-${{ env.cache-name }}-${{env.MONGODB_VERSION}}-${{env.MINICONDA_VERSION}}-${{env.FREEBAYES_VERSION}}-${{env.BIOBAMBAM_VERSION}}-${{env.SAMTOOLS1_VERSION}} | |
| - name: Setup dependencies | |
| run: | | |
| ./scripts/CI-install.sh | |
| export PATH="/tmp/usr/bin:${PATH}" | |
| npm install | |
| npm install -g grunt-cli | |
| npm --version | |
| mongo --version | |
| conda --version | |
| bamstreamingmarkduplicates --version | |
| samtools --version | |
| - name: Run tests | |
| run: grunt -v |