fix!: fix broken fastqc fixture #306
Workflow file for this run
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| name: ci | |
| on: | |
| pull_request: | |
| branches: | |
| - "main" | |
| - "alpha" | |
| push: | |
| branches: | |
| - "main" | |
| - "alpha" | |
| jobs: | |
| commitlint: | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Commitlint | |
| uses: wagoid/commitlint-github-action@v5 | |
| test: | |
| runs-on: ubuntu-22.04 | |
| services: | |
| redis: | |
| image: redis:6.0 | |
| ports: | |
| - 6379:6379 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Install FastQC | |
| run: | | |
| wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip | |
| unzip fastqc_v0.11.9.zip | |
| mv FastQC /opt/fastqc | |
| chmod ugo+x /opt/fastqc/fastqc | |
| ln -s /opt/fastqc/fastqc /usr/local/bin | |
| fastqc --version | |
| - name: Install Bowtie2 | |
| run: | | |
| wget https://github.com/BenLangmead/bowtie2/releases/download/v2.3.2/bowtie2-2.3.2-legacy-linux-x86_64.zip | |
| unzip bowtie2-2.3.2-legacy-linux-x86_64.zip | |
| cp -rv bowtie2-2.3.2-legacy /opt/bowtie2 | |
| ln -s /opt/bowtie2/bowtie* /usr/local/bin | |
| - name: Install HMMER | |
| run: | | |
| wget http://eddylab.org/software/hmmer/hmmer-3.2.1.tar.gz | |
| tar -xf hmmer-3.2.1.tar.gz | |
| cd hmmer-3.2.1 | |
| ./configure --prefix /opt/hmmer | |
| make | |
| make install | |
| ln -s /opt/hmmer/bin/* /usr/local/bin | |
| - name: Install Skewer | |
| run: cp vendor/skewer /usr/local/bin | |
| - name: Setup Java | |
| uses: actions/setup-java@v2 | |
| with: | |
| distribution: 'zulu' | |
| java-version: '11' | |
| - name: Setup Python | |
| uses: actions/setup-python@v4 | |
| - name: Install Poetry | |
| uses: snok/install-poetry@v1 | |
| with: | |
| python-version: '3.10' | |
| - name: Install Dependencies | |
| run: poetry install | |
| - name: Test | |
| run: poetry run pytest --redis-connection-string redis://localhost:6379 | |
| build: | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Setup Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| - name: Install Poetry | |
| uses: snok/install-poetry@v1 | |
| - name: Poetry Build | |
| run: | | |
| poetry check | |
| poetry build | |
| release: | |
| runs-on: ubuntu-22.04 | |
| if: github.event_name == 'push' | |
| needs: | |
| - commitlint | |
| - build | |
| - test | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Setup NodeJS | |
| uses: actions/setup-node@v2 | |
| with: | |
| node-version: 18 | |
| - name: Install semantic-release | |
| run: npm i semantic-release@^22.0.12 conventional-changelog-conventionalcommits@^7.0.2 | |
| - name: Release | |
| env: | |
| GITHUB_USERNAME: ${{ secrets.GH_USERNAME }} | |
| GITHUB_TOKEN: ${{ secrets.GH_TOKEN }} | |
| run: npx semantic-release |