Add back a missing run()
#7
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| name: CI-main | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| env: | |
| SENTIEON_VERSION: "202308.01" | |
| jobs: | |
| smoke: | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| python-version: ["3.12"] | |
| poetry-version: ["1.5.1"] | |
| os: [ubuntu-22.04] #, macos-latest, windows-latest] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Run image | |
| uses: abatilo/actions-poetry@v2 | |
| with: | |
| poetry-version: ${{ matrix.poetry-version }} | |
| - name: Install the project dependencies | |
| run: | | |
| poetry config virtualenvs.in-project true | |
| poetry install | |
| - name: Install bcftools | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y bcftools | |
| - name: Install bedtools | |
| run: | | |
| sudo curl -L -o /usr/local/bin/bedtools "https://github.com/arq5x/bedtools2/releases/download/v2.31.0/bedtools.static" | |
| sudo chmod ugo+x /usr/local/bin/bedtools | |
| - name: Install sentieon | |
| run: | | |
| curl -L https://s3.amazonaws.com/sentieon-release/software/sentieon-genomics-$SENTIEON_VERSION.tar.gz | tar -zxf - | |
| - name: Download model | |
| run: | | |
| curl -L "https://s3.amazonaws.com/sentieon-release/other/DNAscopePacBio2.1.bundle" \ | |
| > "DNAscope PacBio2.1.bundle" | |
| - name: Smoke test | |
| run: | | |
| SENTIEON_AUTH_DATA=$(python3 .github/scripts/license_message.py encrypt --key "$ENCRYPTION_KEY" --message "$LICENSE_MESSAGE") | |
| export SENTIEON_AUTH_DATA | |
| . .venv/bin/activate | |
| export PATH=$(pwd)/sentieon-genomics-$SENTIEON_VERSION/bin:$PATH | |
| gzip -dc tests/smoke/ref.fa.bgz > "tests/smoke/r ef.fa" | |
| mv tests/smoke/ref.fa.fai "tests/smoke/r ef.fa.fai" | |
| mv tests/smoke/sample.cram "tests/smoke/sam ple.cram" | |
| mv tests/smoke/sample.cram.crai "tests/smoke/sam ple.cram.crai" | |
| sentieon-cli dnascope-longread -r "tests/smoke/r ef.fa" \ | |
| -i "tests/smoke/sam ple.cram" -m "DNAscope PacBio2.1.bundle" \ | |
| --repeat-model tests/smoke/sample_repeat.model -g "output hifi.vcf.gz" | |
| sentieon driver -r "tests/smoke/r ef.fa" --algo GVCFtyper \ | |
| -v "output hifi.g.vcf.gz" output_hifi_gvcftyper.vcf.gz | |
| sentieon-cli dnascope-longread --tech ONT -r "tests/smoke/r ef.fa" \ | |
| -i "tests/smoke/sam ple.cram" -m "DNAscope PacBio2.1.bundle" \ | |
| --repeat-model tests/smoke/sample_repeat.model -g "output ont.vcf.gz" | |
| sentieon driver -r "tests/smoke/r ef.fa" --algo GVCFtyper \ | |
| -v "output ont.g.vcf.gz" output_hifi_gvcftyper.vcf.gz | |
| env: | |
| SENTIEON_LICENSE: ${{ secrets.SENTIEON_LICENSE }} | |
| SENTIEON_AUTH_MECH: "GitHub Actions - token" | |
| ENCRYPTION_KEY: ${{ secrets.ENCRYPTION_KEY }} | |
| LICENSE_MESSAGE: ${{ secrets.LICENSE_MESSAGE }} | |