Fix a CI failure in some python versions #1
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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: ${{ matrix.poetry-version }} | |
- name: Install the project dependencies | |
run: | | |
poetry config virtualenvs.in-project true | |
poetry install | |
- name: Install bcftools | |
run: | | |
apt-get update | |
apt-get install -y bcftools | |
- name: Install bedtools | |
run: | | |
curl -L -o /usr/local/bin/bedtools "https://github.com/arq5x/bedtools2/releases/download/v2.31.0/bedtools.static" | |
chmod ugo+x /usr/local/bin/bedtools | |
- name: Install sentieon | |
run: | | |
curl -L https://s3.amazonaws.com/sentieon-release/software/sentieon-genomics-$SENTIEON_VERSION.tar.gz | tar -zxf - | |
- name: Download model | |
run: curl -LO "https://s3.amazonaws.com/sentieon-release/other/DNAscopePacBio2.0.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/ref.fa | |
sentieon-cli dnascope-longread -r tests/smoke/ref.fa -i tests/smoke/sample.cram -m DNAscopePacBio2.0.bundle --repeat-model tests/smoke/sample_repeat.model -g output_hifi.vcf.gz | |
sentieon-cli dnascope-longread --tech ONT -r tests/smoke/ref.fa -i tests/smoke/sample.cram -m DNAscopePacBio2.0.bundle --repeat-model tests/smoke/sample_repeat.model -g output_ont.vcf.gz | |
env: | |
SENTIEON_LICENSE: ${{ secrets.SENTIEON_LICENSE }} | |
SENTIEON_AUTH_MECH: "GitHub Actions - token" | |
ENCRYPTION_KEY: ${{ secrets.ENCRYPTION_KEY }} | |
LICENSE_MESSAGE: ${{ secrets.LICENSE_MESSAGE }} | |