Merge pull request #230 from abyzovlab/master #26
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| name: Test python versions | |
| on: [push, pull_request] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.11"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| pip install -r requirements.txt | |
| pip install . | |
| pip install pytest | |
| - name: Install `gcsfuse` | |
| run: | | |
| echo "deb http://packages.cloud.google.com/apt gcsfuse-$(lsb_release -c -s) main" | sudo tee /etc/apt/sources.list.d/gcsfuse.list | |
| curl -fsSL https://packages.cloud.google.com/apt/doc/apt-key.gpg | gpg --dearmor -o /tmp/packages-cloud-google-com-apt-keyring.gpg | |
| sudo mv /tmp/packages-cloud-google-com-apt-keyring.gpg /etc/apt/trusted.gpg.d/ | |
| sudo apt-get update | |
| sudo apt-get install gcsfuse -y | |
| - name: Mount Google Cloud Storage bucket | |
| run: | | |
| sudo mkdir -p /mnt/gcs-bucket | |
| sudo chown $USER:$USER /mnt/gcs-bucket | |
| gcsfuse --implicit-dirs --anonymous-access --only-dir platinum-genomes genomics-public-data /mnt/gcs-bucket | |
| - name: List bucket contents | |
| run: ls /mnt/gcs-bucket | |
| - name: check cnvpytor | |
| run: | | |
| cnvpytor -h | |
| - name: run cnvpytor RD | |
| run: | | |
| cnvpytor -root test.pytor -rd /mnt/gcs-bucket/bam/NA12877_S1.bam -v d | |
| - name: run cnvpytor SNP | |
| run: | | |
| cnvpytor -root test.pytor -snp /mnt/gcs-bucket/vcf/NA12877_S1.genome.vcf -v d | |
| - name: run cnvpytor mask_snps | |
| run: | | |
| cnvpytor -root test.pytor -mask_snps | |
| - name: run cnvpytor pileup | |
| run: | | |
| cnvpytor -root test.pytor -pileup /mnt/gcs-bucket/bam/NA12877_S1.bam -v d | |
| - name: run cnvpytor his, baf, call combined | |
| run: | | |
| cnvpytor -root test.pytor -his 100000 -v d | |
| cnvpytor -root test.pytor -baf 100000 -v d | |
| cnvpytor -root test.pytor -call combined 100000 -v d > output | |
| cat output | |
| - name: run cnvptor ls | |
| run: | | |
| cnvpytor -root test.pytor -ls | |
| echo "rdstat" | cnvpytor -root test.pytor -view 100000 -o prefix.png | |
| - name: check calls | |
| run: | | |
| md5 < output | |
| if [ "$(md5 < output)" == "cf2496a1f86cc22500825493a27f0d95" ] ; then echo PASS; else echo FAIL; fi | |
| - name: Run tests | |
| run: | | |
| pytest -s |