Updating the list of Python versions for testing. #41
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| name: Test python versions | |
| on: [push] | |
| jobs: | |
| build: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-20.04, ubuntu-latest] | |
| include: | |
| - os: ubuntu-20.04 | |
| python-version: "3.3" | |
| - os: ubuntu-20.04 | |
| python-version: "3.4" | |
| - os: ubuntu-20.04 | |
| python-version: "3.5" | |
| - os: ubuntu-20.04 | |
| python-version: "3.6" | |
| - os: ubuntu-latest | |
| python-version: "3.7" | |
| - os: ubuntu-latest | |
| python-version: "3.8" | |
| - os: ubuntu-latest | |
| python-version: "3.9" | |
| - os: ubuntu-latest | |
| python-version: "3.10" | |
| - os: ubuntu-latest | |
| python-version: "3.11" | |
| - os: ubuntu-latest | |
| python-version: "3.12" | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| pip install -r requirements.txt | |
| pip install . | |
| - name: cnvpytor Usage | |
| run: | | |
| cnvpytor -h | |
| - name: Install `gcsfuse` | |
| run: | | |
| echo "deb http://packages.cloud.google.com/apt gcsfuse-$(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: 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 | |
| run: | | |
| cnvpytor -root test.pytor -his 100000 -v d | |
| cnvpytor -root test.pytor -baf 100000 -v d | |
| - name: run cnvpytor call combined | |
| run: | | |
| cnvpytor -root test.pytor -call combined 100000 -v d > output_2D.tsv | |
| cat output_2D.tsv | |
| - name: check combined calls | |
| run: | | |
| md5sum output_2D.tsv | |
| [ "$(md5sum output_2D.tsv | awk '{ print $1 }')" == "c7a07af67cb38337f5df012cef304e66" ] && echo PASS || echo FAIL | |
| - name: run cnvpytor call meanShift | |
| run: | | |
| cnvpytor -root test.pytor -partition 100000 -v d | |
| cnvpytor -root test.pytor -call 100000 -v d > output_meanShift.tsv | |
| cat output_meanShift.tsv | |
| - name: check meanShift calls | |
| run: | | |
| md5sum output_meanShift.tsv | |
| [ "$(md5sum output_meanShift.tsv | awk '{ print $1 }')" == "7dd1d5297e57ae1a89f0d58c2a604bb6" ] && echo PASS || echo FAIL | |
| - name: run cnvptor ls | |
| run: | | |
| cnvpytor -root test.pytor -ls | |
| - name: run cnvptor rdstat | |
| run: | | |
| echo "rdstat" | cnvpytor -root test.pytor -view 100000 -o NA12877.png | |
| - name: run cnvptor manhattan | |
| run: | | |
| echo -e "set panels rd likelihood\n manhattan" | cnvpytor -root test.pytor -view 100000 -o NA12877.png | |
| - name: Upload data | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: NA12877 Python ${{ matrix.python-version }} | |
| path: | | |
| output_2D.tsv | |
| output_meanShift.tsv | |
| NA12877.stat.0000.png | |
| NA12877.global.0000.png |