Merge pull request #199 from eastgenomics/IN-500-update-report-text #146
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: pytest | |
| on: [push] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v1 | |
| with: | |
| python-version: 3.8 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install pipenv codecov | |
| pip install -r requirements.txt | |
| pipenv install --dev | |
| - name: Build bcftools | |
| run: | | |
| wget https://github.com/samtools/bcftools/releases/download/1.18/bcftools-1.18.tar.bz2 | |
| tar xf bcftools-1.18.tar.bz2 | |
| cd bcftools-1.18 | |
| ./configure --prefix=/usr/local/ | |
| sudo make | |
| sudo make install | |
| - name: Build htslib | |
| run: | | |
| wget https://github.com/samtools/htslib/releases/download/1.18/htslib-1.18.tar.bz2 | |
| tar xf htslib-1.18.tar.bz2 | |
| cd htslib-1.18 | |
| ./configure --prefix=/usr/local/ | |
| sudo make | |
| sudo make install | |
| - name: Test with pytest | |
| run: | | |
| pytest -vv --cov resources/home/dnanexus/generate_workbook/ |