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| name: CI | |
| on: [push] | |
| jobs: | |
| build-and-test: | |
| name: Build & test on ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, ubuntu-20.04] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: false | |
| use-only-tar-bz2: true | |
| miniforge-version: latest | |
| - name: Install cnv_facets | |
| run: | | |
| mamba init | |
| source ~/.bashrc | |
| mamba create --yes -n cnv_facets | |
| mamba activate cnv_facets | |
| mamba install --yes -c bioconda -c conda-forge cnv_facets | |
| - name: Install vcf_validator | |
| run: | | |
| curl -L -o test/vcf_validator -s https://github.com/EBIvariation/vcf-validator/releases/download/v0.9.1/vcf_validator_linux | |
| chmod a+x test/vcf_validator | |
| ./test/vcf_validator --help | |
| - name: Run tests | |
| run: | | |
| source ~/.bashrc | |
| mamba activate cnv_facets | |
| cd test | |
| Rscript testthat.R | |
| python3 test_cnv_facets.py |