Added ps to dockerfile #101
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| # Build dockerfile on change | |
| name: Build and Test | |
| on: | |
| - push | |
| jobs: | |
| test_and_publish: | |
| strategy: | |
| matrix: | |
| python-version: ["3.7"] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install curl headers | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install --fix-missing libcurl4-openssl-dev | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| channels: conda-forge,bioconda,defaults | |
| - name: Install dependencies | |
| run: | | |
| conda create -n vcf-kit \ | |
| python=${{ matrix.python-version }} \ | |
| pytest \ | |
| pytest-cov \ | |
| coveralls \ | |
| numpy \ | |
| scipy \ | |
| cython \ | |
| biopython \ | |
| matplotlib \ | |
| clint \ | |
| "cyvcf2>=0.6.5" \ | |
| "intervaltree" \ | |
| jinja2 \ | |
| "pomegranate" \ | |
| "bwa>=0.7.12" \ | |
| "samtools>=1.10" \ | |
| "bcftools>=1.10" \ | |
| "blast>=2.2.31" \ | |
| "muscle>=3.8.31" \ | |
| "primer3>=2.5.0" \ | |
| "vcftools>=0.1.16" | |
| - name: Install | |
| shell: bash -l {0} | |
| run: | | |
| conda activate vcf-kit | |
| python setup.py install | |
| python setup.py sdist bdist_wheel --universal | |
| - name: Test vcf-kit | |
| shell: bash -l {0} | |
| run: | | |
| conda activate vcf-kit | |
| py.test --verbose --cov-report=term --cov=vcfkit tests | |
| coveralls | |
| - uses: actions/upload-artifact@v2 | |
| with: | |
| name: genome | |
| path: .genome/ | |
| - name: Create Release | |
| id: create_release | |
| uses: actions/create-release@v1 | |
| if: startsWith(github.ref, 'refs/tags') | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| tag_name: ${{ github.ref }} | |
| release_name: ${{ github.ref }} | |
| draft: true | |
| prerelease: false | |
| - name: Publish a Python distribution to PyPI | |
| uses: pypa/gh-action-pypi-publish@master | |
| if: startsWith(github.ref, 'refs/tags') | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_PASSWORD }} | |
| # - name: publish-to-conda | |
| # uses: fcakyon/[email protected] | |
| # with: | |
| # subdir: 'conda' | |
| # anacondatoken: ${{ secrets.ANACONDA_TOKEN }} | |
| # platforms: 'win osx linux' |