Upadated dockerfile version #108
Workflow file for this run
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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' |