Updated GitHub Actions workflow. #664
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: chewbbaca | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.8', '3.9', '3.10', '3.11', '3.12'] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| # Install setuptools to provide distutils for Python >3.12 | |
| pip install setuptools | |
| pip install pytest | |
| pip install py | |
| - name: install blast | |
| run: | | |
| mkdir $GITHUB_WORKSPACE/blast | |
| pushd $GITHUB_WORKSPACE/blast | |
| wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.9.0/ncbi-blast-2.9.0+-x64-linux.tar.gz \ | |
| && tar -xzvf ncbi-blast-2.9.0+-x64-linux.tar.gz && rm ncbi-blast-2.9.0+-x64-linux.tar.gz | |
| echo "$GITHUB_WORKSPACE/blast/ncbi-blast-2.9.0+/bin" >> $GITHUB_PATH | |
| popd | |
| - name: check blast | |
| run: | | |
| which blastp | |
| blastp -version | |
| - name: install mafft | |
| run: | | |
| mkdir $GITHUB_WORKSPACE/mafft | |
| pushd $GITHUB_WORKSPACE/mafft | |
| wget https://mafft.cbrc.jp/alignment/software/mafft_7.475-1_amd64.deb | |
| sudo dpkg -i mafft_7.475-1_amd64.deb | |
| popd | |
| - name: check mafft | |
| run: | | |
| which mafft | |
| mafft --version | |
| - name: install fasttree2 | |
| run: | | |
| mkdir $GITHUB_WORKSPACE/fasttree2 | |
| pushd $GITHUB_WORKSPACE/fasttree2 | |
| wget https://anaconda.org/bioconda/fasttree/2.1.11/download/linux-64/fasttree-2.1.11-h031d066_2.tar.bz2 | |
| bzip2 -d fasttree-2.1.11-h031d066_2.tar.bz2 && tar -xvf fasttree-2.1.11-h031d066_2.tar && rm fasttree-2.1.11-h031d066_2.tar | |
| echo "$GITHUB_WORKSPACE/fasttree2/bin" >> $GITHUB_PATH | |
| popd | |
| - name: check fasttree2 | |
| run: | | |
| which FastTree | |
| FastTree -help | |
| - name: checkout chewbbaca | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: B-UMMI/chewBBACA | |
| path: chewbbaca | |
| - name: install chewbbaca | |
| run: | | |
| pushd $GITHUB_WORKSPACE/chewbbaca | |
| python -m pip install . | |
| - name: check chewbbaca | |
| run: | | |
| which chewBBACA.py | |
| - name: run pytest | |
| run: | | |
| pushd CHEWBBACA/tests | |
| pytest | |
| popd |