Fixed issue when creating FASTA files with novel alleles. #697
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| 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'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| 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@v4 | |
| 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 |