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| name: Python Package using Conda | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - release/* | |
| jobs: | |
| build-linux: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 5 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: '3.10' | |
| - name: Add conda to system path | |
| run: | | |
| # $CONDA is an environment variable pointing to the root of the miniconda directory | |
| echo $CONDA/bin >> $GITHUB_PATH | |
| - name: Install dependencies | |
| run: | | |
| conda config --set solver classic | |
| conda install phabox=2.1.5 python=3.10 -c bioconda -c conda-forge -y | |
| conda install flake8 | |
| - name: Lint with flake8 | |
| run: | | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Test PhaBOX utilities | |
| run: | | |
| git clone https://github.com/KennthShang/PhaBOX.git | |
| cd PhaBOX | |
| python -m pip install . | |
| cd .. | |
| wget https://github.com/KennthShang/PhaBOX/releases/download/v2/example_contigs.fa | |
| wget https://github.com/KennthShang/PhaBOX/releases/download/v2/phabox_db_v2.zip | |
| unzip phabox_db_v2.zip > /dev/null | |
| phabox2 --task end_to_end --contigs example_contigs.fa -o end_to_end -d phabox_db_v2 | |
| head end_to_end/final_prediction/final_prediction_summary.tsv | |
| phabox2 --task phamer --contigs example_contigs.fa -o phamer -d phabox_db_v2 | |
| head phamer/final_prediction/phamer_prediction.tsv | |
| phabox2 --task phagcn --contigs example_contigs.fa -o phagcn -d phabox_db_v2 | |
| head phagcn/final_prediction/phagcn_prediction.tsv | |
| phabox2 --task phatyp --contigs example_contigs.fa -o phatyp -d phabox_db_v2 | |
| head phatyp/final_prediction/phatyp_prediction.tsv | |
| phabox2 --task cherry --contigs example_contigs.fa -o cherry -d phabox_db_v2 | |
| head cherry/final_prediction/cherry_prediction.tsv | |
| phabox2 --task contamination --contigs example_contigs.fa -o contamination -d phabox_db_v2 | |
| head contamination/final_prediction/contamination_prediction.tsv | |
| phabox2 --task votu --contigs example_contigs.fa -o votu -d phabox_db_v2 --mode AAI | |
| head votu/final_prediction/AAI_based_vOTU.tsv | |
| phabox2 --task votu --contigs example_contigs.fa -o votu -d phabox_db_v2 --mode ANI | |
| head votu/final_prediction/ANI_based_vOTU.tsv | |
| phabox2 --task tree --contigs example_contigs.fa -o tree -d phabox_db_v2 --msa Y --tree N | |
| head tree/final_prediction/combined_marker.msa |