Update python-package-conda.yml #52
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: 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 python=3.10 phabox -c conda-forge -c bioconda | |
| conda install diamond=0.9 flake8 -c conda-forge -c bioconda | |
| - 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 |