Update README.md #290
Workflow file for this run
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| name: Command line interface tests | |
| on: | |
| push: | |
| branches: [ "master" ] | |
| pull_request: | |
| branches: [ "master" ] | |
| workflow_dispatch: | |
| inputs: | |
| permissions: | |
| contents: read | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.11"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' # caching pip dependencies | |
| cache-dependency-path: '**/pyproject.toml' | |
| - name: Download fixtures | |
| run: | | |
| wget https://www.dropbox.com/scl/fi/xzc0tro7oe6tfm3igygpj/ci_data.zip\?rlkey\=xuv6b5eoynfryp4fba1kfp5jm\&st\=9oz24ych\&dl\=0 -O ci_data.zip | |
| unzip -o ci_data.zip | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install flake8 pytest | |
| pip install -e . | |
| - name: Run VAMB | |
| run: | | |
| vamb bin default --outdir outdir_vamb --fasta catalogue_mock.fna.gz --abundance abundance_mock.npz -l 32 -e 10 -q 2 -o C --minfasta 200000 -t 10 | |
| ls -la outdir_vamb | |
| cat outdir_vamb/log.txt | |
| - name: Run TaxVAMB | |
| run: | | |
| vamb bin taxvamb --outdir outdir_taxvamb --fasta catalogue_mock.fna.gz --abundance abundance_mock.npz --taxonomy taxonomy_mock.tsv -pe 10 -pt 10 -e 10 -q -t 10 -o C --minfasta 200000 | |
| ls -la outdir_taxvamb | |
| cat outdir_taxvamb/log.txt | |
| vamb bin taxvamb --outdir outdir_taxvamb_no_predict --no_predictor --fasta catalogue_mock.fna.gz --abundance abundance_mock.npz --taxonomy taxonomy_mock.tsv -e 10 -q -t 10 -o C --minfasta 200000 | |
| ls -la outdir_taxvamb_no_predict | |
| cat outdir_taxvamb_no_predict/log.txt | |
| vamb bin taxvamb --outdir outdir_taxvamb_preds --fasta catalogue_mock.fna.gz --abundance abundance_mock.npz --no_predictor --taxonomy outdir_taxvamb/results_taxometer.tsv -e 10 -q -t 10 -o C --minfasta 200000 | |
| ls -la outdir_taxvamb_preds | |
| cat outdir_taxvamb_preds/log.txt | |
| - name: Run Taxometer | |
| run: | | |
| vamb taxometer --outdir outdir_taxometer --fasta catalogue_mock.fna.gz --abundance abundance_mock.npz --taxonomy taxonomy_mock.tsv -pe 10 -pt 10 | |
| ls -la outdir_taxometer | |
| cat outdir_taxometer/log.txt | |
| vamb taxometer --outdir outdir_taxometer_pred --fasta catalogue_mock.fna.gz --abundance abundance_mock.npz --taxonomy outdir_taxometer/results_taxometer.tsv -pe 10 -pt 10 | |
| ls -la outdir_taxometer_pred | |
| cat outdir_taxometer/log.txt | |
| - name: Run k-means reclustering | |
| run: | | |
| vamb recluster --outdir outdir_recluster --fasta catalogue_mock.fna.gz --abundance abundance_mock.npz --latent_path outdir_taxvamb/vaevae_latent.npz --clusters_path outdir_taxvamb/vaevae_clusters_split.tsv --hmmout_path markers_mock.hmmout --algorithm kmeans --minfasta 200000 | |
| ls -la outdir_recluster | |
| cat outdir_recluster/log.txt |