Update runTest.yml #11
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| name: runTest | |
| on: [push] | |
| jobs: | |
| test-python-app: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: yacht | |
| environment-file: env/yacht_env.yaml | |
| auto-activate-base: false | |
| auto-update-conda: true | |
| - run: | | |
| conda info | |
| conda list | |
| printenv | sort | |
| - name: make training data | |
| run: python make_training_data_from_sketches.py --ref_file 'tests/testdata/20_genomes_sketches.zip' --ksize 31 --out_prefix 'gtdb_ani_thresh_0.95' --ani_thresh 0.95 | |
| - name: run YACHT | |
| run: python run_YACHT.py --ref_matrix 'gtdb_ani_thresh_0.95_ref_matrix_processed.npz' --ksize 31 --sample_file 'tests/testdata/sample.sig' --ani_thresh 0.95 --significance 0.99 --min_coverage 1 --outfile 'yacht_results.csv' |