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Set up CI. Part 1. Running the code on GitHub Actions. (#18) #17

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Set up CI. Part 1. Running the code on GitHub Actions. (#18)

Set up CI. Part 1. Running the code on GitHub Actions. (#18) #17

Workflow file for this run

.github/workflows/runTest.yml at e7e1629
name: runTest
on: [push]
jobs:
test-python-app:
runs-on: ubuntu-20.04
defaults:
run:
shell: bash -el {0}
steps:
- uses: actions/checkout@v4
- uses: conda-incubator/setup-miniconda@v2
with:
activate-environment: yacht
environment-file: env/yacht_env.yaml
- 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 --json 'gtdb_ani_thresh_0.95_config.json' --sample_file 'tests/testdata/sample.sig' --significance 0.99 --min_coverage 1 --outdir './'