Add entries for pangolin-data/-assignment v1.27 (#543) #258
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: pangolin-macosx | |
| on: [push, pull_request] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| run_pangolin_test: | |
| name: Pangolin test on ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: ["macos-latest"] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| environment-file: environment.yml | |
| activate-environment: pangolin | |
| channels: conda-forge,bioconda,defaults | |
| conda-version: "23.5.0" | |
| mamba-version: "*" | |
| - name: Install pangolin | |
| run: pip install -e . | |
| - name: Check pangolin version | |
| run: pangolin --version | |
| - name: Run pangolin with test data | |
| run: pangolin pangolin/test/test_seqs.fasta 2>&1 | tee pangolin.log | |
| - name: Run pangolin with test zip data | |
| run: pangolin pangolin/test/test_seqs.fasta.gz 2>&1 | tee pangolin_zip.log | |
| - name: Run pangolin with test all cache data | |
| run: pangolin pangolin/test/all_bad_seqs.fasta 2>&1 | tee pangolin_all_bad.log | |
| - name: Run pangolin with test all bad data | |
| run: pangolin pangolin/test/all_hash.fasta 2>&1 | tee pangolin_cache.log | |
| - name: Run pangolin usher with test data | |
| run: pangolin --analysis-mode usher pangolin/test/test_seqs.fasta 2>&1 | tee pangolin_usher.log | |
| - name: Run pangolin pangolearn with test data | |
| run: pangolin --analysis-mode pangolearn pangolin/test/test_seqs.fasta 2>&1 | tee pangolin_panolearn.log | |
| - name: Run pangolin fast with test data | |
| run: pangolin --analysis-mode fast pangolin/test/test_seqs.fasta 2>&1 | tee pangolin_fast.log | |
| - name: Run pangolin accurate with test data | |
| run: pangolin --analysis-mode accurate pangolin/test/test_seqs.fasta 2>&1 | tee pangolin_accurate.log | |
| - name: Run pangolin with outdir and outfile | |
| run: pangolin pangolin/test/test_seqs.fasta -o my_test --outfile pangolin_out.txt 2>&1 | tee pangolin_outdir_outfile.log | |
| - name: Run pangolin with out alignment | |
| run: pangolin pangolin/test/test_seqs.fasta --alignment --alignment-file my_alignment.fasta 2>&1 | tee pangolin_alignment.log | |
| - name: Run pangolin aliases | |
| run: pangolin --aliases 2>&1 | tee pangolin_alias.log | |
| - name: Run pangolin all versions | |
| run: pangolin --all-versions 2>&1 | tee pangolin_versions.log | |
| - name: Run pangolin skip designation cache | |
| run: pangolin pangolin/test/test_seqs.fasta --skip-designation-cache 2>&1 | tee pangolin_no_cache.log | |
| - name: Run pangolin verbose mode | |
| run: pangolin --verbose pangolin/test/test_seqs.fasta 2>&1 | tee pangolin_verbose.log | |