update to use camlhmp #26
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| name: pbptyper-test | |
| on: | |
| push: | |
| branches: [ main, dev ] | |
| pull_request: | |
| branches: [ main, dev ] | |
| jobs: | |
| pbptyper-tests: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout rpetit3/pbptyper | |
| uses: actions/checkout@v2 | |
| - name: Setup miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: pbptyper | |
| auto-activate-base: false | |
| - name: Setup pbptyper Environment | |
| run: | | |
| conda install -y -c conda-forge -c bioconda 'camlhmp>=0.3.1' | |
| - name: Environment Information | |
| run: uname -a && env | |
| - name: Test pbptyper basics | |
| run: | | |
| echo "Testing pbptyper" | |
| bin/pbptyper --version | |
| bin/pbptyper --help | |
| - name: Test pbptyper | |
| run: | | |
| echo "ERR1065617" | |
| bin/pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/ERR1065617.fna.gz --prefix ERR1065617 | |
| cat ERR1065617.tsv | |
| head ERR1065617.tblastn.tsv | |
| echo "SRR2912551" | |
| bin/pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/SRR2912551.fna.gz --prefix SRR2912551 | |
| cat SRR2912551.tsv | |
| head SRR2912551.tblastn.tsv | |
| echo "SRR8654742" | |
| bin/pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/SRR8654742.fna --prefix SRR8654742 --outdir SRR8654742 | |
| cat SRR8654742/SRR8654742.tsv | |
| head SRR8654742/SRR8654742.tblastn.tsv | |
| echo "S. pseudopneumoniae" | |
| bin/pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/spseudopneumoniae.fna.gz --prefix spseudopneumoniae --outdir spseudopneumoniae | |
| cat spseudopneumoniae/spseudopneumoniae.tsv | |
| head spseudopneumoniae/spseudopneumoniae.tblastn.tsv | |
| echo "S. mitis" | |
| bin/pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/smitis.fna.gz --prefix smitis --outdir smitis | |
| cat smitis/smitis.tsv | |
| head smitis/smitis.tblastn.tsv | |
| echo "S. suis" | |
| bin/pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/ssuis.fna.gz --prefix ssuis --outdir ssuis | |
| cat ssuis/ssuis.tsv | |
| head ssuis/ssuis.tblastn.tsv | |
| echo "not-spn" | |
| bin/pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/not-spn.fna.gz --prefix not-spn | |
| cat not-spn.tsv | |
| head not-spn.tblastn.tsv | |
| echo "empty" | |
| bin/pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/empty.fasta --prefix empty | |
| cat empty.tsv | |
| head empty.tblastn.tsv | |
| echo "not-a-fasta" | |
| bin/pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/not-a-fasta.fasta --prefix not-a-fasta | |
| cat not-a-fasta.tsv | |
| head not-a-fasta.tblastn.tsv | |
| echo "poor" | |
| bin/pbptyper --yaml data/pbptyper.yaml --targets data/pbptyper.fasta --input test/poor.fasta --prefix poor --outdir poor | |
| cat poor/poor.tsv | |
| head poor/poor.tblastn.tsv |