update pasty to use camlhmp #34
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| name: pasty-test | |
| on: | |
| push: | |
| branches: [ main, dev ] | |
| pull_request: | |
| branches: [ main, dev ] | |
| jobs: | |
| pasty-tests: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout rpetit3/pasty | |
| uses: actions/checkout@v2 | |
| - name: Setup miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: pasty | |
| auto-activate-base: false | |
| - name: Setup pasty Environment | |
| run: | | |
| conda install -y -c conda-forge -c bioconda rich-click executor 'python>=3.7' blast | |
| - name: Environment Information | |
| run: uname -a && env | |
| - name: Test pasty basics | |
| run: | | |
| echo "Testing patsy" | |
| bin/pasty --version | |
| bin/pasty --help | |
| bin/pasty --check | |
| - name: Test patsy | |
| run: | | |
| echo "O1-GCF_000504045" | |
| bin/pasty --assembly test/O1-GCF_000504045.fna.gz --prefix O1-GCF_000504045 --db db/OSAdb.fasta | |
| cat O1-GCF_000504045.tsv | |
| cat O1-GCF_000504045.details.tsv | |
| echo "O2-GCF_000006765" | |
| bin/pasty --assembly test/O2-GCF_000006765.fna.gz --prefix O2-GCF_000006765 --outdir O2 | |
| cat O2/O2-GCF_000006765.tsv | |
| cat O2/O2-GCF_000006765.details.tsv | |
| echo "O3-GCF_000271365" | |
| bin/pasty --assembly test/O3-GCF_000271365.fna.gz --prefix O3-GCF_000271365 --outdir O3 | |
| cat O3/O3-GCF_000271365.tsv | |
| cat O3/O3-GCF_000271365.details.tsv | |
| echo "O4-GCF_024652945" | |
| bin/pasty --assembly test/O4-GCF_024652945.fna.gz --prefix O4-GCF_024652945 --outdir O4 | |
| cat O4/O4-GCF_024652945.tsv | |
| cat O4/O4-GCF_024652945.details.tsv | |
| echo "O6-GCF_001457615" | |
| bin/pasty --assembly test/O6-GCF_001457615.fna.gz --prefix O6-GCF_001457615 | |
| cat O6-GCF_001457615.tsv | |
| cat O6-GCF_001457615.details.tsv | |
| echo "O7-GCF_001482325" | |
| bin/pasty --assembly test/O7-GCF_001482325.fna.gz --prefix O7-GCF_001482325 | |
| cat O7-GCF_001482325.tsv | |
| cat O7-GCF_001482325.details.tsv | |
| echo "O9-GCF_002075065" | |
| bin/pasty --assembly test/O9-GCF_002075065.fna.gz --prefix O9-GCF_002075065 | |
| cat O9-GCF_002075065.tsv | |
| cat O9-GCF_002075065.details.tsv | |
| echo "O10-GCF_009676765" | |
| bin/pasty --assembly test/O10-GCF_009676765.fna.gz --prefix O10-GCF_009676765 | |
| cat O10-GCF_009676765.tsv | |
| cat O10-GCF_009676765.details.tsv | |
| echo "O11-GCF_002192495" | |
| bin/pasty --assembly test/O11-GCF_002192495.fna.gz --prefix O11-GCF_002192495 | |
| cat O11-GCF_002192495.tsv | |
| cat O11-GCF_002192495.details.tsv | |
| echo "O12-GCF_000981825" | |
| bin/pasty --assembly test/O12-GCF_000981825.fna.gz --prefix O12-GCF_000981825 | |
| cat O12-GCF_000981825.tsv | |
| cat O12-GCF_000981825.details.tsv | |
| echo "NT-GCF_000292685" | |
| bin/pasty --assembly test/NT-GCF_000292685.fna.gz --prefix NT-GCF_000292685 --db db/OSAdb.fasta | |
| cat NT-GCF_000292685.tsv | |
| cat NT-GCF_000292685.details.tsv | |
| echo "empty" | |
| bin/pasty --assembly test/empty.fasta --prefix empty | |
| cat empty.tsv | |
| cat empty.details.tsv | |
| echo "not-a-fasta" | |
| bin/pasty --assembly test/not-a-fasta.fasta --prefix not-a-fasta | |
| cat not-a-fasta.tsv | |
| cat not-a-fasta.details.tsv | |
| echo "poor" | |
| bin/pasty --assembly test/poor.fasta --prefix poor --outdir poor | |
| cat poor/poor.tsv | |
| cat poor/poor.details.tsv | |
| echo "O2-GCF_001444895-int-bug" | |
| bin/pasty --assembly test/O2-GCF_001444895-int-bug.fna.gz --prefix O2-GCF_001444895-int-bug --outdir O2 | |
| cat O2/O2-GCF_001444895-int-bug.tsv | |
| cat O2/O2-GCF_001444895-int-bug.details.tsv |