fix: ensure pulp version 2.7.0 is installed with Snakemake #10
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| name: Test GHCR Container | |
| on: | |
| push: | |
| pull_request: | |
| jobs: | |
| test-container: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Pull container presto-0.7.4:latest from GHCR | |
| run: | | |
| docker pull ghcr.io/lewisl23/presto-0.7.4:latest | |
| - name: Test container presto-0.7.4:latest runs | |
| run: | | |
| docker run --rm ghcr.io/lewisl23/presto-0.7.4:latest AssemblePairs.py --help | |
| echo "Container works" | |
| - name: Pull container igblast-1.21.0:latest from GHCR | |
| run: | | |
| docker pull ghcr.io/lewisl23/igblast-1.21.0:latest | |
| - name: Test container igblast-1.21.0:latest runs | |
| run: | | |
| docker run --rm ghcr.io/lewisl23/igblast-1.21.0:latest igblastn -help | |
| echo "Container works" | |
| test-workflow: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.9" | |
| - name: Install Snakemake | |
| run: | | |
| pip install snakemake | |
| pip install pulp==2.7.0 | |
| - name: Run test pipeline | |
| run: | | |
| snakemake --cores 1 \ | |
| --configfile tests/config/test_config.yaml \ | |
| --use-singularity \ | |
| --printshellcmds \ | |
| --reason |