Run test workflow #7
Workflow file for this run
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| name: Python Package using Conda | |
| on: [push] | |
| jobs: | |
| build-linux: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 5 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: '3.10' | |
| - name: Add conda to system path | |
| run: | | |
| # $CONDA is an environment variable pointing to the root of the miniconda directory | |
| echo $CONDA/bin >> $GITHUB_PATH | |
| - name: Install dependencies | |
| run: | | |
| conda install -c conda-forge -c bioconda snakemake pip | |
| pip install . | |
| - name: Deploy panoptes | |
| run: | | |
| panoptes & | |
| - name: Test panoptes | |
| run: | | |
| response=$(curl http://127.0.0.1:5000/api/service-info) | |
| if [ "$response" = "{\"status\":\"running\"}" ]; then | |
| echo "Success"; | |
| exit 0; | |
| else | |
| echo "Fail"; | |
| exit 1; | |
| fi | |
| - name: Run test workflow | |
| run: | | |
| cd .. | |
| git clone https://github.com/panoptes-organization/snakemake_example_workflow.git | |
| cd snakemake_example_workflow | |
| bash run_local.sh | |