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name: Python Package using Conda | ||
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on: [push] | ||
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jobs: | ||
build-linux: | ||
runs-on: ubuntu-latest | ||
strategy: | ||
max-parallel: 5 | ||
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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 >> $GITHUB_PATH | ||
- name: Install dependencies | ||
run: | | ||
conda install -c conda-forge -c bioconda snakemake pip mamba | ||
pip install . | ||
- name: Deploy panoptes | ||
run: | | ||
panoptes & | ||
- name: Test panoptes | ||
run: | | ||
response=$(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: | | ||
snakemake --version | ||
cd .. | ||
git clone https://github.com/panoptes-organization/snakemake_example_workflow.git | ||
cd snakemake_example_workflow | ||
ls | ||
bash run_local.sh | ||
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