Fix sidecar index out of range issues #97
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| name: Test SnakemakeProfiles/slurm | |
| env: | |
| SNAKEMAKE_IMAGE: quay.io/biocontainers/snakemake:7.30.1--hdfd78af_0 | |
| SLURM_IMAGE: giovtorres/docker-centos7-slurm:20.11.8 | |
| DOCKER_COMPOSE: tests/docker-compose.yaml | |
| on: [push, pull_request] | |
| jobs: | |
| slurmtest: | |
| name: Test slurm profile in docker containers | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 30 | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - run: mkdir -p ~/image-cache | |
| - name: cache conda environment | |
| uses: actions/cache@v3 | |
| env: | |
| CACHE_NUMBER: 0 | |
| with: | |
| path: ~/conda_pkgs_dir | |
| key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('conda-linux-64.lock') }} | |
| - name: cache images | |
| uses: actions/cache@v3 | |
| id: cache-images | |
| env: | |
| CACHE_NUMBER: 0 | |
| with: | |
| path: ~/image-cache | |
| key: image-cache-${{ runner.os }}-${{ env.CACHE_NUMBER }}-${{ env.SNAKEMAKE_IMAGE }}-${{ env.SLURM_IMAGE }} | |
| - name: install miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniconda-version: "latest" | |
| environment-file: conda-linux-64.lock | |
| use-only-tar-bz2: true | |
| - name: docker swarm init | |
| run: docker swarm init | |
| - if: steps.cache-images.outputs.cache-hit == 'true' | |
| run: docker load -i ~/image-cache/snakemake.tar | |
| - if: steps.cache-images.outputs.cache-hit == 'true' | |
| run: docker load -i ~/image-cache/slurm.tar | |
| - name: docker deploy | |
| shell: bash -l {0} | |
| env: | |
| DOCKER_COMPOSE: ${{ env.DOCKER_COMPOSE }} | |
| SNAKEMAKE_IMAGE: ${{ env.SNAKEMAKE_IMAGE }} | |
| SLURM_IMAGE: ${{ env.SLURM_IMAGE }} | |
| run: ./tests/deploystack.sh | |
| - if: steps.cache-images.outputs.cache-hit != 'true' | |
| run: docker save -o ~/image-cache/snakemake.tar ${{ env.SNAKEMAKE_IMAGE }} | |
| - if: steps.cache-images.outputs.cache-hit != 'true' | |
| run: docker save -o ~/image-cache/slurm.tar ${{ env.SLURM_IMAGE }} | |
| - name: run tests | |
| shell: bash -l {0} | |
| run: | | |
| pytest -v -s tests/test_cookie.py | |
| pytest -v -s tests/test_utils.py | |
| pytest -v -s tests/test_slurm.py --slow | |
| pytest -v -s tests/test_sidecar.py |