GH actions: bash env #217
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| name: Workflow CI | |
| on: | |
| push: | |
| branches: "main" | |
| pull_request: | |
| branches: [ main ] | |
| workflow_dispatch: | |
| jobs: | |
| run_workflow: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: setup-mamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| mamba-version: "*" | |
| channels: bioconda,conda-forge | |
| channel-priority: true | |
| auto-update-conda: true | |
| - name: Cache generated inputs | |
| id: cache-inputs | |
| uses: actions/cache@v3 | |
| with: | |
| path: tests/rawdata | |
| key: rawdata-${{ hashFiles('tests/Snakefile.generate-rawdata') }}-${{ hashFiles('acanthophis/template/environment.yml') }}-${{ hashFiles('acanthophis/template/workflow/rules/envs/*.yml') }} | |
| - name: setup mamba | |
| shell: bash -el {0} | |
| run: | | |
| mamba init | |
| - name: setup data | |
| shell: bash -el {0} | |
| run: | | |
| export BASH_ENV=~/.bashrc | |
| mamba info | |
| pushd tests | |
| bash setup.sh | |
| popd | |
| - name: run workflow | |
| shell: bash -el {0} | |
| run: | | |
| export BASH_ENV=~/.bashrc | |
| pushd tests | |
| bash test.sh | |
| popd | |
| - name: cat all log files on failure | |
| if: ${{ failure() }} | |
| run: | | |
| find tests/ -name '*.log' -exec tail -n 1000 {} \; |