GH actions: mamba init #216
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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: | | |
| mamba info | |
| pushd tests | |
| bash setup.sh | |
| popd | |
| - name: run workflow | |
| shell: bash -el {0} | |
| run: | | |
| pushd tests | |
| source test.sh | |
| popd | |
| - name: cat all log files on failure | |
| if: ${{ failure() }} | |
| run: | | |
| find tests/ -name '*.log' -exec tail -n 1000 {} \; |