Update medaka.yaml #110
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches_ignore: [] | |
| jobs: | |
| Formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Formatting | |
| uses: github/super-linter@v4 | |
| env: | |
| VALIDATE_ALL_CODEBASE: false | |
| DEFAULT_BRANCH: master | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| VALIDATE_SNAKEMAKE_SNAKEFMT: true | |
| Testing: | |
| runs-on: ubuntu-latest | |
| needs: Formatting | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 # we need tags for versioneer to work | |
| - name: Setup LACA environment | |
| run: | | |
| wget -O Mambaforge.sh https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh --quiet | |
| bash Mambaforge.sh -b -p "${HOME}/conda" | |
| source "${HOME}/conda/etc/profile.d/conda.sh" | |
| source "${HOME}/conda/etc/profile.d/mamba.sh" | |
| # ensure that mamba is happy to write into the cache | |
| sudo chown -R runner:docker "${HOME}/conda/pkgs/cache" | |
| conda config --set channel_priority flexible | |
| mamba env create -q --name laca --file env.yaml | |
| - name: Install LACA | |
| run: | | |
| export PATH="${HOME}/conda/bin:$PATH" | |
| source activate laca | |
| pip install --editable . | |
| laca -h | |
| laca init -h | |
| laca run -h | |
| - name: Dry-run LACA | |
| run: | | |
| export PATH="${HOME}/conda/bin:$PATH" | |
| source activate laca | |
| laca init -b laca/workflow/resources/data -d test/Database -w test | |
| laca run all -w test -n | |