docs: add reat transcriptome, homology, and prediction workflows #252
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: REAT | |
| on: | |
| [ push, pull_request ] | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| matrix: | |
| python-version: [ 3.8 ] | |
| os: [ubuntu-latest] | |
| steps: | |
| - name: Install system development tools | |
| if: startsWith(runner.os, 'Linux') | |
| run: | | |
| export DEBIAN_FRONTEND=noninteractive | |
| sudo apt update | |
| sudo apt install -y build-essential zlib1g-dev zlib1g | |
| - uses: actions/checkout@v2 | |
| - uses: actions/cache@v2 | |
| if: startsWith(runner.os, 'Linux') | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - uses: actions/cache@v2 | |
| if: startsWith(runner.os, 'macOS') | |
| with: | |
| path: ~/Library/Caches/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Cache conda | |
| id: cache-miniconda | |
| uses: actions/cache@v2 | |
| env: | |
| CACHE_NUMBER: 0 | |
| with: | |
| path: ~/conda_pkgs_dir | |
| key: | |
| ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('./reat.yml') }} | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| miniconda-version: "latest" | |
| environment-file: ./reat.yml | |
| mamba-version: "*" | |
| use-mamba: true | |
| channels: conda-forge, defaults | |
| use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly! | |
| activate-environment: "REAT" | |
| - name: Install dependencies | |
| run: | | |
| wget -q -O cromwell.jar https://github.com/broadinstitute/cromwell/releases/download/63/cromwell-63.jar | |
| pip install pytest==6.2.5 pytest-workflow | |
| pip install . | |
| reat --help | |
| - name: CLI test | |
| run: | | |
| export CROMWELL_JAR=$(readlink -f cromwell.jar) | |
| export CROMWELL_RUNTIME_CONFIG=$(readlink -f cromwell_configuration/cromwell.local.conf) | |
| pytest --tag cli --symlink --kwd --basetemp ../pytest_temp | |
| - name: Homology test | |
| run: | | |
| export CROMWELL_JAR=$(readlink -f cromwell.jar) | |
| export CROMWELL_RUNTIME_CONFIG=$(readlink -f cromwell_configuration/cromwell.local.conf) | |
| pytest --tag homology --symlink --kwd --basetemp ../pytest_temp | |
| - name: Transcriptome test | |
| run: | | |
| export CROMWELL_JAR=$(readlink -f cromwell.jar) | |
| export CROMWELL_RUNTIME_CONFIG=$(readlink -f cromwell_configuration/cromwell.local.conf) | |
| pytest --tag transcriptome --symlink --kwd --basetemp ../pytest_temp |