fix viral_assemble #1044
Workflow file for this run
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| name: CI | |
| on: [push, pull_request] | |
| jobs: | |
| target: | |
| strategy: | |
| matrix: | |
| ci_target: | |
| - ci_housekeeping | |
| - ci_unit_tests | |
| - integration_tests | |
| - viral_refbased | |
| - viral_assemble | |
| # disabled due to test data bitrot (Apr 2023) | |
| # - skylab_bulk_rna | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Maximize build space | |
| uses: easimon/maximize-build-space@master | |
| if: ${{ matrix.ci_target == 'viral_assemble' }} | |
| - name: Login to GitHub Packages Docker Registry | |
| uses: docker/login-action@v1 | |
| with: | |
| registry: docker.pkg.github.com | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| submodules: recursive | |
| - name: docker build | |
| run: | | |
| # Cache the dependency-installation image layer on GitHub Packages to speed up CI. Use a | |
| # year/month tag to ensure we do refresh them occasionally. | |
| DOCKER_TAG="docker.pkg.github.com/${GITHUB_REPOSITORY}/miniwdl_ci:$(date +%Y%m)" | |
| echo "DOCKER_TAG=${DOCKER_TAG}" >> $GITHUB_ENV | |
| if docker pull "$DOCKER_TAG"; then | |
| docker build -t "$DOCKER_TAG" --cache-from "$DOCKER_TAG" . | |
| else | |
| docker build -t "$DOCKER_TAG" . | |
| fi | |
| if [ "${{ matrix.ci_target }}" == "ci_housekeeping" ]; then | |
| docker push "$DOCKER_TAG" || true # allow failure for third-party PRs | |
| fi | |
| - name: make ${{ matrix.ci_target }} | |
| run: | | |
| chmod -R ugo+rw . | |
| # AWS_EC2_METADATA_DISABLED needed on Azure: https://github.com/aws/aws-cli/issues/5623 | |
| docker run \ | |
| --group-add $(stat -c %g /var/run/docker.sock) -v /var/run/docker.sock:/var/run/docker.sock \ | |
| -v $(pwd):/home/wdler/miniwdl -v /tmp:/tmp \ | |
| -e AWS_EC2_METADATA_DISABLED=true -e CI=true \ | |
| "$DOCKER_TAG" make -C miniwdl ${{ matrix.ci_target }} | |
| - name: Coveralls | |
| if: ${{ matrix.ci_target == 'ci_unit_tests' }} | |
| # https://github.com/coverallsapp/github-action/issues/30 | |
| # https://github.com/marketplace/actions/coveralls-python | |
| uses: AndreMiras/coveralls-python-action@develop | |
| bionic_self_test: | |
| # run_self_test in a ubuntu:18.04 image with only the minimal runtime dependencies installed | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: docker build | |
| run: | | |
| mkdir bionic_self_test | |
| cp requirements.txt bionic_self_test | |
| cat << 'EOF' > bionic_self_test/Dockerfile | |
| FROM ubuntu:18.04 | |
| ENV LC_ALL C.UTF-8 | |
| ENV LANG C.UTF-8 | |
| RUN apt-get -qq update && DEBIAN_FRONTEND=noninteractive apt-get -qq install -y python3-pip | |
| RUN useradd -ms /bin/bash -u 1337 wdler | |
| USER wdler | |
| WORKDIR /home/wdler | |
| RUN mkdir miniwdl | |
| COPY requirements.txt /home/wdler/ | |
| RUN pip3 install --user -r requirements.txt | |
| ENV PYTHONPATH $PYTHONPATH:/home/wdler/.local/lib/python3.6 | |
| ENV PATH $PATH:/home/wdler/.local/bin | |
| # expectation -- mount miniwdl source tree at /home/wdler/miniwdl | |
| CMD env -C miniwdl python3 -m WDL run_self_test | |
| EOF | |
| docker build -t miniwdl_bionic_self_test bionic_self_test | |
| - name: miniwdl run_self_test | |
| run: | | |
| docker run \ | |
| --group-add $(stat -c %g /var/run/docker.sock) -v /var/run/docker.sock:/var/run/docker.sock \ | |
| -v $(pwd):/home/wdler/miniwdl -v /tmp:/tmp \ | |
| -e AWS_EC2_METADATA_DISABLED=true \ | |
| miniwdl_bionic_self_test |