[pull] master from bcbio:master #2
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| jobs: | |
| build: | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| matrix: | |
| include: | |
| - name: Variant standard | |
| env: | |
| BCBIO_DOCKER_PRIVILEGED: True | |
| ARVADOS_API_HOST: qr1hi.arvadosapi.com | |
| - name: Variant CWL | |
| - name: RNA-seq CWL | |
| env: | |
| ANACONDA_INSTALL_DIR: ~/install/bcbio-vm/anaconda | |
| steps: | |
| - name: Check if only Markdown files changed | |
| run: | | |
| if ! git diff --name-only ${{ github.event.before }}..${{ github.sha }} | grep -qvE '(.md)' | |
| then | |
| echo "Not running CI since only docs were changed" | |
| exit 0 | |
| fi | |
| - name: Update packages and install Miniconda | |
| run: | | |
| sudo apt update | |
| wget --progress=dot:giga https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.2-Linux-x86_64.sh | |
| bash Miniconda3-py37_4.8.2-Linux-x86_64.sh -b -p ${{ env.ANACONDA_INSTALL_DIR }} | |
| - name: Install bcbio-nextgen and bcbio-nextgen-vm | |
| run: | | |
| export PATH=${{ env.ANACONDA_INSTALL_DIR }}/bin:$PATH | |
| conda install --yes nomkl | |
| conda install --yes -c conda-forge -c bioconda bcbio-nextgen python=3 | |
| conda install --yes -c conda-forge -c bioconda bcbio-nextgen-vm python=3 | |
| conda clean --yes --tarballs --index-cache | |
| rm -rf ${{ env.ANACONDA_INSTALL_DIR }}/pkgs/qt-* | |
| du -sch ${{ env.ANACONDA_INSTALL_DIR }}/pkgs/* | sort -h | |
| - name: Update bcbio-nextgen code | |
| run: | | |
| rm -rf ${{ env.ANACONDA_INSTALL_DIR }}/lib/python*/site-packages/bcbio | |
| rm -rf ${{ env.ANACONDA_INSTALL_DIR }}/lib/python*/site-packages/bcbio_nextgen-* | |
| ${{ env.ANACONDA_INSTALL_DIR }}/bin/python setup.py install | |
| - name: Variant tests | |
| if: matrix.name == 'Variant standard' || matrix.name == 'Variant CWL' | |
| run: | | |
| docker pull quay.io/bcbio/bcbio-vc | |
| docker images | |
| bcbio_vm.py devel setup_install -i quay.io/bcbio/bcbio-vc | |
| py.test -p no:cacheprovider -p no:stepwise tests/bcbio_vm -v -s | |
| docker ps -a -q | xargs --no-run-if-empty docker rm | |
| docker rmi -f quay.io/bcbio/bcbio-vc | |
| docker images | grep '<none>' | awk '{print $3}' | xargs --no-run-if-empty docker rmi | |
| - name: RNA-seq tests | |
| if: matrix.name == 'RNA-seq CWL' | |
| run: | | |
| docker pull quay.io/bcbio/bcbio-rnaseq | |
| docker images | |
| bcbio_vm.py devel setup_install -i quay.io/bcbio/bcbio-rnaseq | |
| py.test -p no:cacheprovider -p no:stepwise tests/bcbio_vm -v -s | |
| docker ps -a -q | xargs --no-run-if-empty docker rm | |
| docker rmi -f quay.io/bcbio/bcbio-rnaseq | |
| docker images | grep '<none>' | awk '{print $3}' | xargs --no-run-if-empty docker rmi | |
| - name: Cleanup | |
| run: df -h | |
| - name: Notify on failure | |
| if: failure() | |
| run: echo "Build failed" | |