Update index.md #3
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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" | |