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fix branch

fix branch #1

Workflow file for this run

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"