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|
os: linux
dist: bionic
language: generic
addons:
apt:
update: true
env:
global:
- secure: "VJSdyR3BUpDGf7ot0I+GvSVR77TaMgxgscW1pFgxeitr3XvZ9la+PMuSqKH1B1TR/8Gq+l507FnQb1I/zjzUOvomX2gnsL6CcbTml8DKUz12kmQ0ixGT5IxZjDuBDvJwOJlRg1JLgJkcxMHa9EEmDZTh7Feyu7jJC9qeGKSyjFw="
matrix:
- BCBIO_DOCKER_PRIVILEGED=True ARVADOS_API_HOST=qr1hi.arvadosapi.com
before_install:
# exit the build if it only includes Markdown files
- |
if ! git diff --name-only $TRAVIS_COMMIT_RANGE | grep -qvE '(.md)'
then
echo "Not running CI since only docs were changed"
exit
fi
# Get and install anaconda for custom Python installation
- wget --progress=dot:giga https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.2-Linux-x86_64.sh
- bash Miniconda3-py37_4.8.2-Linux-x86_64.sh -b -p ~/install/bcbio-vm/anaconda
install:
# Install bcbio-nextgen and bcbio-nextgen-vm
- df -h
- export PATH=~/install/bcbio-vm/anaconda/bin:$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
# Clean up space with external tools we don't need for tests
- conda clean --yes --tarballs --index-cache
- rm -rf ~/install/bcbio-vm/anaconda/pkgs/qt-*
- du -sch ~/install/bcbio-vm/anaconda/pkgs/* | sort -h
- df -h
# Update to latest bcbio-nextgen code externally
- rm -rf ~/install/bcbio-vm/anaconda/lib/python*/site-packages/bcbio
- rm -rf ~/install/bcbio-vm/anaconda/lib/python*/site-packages/bcbio_nextgen-*
- ~/install/bcbio-vm/anaconda/bin/python setup.py install
jobs:
include:
- stage: test
name: "Variant standard"
script:
# -- Prepare variant docker image
- docker pull quay.io/bcbio/bcbio-vc
- docker images
- df -h
# Update to latest bcbio-nextgen code within the container
- bcbio_vm.py devel setup_install -i quay.io/bcbio/bcbio-vc
# -- Standard bcbio variant tests
- docker run -v `pwd`:`pwd` quay.io/bcbio/bcbio-vc bash -c "cd `pwd` && /usr/local/share/bcbio-nextgen/anaconda/bin/py.test -p no:cacheprovider -p no:stepwise tests/unit --cov=bcbio"
- py.test -p no:cacheprovider -p no:stepwise tests/bcbio_vm -v -m docker_multicore
# XXX Arvados tests failing with 404 when contacting from Travis
# - sudo mkdir -p /etc/pki/tls/certs && sudo ln -s /etc/ssl/certs/ca-certificates.crt /etc/pki/tls/certs/ca-bundle.crt
# - py.test -p no:cacheprovider -p no:stepwise tests/bcbio_vm -v -s -m cwl_arvados
- stage: test
name: "Variant CWL"
script:
- docker pull quay.io/bcbio/bcbio-vc
- docker images
- df -h
# Update to latest bcbio-nextgen code within the container
- bcbio_vm.py devel setup_install -i quay.io/bcbio/bcbio-vc
# XXX Currently commented out joint test, taking too long and causing Travis timeouts
# - py.test -p no:cacheprovider -p no:stepwise tests/bcbio_vm -v -s -m cwl_docker_joint
- py.test -p no:cacheprovider -p no:stepwise tests/bcbio_vm -v -s -m cwl_docker_somatic
# -- Cleanup variant docker image
- 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
- docker images
- stage: test
name: "RNA-seq CWL"
script:
- docker pull quay.io/bcbio/bcbio-rnaseq
- docker images
- df -h
- 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 -m cwl_docker_rnaseq
# -- Cleanup RNA-seq docker image
- 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
- docker images
after_failure:
- df -h
notifications:
email: false
slack:
secure: iMn3Iih7cVmWci7A/Rpozc9Fn5IDKr3o6Y7XAWHEBiOEFlBwkC3oHFZxTC1+wZQiDNR87yVF9z3+FhYTYizpUeCPMddfNLMzdcO0EGtpckZOzX7aaFjqQCWhtucDnDQYaHhZIPKATrWvpPSYm7bpyp/p9cqgE/a9uvFLRMrIyzM=
|
