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.travis.yml
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.travis.yml
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sudo: required
dist: trusty
language: generic
env:
global:
- secure: "VJSdyR3BUpDGf7ot0I+GvSVR77TaMgxgscW1pFgxeitr3XvZ9la+PMuSqKH1B1TR/8Gq+l507FnQb1I/zjzUOvomX2gnsL6CcbTml8DKUz12kmQ0ixGT5IxZjDuBDvJwOJlRg1JLgJkcxMHa9EEmDZTh7Feyu7jJC9qeGKSyjFw="
matrix:
- BCBIO_DOCKER_PRIVILEGED=True ARVADOS_API_HOST=qr1hi.arvadosapi.com
before_install:
# Fix issue with boto2 and gce https://github.com/travis-ci/travis-ci/issues/7940#issuecomment-311046316
- export BOTO_CONFIG=/dev/null
# Temporal fix for networking problem: https://github.com/travis-ci/travis-ci/issues/1484
- echo "127.0.1.1 "`hostname` | sudo tee /etc/hosts
# Get and install anaconda for custom Python installation
- wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
- bash Miniconda2-latest-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
- conda install --yes -c conda-forge -c bioconda bcbio-nextgen-vm
- conda install --yes -c conda-forge -c bioconda cwltool toil rabix-bunny
# Clean up space with external tools we don't need for tests
- conda clean --yes --tarballs --index-cache
- conda remove --yes --force qt
- 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 and within the container
- rm -rf ~/install/bcbio-vm/anaconda/lib/python2.7/site-packages/bcbio
- rm -rf ~/install/bcbio-vm/anaconda/lib/python2.7/site-packages/bcbio_nextgen-*
- ~/install/bcbio-vm/anaconda/bin/python setup.py install
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 tests/unit --cov=bcbio"
- py.test -p no:cacheprovider tests/bcbio_vm -v -m docker_multicore
# -- bcbio variant CWL tests
- py.test -p no:cacheprovider tests/bcbio_vm -v -s -m cwl_docker_joint
- py.test -p no:cacheprovider tests/bcbio_vm -v -s -m cwl_docker_somatic
# -- platform integration
- 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 tests/bcbio_vm -v -s -m cwl_arvados
# -- 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
# -- bcbio RNA-seq CWL tests
- 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 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=