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| sudo: required | |
| dist: trusty | |
| language: generic | |
| env: | |
| - BCBIO_DOCKER_PRIVILEGED=True | |
| before_install: | |
| # 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 http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh | |
| - bash Miniconda-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/:$PATH | |
| - conda install --yes -c conda-forge -c bioconda bcbio-nextgen-vm bcbio-nextgen -q | |
| - conda install --yes -c conda-forge -c bioconda cwltool | |
| # Clean up space with external tools we don't need for tests | |
| - conda clean --yes --tarballs --index-cache | |
| - conda remove --yes --force qt openjdk nodejs | |
| - rm -rf ~/install/bcbio-vm/anaconda/pkgs/qt-* | |
| - rm -rf ~/install/bcbio-vm/anaconda/pkgs/openjdk-* | |
| - rm -rf ~/install/bcbio-vm/anaconda/pkgs/nodejs-* | |
| - du -sch ~/install/bcbio-vm/anaconda/pkgs/* | sort -h | |
| - df -h | |
| # Get docker container | |
| - bcbio_vm.py --datadir=${TRAVIS_BUILD_DIR}/tests/data install --tools | |
| - df -h | |
| - docker images | |
| # 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 | |
| - bcbio_vm.py devel setup_install | |
| script: | |
| - docker run -v `pwd`:`pwd` bcbio/bcbio bash -c "cd `pwd` && /usr/local/share/bcbio-nextgen/anaconda/bin/py.test tests/unit --cov=bcbio" | |
| # Currently turned off to reduce test run times on Travis | |
| #- docker run -v `pwd`:`pwd` bcbio/bcbio bash -c "cd `pwd` && /usr/local/share/bcbio-nextgen/anaconda/bin/py.test tests/integration -v -m 'not install_required' --cov=bcbio" | |
| - py.test tests/bcbio_vm -v -m docker | |
| # TODO: switch to use CWL docker runs instead of full bcbio/bcbio images | |
| #- py.test tests/bcbio_vm -v -m cwl | |
| after_failure: | |
| - df -h | |
| notifications: | |
| email: false | |
| slack: | |
| secure: iMn3Iih7cVmWci7A/Rpozc9Fn5IDKr3o6Y7XAWHEBiOEFlBwkC3oHFZxTC1+wZQiDNR87yVF9z3+FhYTYizpUeCPMddfNLMzdcO0EGtpckZOzX7aaFjqQCWhtucDnDQYaHhZIPKATrWvpPSYm7bpyp/p9cqgE/a9uvFLRMrIyzM= |