.travis.yml

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
  - export PATH=~/install/bcbio-vm/anaconda/bin/:$PATH
  - conda install --yes -c bioconda -c conda-forge bcbio-nextgen-vm bcbio-nextgen -q
  # Get docker container
  - bcbio_vm.py --datadir=${TRAVIS_BUILD_DIR}/tests/data install --tools
  # 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
  - pip install cwl_runner

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

notifications:
  email: false
  slack:
    secure: iMn3Iih7cVmWci7A/Rpozc9Fn5IDKr3o6Y7XAWHEBiOEFlBwkC3oHFZxTC1+wZQiDNR87yVF9z3+FhYTYizpUeCPMddfNLMzdcO0EGtpckZOzX7aaFjqQCWhtucDnDQYaHhZIPKATrWvpPSYm7bpyp/p9cqgE/a9uvFLRMrIyzM=