.travis.yml

language: python
python:
  - "2.7"
  - "3.5"
script:
    - source activate travis
    - ./scripts/lumpyexpress -h
    - python scripts/cnvanator_to_bedpes.py --cnvkit  -b 100 --del_o delo2 --dup_o dupo2 -c data/example.cns
    - bash test/functional-test.sh
    - cd lumpy_tests && bash test.sh

install:
    - sudo apt-get update
    - sudo apt-get install libssl-dev gettext gettext-base libtool autoconf gawk
    - unset PYTHONPATH
    - unset PYTHONHOME
    - unset PYTHONUSER
    - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
        wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
      else
        wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
      fi
    - bash miniconda.sh -b -p $HOME/miniconda
    - export PATH="$HOME/miniconda/bin:$PATH"
    - hash -r
    - conda config --set always_yes yes --set changeps1 no
    - conda update -q conda
    - conda config --add channels bioconda
    - conda create -q -n travis python=$TRAVIS_PYTHON_VERSION pysam samtools htslib bedtools
    - source activate travis
    - git clone https://github.com/hall-lab/svtyper.git
    - cd svtyper && sudo python setup.py install && cd ..
    - autoconf --version
    - make