.travis.yml

language: python
python:
  - "2.7"
sudo: false
install:
  - case "$TRAVIS_PYTHON_VERSION" in
    2*)
      wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
      PYTHON="python"
      ;;
    3*)
      wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
      PYTHON="python3"
      ;;
    esac
  - 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 info -a
  - conda config --add channels r
  - conda config --add channels bioconda 
  - conda config --add channels auto
  - conda config --add channels jrderuiter
  - conda config --add channels biobuilds
  - conda create -q -n jrflab --file conda_env/jrflab_modules_env.txt
  - conda create -q -n r-env --file conda_env/R3.2.2.txt
script:
# TODO: copy number heatmap test not working:
# source activate r-env
# bash -x test/copy_number/test_copynumber_heatmap.sh
  - source activate jrflab
  - bash -x test/vcf_tools/test_common_filter.sh
  - bash -x test/vcf_tools/test_hotspot.sh
  - bash -x test/vcf_tools/test_pathogenicity.sh
  - bash -x test/scripts/test_create_sample_yaml.sh
  - bash -x test/scripts/test_configure.sh