.travis.yml

language: julia
os:
    - linux
julia:
    - 1.1
addons:
  apt:
    packages:
      - python3-numpy
env:
  matrix:
    - PYTHON=python3
before_install:
    ## install conda
  - sudo apt-get update
  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
  - 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
  # Useful for debugging any issues with conda
  - conda info -a
  - conda install scipy pandas
  - conda install -c https://conda.anaconda.org/bioconda pysam

  ## instal R
  - sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
  - sudo add-apt-repository -y "deb http://cran.rstudio.com/bin/linux/ubuntu $(lsb_release -s -c)/"
  - sudo apt-get update -qq -y
  - sudo apt-get install git r-base r-recommended -y --allow-unauthenticated
  - sudo R -e "install.packages(c(\"neldermead\",\"data.table\"), repos=\"https://cran.rstudio.com\")"
  - sudo R -e "source(\"http://bioconductor.org/biocLite.R\"); biocLite(\"Rsamtools\")"

after_success:
    - julia -e 'using Pkg; Pkg.add("Coverage"); using Coverage; Codecov.submit(process_folder())'
notifications:
    email: false