.travis.yml

os:
  - linux

# language: python sets up virtualenv and pip that we don't need.
# omitting language gives us ruby stuff. c seems likely to be a minimal setup.
language: c

install:
  # Install dependencies for Conda
  - printenv | sort
  - |
    if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
      MINICONDA_OS=Linux ;
    else
      MINICONDA_OS=MacOSX ;
    fi ;
    echo "Fetching miniconda for $MINICONDA_OS" ;
    wget https://repo.continuum.io/miniconda/Miniconda3-latest-$MINICONDA_OS-x86_64.sh -O miniconda.sh
  - bash miniconda.sh -b -p $HOME/miniconda
  - export PATH="$HOME/miniconda/bin:$PATH"
  - hash -r
  - source "$HOME"/miniconda/bin/activate root
  - printenv | sort
  - conda config --set always_yes yes --set changeps1 no
  - conda config --add channels r
  - conda config --add channels bioconda
  - conda config --add channels conda-forge
  - conda config --add channels grst
  - conda update -q conda
  - conda install snakemake
  # Useful for debugging any issues with conda
  - conda info -a

script:
  # Run pipeline
  - travis_wait 40 snakemake --use-conda book

# sudo = true gives a little bit more RAM 
sudo: true 
cache: packages