.travis.yml

language: python
cache:
    directories:
     - $HOME/miniconda
python:
  # We don't actually use the Travis Python, but this keeps it organized.
  - "3.6"
before_install:
  - |
    if [ -d "$HOME/miniconda" ]; then
      echo "conda exist already";
      source activate atlasenv
      conda list
    else:
      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 config --add channels defaults
      conda config --add channels bioconda
      conda config --add channels conda-forge
      conda env create -n atlasenv --file atlasenv.yml
    fi

install:
  - source activate atlasenv
  - python setup.py install
  - atlas --help
  - atlas --version
script:
  - N_THREADS=2 ; MEM=7
  - test/dryrun.sh
  - test/test_assembly.sh --resources mem=$MEM java_mem=$MEM --jobs=$N_THREADS --restart-times=2