language: python
python:
  - "2.7"
cache:
  - pip
  

install: 
  - pip install Cython
  - pip install -r requirements.txt
  - python setup.py install
addons:
  apt:
    packages:
    - bwa
    - samtools
    - tabix
    - ncbi-blast+
    - muscle

script: 
  - py.test 
language: python
python:
  - "2.7"
cache:
  - pip
  

before_install:
  - git clone https://github.com/Linuxbrew/brew.git ~/.linuxbrew
  - export PATH="$HOME/.linuxbrew/bin:$PATH"
  - export MANPATH="$HOME/.linuxbrew/share/man:$MANPATH"
  - export INFOPATH="$HOME/.linuxbrew/share/info:$INFOPATH"
  - brew tap homebrew/science
  - brew install bwa samtools tabix blast muscle

install: 
  - pip install Cython
  - pip install -r requirements.txt
  - python setup.py install

script: 
  - py.test 
Use homebrew for managing dependencies
Use homebrew for managing dependencies
