.travis.yml

language: python

python:
  - "3.6"

cache: pip

before_install:
  - sudo apt-get -qq install ghostscript
  - sudo apt-get -qq install dvipng
  - sudo apt-get -qq install texlive-latex-extra
  - sudo apt-get -qq install texlive-fonts-recommended
  - sudo apt-get -qq install cm-super
  - sudo apt-get install -y r-base
  # install samtools
  - wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
  - tar xvf samtools-1.9.tar.bz2
  - cd samtools-1.9
  - ./configure
  - make
  - cd ..
  - export PATH=$PWD/samtools-1.9:$PATH
  # install minimap2
  - wget https://github.com/lh3/minimap2/releases/download/v2.12/minimap2-2.12_x64-linux.tar.bz2
  - tar xvf minimap2-2.12_x64-linux.tar.bz2
  - export PATH=$PWD/minimap2-2.12_x64-linux:$PATH

install:
  - pip install -e .

# following here: https://docs.travis-ci.com/user/gui-and-headless-browsers/#using-xvfb-to-run-tests-that-require-a-gui
services:
  - xvfb

script: 
  - pytest

branches:
  only:
    - master

notifications:
  slack: jbloomlab:JRB6s9Rw88c7YPaL2VGmVJaq