.travis.yml

sudo: required

services:
    - docker

language: python
python:
  # this dictates the conda python version
  - "3.5"

install:
  - 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:$PATH"
  - hash -r
  - conda config --set always_yes yes --set changeps1 no
  - conda update -q conda
  - conda info -a
  - conda config --add channels defaults
  - conda config --add channels conda-forge
  - conda config --add channels bioconda
  - conda create -q -n snakemake_env python=$TRAVIS_PYTHON_VERSION snakemake-minimal pandas

script:
  - source activate snakemake_env
  # run the assembly workflow on a cell in the .test directory
  - snakemake --use-conda --directory .test combined_assemblies.tsv
  # output should contain functional heavy and light chain assemblies
  - python .test/check_assemblies.py .test/combined_assemblies.tsv