language: python

python:

- "3.6"

branches:

only:

- master

- develop

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

# Useful for debugging any issues with conda

- conda info -a

- conda config --add channels defaults

- conda config --add channels conda-forge

- conda config --add channels bioconda

- conda install -c bioconda -c conda-forge snakemake

- conda create -q -n snakemake snakemake>=5.3.1 python=$TRAVIS_PYTHON_VERSION

script:

# run the workflow

- snakemake --use-conda --directory .test -p

after_success:

- cd docs && snakemake --use-conda build_docs

deploy:

provider: pages

skip-cleanup: true

github-token: $GITHUB_PAT

keep-history: true

local-dir: docs/site

on:

branch: master