.travis.yml

sudo: required

language: python
python:
  - "3.6"  # required, otherwise conda will try to clash with py2 packages

services:
  - docker

before_install:
  # Get and install anaconda (https://conda.io/docs/travis.html)
  - wget -nv 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  # Useful for debugging any issues with conda

install:
  # Set up conda
  - export PACKAGE_NAME=pcgr
  # Setting up channels and install dependencies
  - conda config --add channels pcgr --add channels bioconda --add channels conda-forge
  - conda install -q python=$TRAVIS_PYTHON_VERSION pip requests conda-build jinja2 anaconda-client
  # Building packages
  - conda build install_no_docker/conda_pkg/${PACKAGE_NAME}
  - conda build install_no_docker/conda_pkg/${PACKAGE_NAME}_dockerized
  #
  # Dockerized installation:
  - docker pull sigven/pcgr:dev
  - conda install --use-local ${PACKAGE_NAME}_dockerized
  # Download the data bundle (usable for both version)
  - gdown https://drive.google.com/uc?id=1vIESS8NxiITUnrqZoWOdNk1YsklH8f1C -O - | tar xzf - # grch37

script:
  # Dockerized installation:
  - pcgr.py --version
  - python -c "import pcgr"
  - pcgr.py
    --input_vcf examples/tumor_sample.COAD.vcf.gz
    --input_cna examples/tumor_sample.COAD.cna.tsv
    . ./examples grch37 examples/examples_BRCA.toml tumor_sample.COAD
  #
  # Condarized installation:
  - conda install --use-local ${PACKAGE_NAME}
  - pcgr.py --version
  - python -c "import pcgr"
  - pcgr.py
    --input_vcf examples/tumor_sample.BRCA.vcf.gz
    --input_cna examples/tumor_sample.BRCA.cna.tsv
    . ./examples grch37 examples/examples_BRCA.toml tumor_sample.BRCA --no-docker

deploy:
  # Deploy to Anaconda.org
  - provider: script
    script:
      conda convert --platform osx-64 $HOME/miniconda/conda-bld/linux-64/${PACKAGE_NAME}_dockerized-*.tar.bz2 --output-dir $HOME/miniconda/conda-bld/ &&
      anaconda -t ${ANACONDA_TOKEN} upload -u pcgr $HOME/miniconda/conda-bld/**/${PACKAGE_NAME}*.tar.bz2
    on:
      tags: true
    skip_cleanup: true