.appveyor.yml

image: ubuntu

services:
  - docker

install:
  # Pulling the image
  - sudo service docker start
  - docker pull sigven/pcgr:dev
  # Installing wrapper script dependencies
  - 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
  - conda install -y -c conda-forge -c pcgr toml gdown
  # Downloading datab bundle - commenting out because getting "not enough disk space"
  #  - gdown https://drive.google.com/uc?id=1OL5C994HDaeadASz7KzMhPoXfdSiyhNy -O - | tar xzf - # grch37

test_script:
  - python pcgr.py --version
  # Full test - commenting out because getting "not enough disk space" at gdown step
  #  - python pcgr.py --input_vcf examples/tumor_sample.COAD.vcf.gz --input_cna examples/tumor_sample.COAD.cna.tsv . ./examples grch37 examples/pcgr_conf.COAD.toml tumor_sample.COAD

build: off

# TODO: build and push docker from here - see https://stefanscherer.github.io/setup-windows-docker-ci-appveyor/
#environment:
#  DOCKER_USER:
#    secure: xxxxxxx
#  DOCKER_PASS:
#    secure: yyyyyyy
#
#install:
#  - docker version
#
#build_script:
#  - docker build -t me/myfavoriteapp .
#
#test_script:
#  - docker run me/myfavoriteapp
#
#deploy_script:
#  - docker login -u="$env:DOCKER_USER" -p="$env:DOCKER_PASS"
#  - docker push me/myfavoriteapp