.travis.yml

language: python
python:
  - "3.6"
install:
  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
  - bash miniconda.sh -b -p $HOME/miniconda
  - source "$HOME/miniconda/etc/profile.d/conda.sh"
  - 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 env create -f environment.yml
  - conda activate reconCNV
  - conda install codecov
script:
  - coverage run reconCNV.py -x data/hg19_genome_length.txt -c config.json -r data/sample_data/HT-29.cnr  -d . -o test.html -f -g data/sample_data/HT-29.genemetrics.cns -s data/sample_data/HT-29.cns -v data/sample_data/HT-29.vcf -b data/artifact_SNP.bed -t data/artifact_seg.bed -a data/hg19_COSMIC_genes_model.txt -p 0.95 -l 3.04 -z male -y -0.4 -j
after_success:
  - codecov