.travis.yml

language: python
python:
- '3.5'
- '3.6'
install:
- sudo apt-get update
- if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
  -O miniconda.sh; else wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
  -O miniconda.sh; fi
- bash miniconda.sh -b -p $HOME/miniconda
- export PATH="$HOME/miniconda/bin:$PATH"
- hash -r
- conda config --set always_yes yes --set changeps1 no
- conda update -q conda
- conda info -a
- conda env create -q -n test-environment python=$TRAVIS_PYTHON_VERSION -f env.yml
- source activate test-environment
script:
- python helmsman.py --mode vcf --input data/chr22.16050075-16992642.1kg.phase3.vcf.gz
  --fastafile data/chr22.fasta.gz --decomp nmf --rank 4 --package deconstructSigs
  --verbose
- python helmsman.py --mode agg --input data/gsc_LIHC.subtype_count_matrix.txt --decomp
  pca --rank 4 --package SomaticSignatures --verbose
notifications:
  webhooks:
    - secure: 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