/
.travis.yml
34 lines (31 loc) · 1.44 KB
/
.travis.yml
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language: python
python:
- "3.7"
install:
- sudo apt-get update
- sudo apt install build-essential
# We do this conditionally because it saves us some downloading if the
# version is the same.
- 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:$PATH"
- hash -r
- conda config --set always_yes yes --set changeps1 no
- conda update -q conda
# Useful for debugging any issues with conda
- conda info -a
# setup bioconda
- conda config --add channels defaults
- conda config --add channels conda-forge
- conda config --add channels bioconda
- conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION setuptools biopython matplotlib pandas pysam numexpr bcbiogff statsmodels rpy2 bioconductor-deseq2 bioconductor-edger blockbuster
- source activate test-environment
- python setup.py install
script:
- 'peakachu 2>&1 | grep "^usage" > /dev/null'
- time peakachu adaptive -t tests/exp_a.bam tests/exp_b.bam -c tests/ctrl_a.bam -c tests/ctrl_a.bam tests/ctrl_b.bam --output_folder testadaptive
- time peakachu window -t tests/exp_a.bam tests/exp_b.bam -c tests/ctrl_a.bam -c tests/ctrl_a.bam tests/ctrl_b.bam --output_folder testwindow