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## Inspired/copied from https://github.com/snakemake-workflows/ngs-test-data/blob/master/.travis.yml | ||
language: python | ||
python: | ||
# We don't actually use the Travis Python, but this keeps it organized. | ||
- "3.6" | ||
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||
install: | ||
- sudo apt-get update | ||
- wget 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:$PATH" | ||
- hash -r | ||
- conda config --set always_yes yes --set changeps1 no | ||
- conda update -q conda | ||
# Useful for debugging any issues with conda | ||
- conda info -a | ||
- conda config --add channels defaults | ||
- conda config --add channels conda-forge | ||
- conda config --add channels bioconda | ||
- conda create -q -n snakemake snakemake python=$TRAVIS_PYTHON_VERSION | ||
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||
script: | ||
- source activate snakemake | ||
# run the workflow | ||
- snakemake --use-conda runfastqc |