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.travis.yml
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.travis.yml
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language: python
python:
# We don't actually use the Travis Python, but this keeps it organized.
- "3.6"
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:$PATH"
- hash -r
- conda config --set always_yes yes --set changeps1 no
- conda update -q conda
# Useful for debugging any issues with conda
- conda info -a
- conda config --add channels defaults
- conda config --add channels conda-forge
- conda config --add channels bioconda
# create snakemake env
- conda create -q -n snakemake snakemake python=$TRAVIS_PYTHON_VERSION
# add additional stuff to setup below
script:
- source activate snakemake
# run the workflow
# put a test case into the subfolder .test (e.g., use https://github.com/snakemake-workflows/ngs-test-data as a submodule)
- snakemake --use-conda --directory .test