Mercurial > repos > jpetteng > ectyper
comparison ecoli_serotyping/.travis.yml @ 0:7c687720c9e9 draft
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| author | jpetteng |
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| date | Fri, 05 Jan 2018 09:17:33 -0500 |
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| -1:000000000000 | 0:7c687720c9e9 |
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| 1 language: python | |
| 2 python: | |
| 3 # We don't actually use the Travis Python, but this keeps it organized. | |
| 4 - "3.6" | |
| 5 install: | |
| 6 - sudo apt-get update | |
| 7 # We do this conditionally because it saves us some downloading if the | |
| 8 # version is the same. | |
| 9 - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then | |
| 10 wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh; | |
| 11 else | |
| 12 wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; | |
| 13 fi | |
| 14 - bash miniconda.sh -b -p $HOME/miniconda | |
| 15 - export PATH="$HOME/miniconda/bin:$PATH" | |
| 16 - hash -r | |
| 17 - conda config --set always_yes yes --set changeps1 no | |
| 18 - conda update -q conda | |
| 19 # Useful for debugging any issues with conda | |
| 20 - conda info -a | |
| 21 - conda config --add channels bioconda | |
| 22 - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION samtools bowtie2 mash bcftools biopython nose blast pandas seqtk | |
| 23 - source activate test-environment | |
| 24 - python setup.py install | |
| 25 | |
| 26 script: | |
| 27 - nosetests |