/
.travis.yml
32 lines (30 loc) · 1.52 KB
/
.travis.yml
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sudo: required
language: python
compiler:
- clang
env:
- PYTHON_VERSION=3.5
before_install:
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
- chmod +x miniconda.sh
- ./miniconda.sh -b
- export PATH=/home/travis/miniconda3/bin:$PATH
- sudo apt-get install libhdf5-serial-dev hdf5-tools >/dev/null
- sudo sed -i 's/^CXXBASE=.*/CXXBASE=clang++/' `which h5c++`
- sudo sed -i 's/^CXXLINKERBASE=.*/CXXLINKERBASE=clang++/' `which h5c++`
install:
- pushd sucpp; make test main; popd
- sudo cp ssu /usr/bin/
- conda create --yes -n test-env python=$PYTHON_VERSION nose flake8
- source activate test-env
- conda install --yes -c bioconda biom-format scikit-bio
- pip install https://github.com/qiime2/qiime2/archive/master.zip https://github.com/qiime2/q2-types/archive/master.zip https://github.com/qiime2/q2cli/archive/master.zip http://github.com/qiime2/q2templates/archive/master.zip https://github.com/qiime2/q2-feature-table/archive/master.zip https://github.com/qiime2/q2-diversity/archive/master.zip
- git clone https://github.com/qiime2/q2lint
- pip install .
script:
- pushd sucpp; ./test_su; popd
- flake8 q2_state_unifrac setup.py
- python q2lint/q2lint.py
- qiime state-unifrac unweighted --i-table table.qza --i-phylogeny tree.qza --o-distance-matrix ssu_result.qza
- qiime diversity beta-phylogenetic --p-metric unweighted_unifrac --i-table table.qza --i-phylogeny tree.qza --o-distance-matrix sk_result.qza
- python compare_dms.py ssu_result.qza sk_result.qza