Added Travis Xenial to ensure build passes
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93e3b4204e
commit
80417bead0
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.travis.yml
71
.travis.yml
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@ -1,34 +1,48 @@
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services:
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services:
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- mysql
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- mysql
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os: linux
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dist: xenial
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language: python
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language: python
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python:
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python:
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- '3.7'
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- '3.7'
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cache:
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directories:
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- /home/linuxbrew/.linuxbrew
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- $HOME/.local/share/renv
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- $TRAVIS_BUILD_DIR/renv/library
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before_install:
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before_install:
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- sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran40/'
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- /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
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- sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
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- export PATH=/home/linuxbrew/.linuxbrew/bin:$PATH
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- sudo apt-get install -y r-base r-base-dev
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- source ~/.bashrc
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- sudo chmod ugo+rw /usr/local/lib/R/site-library
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- sudo apt-get install linuxbrew-wrapper
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- R -e 'install.packages(c( "rmarkdown"), repos = "http://cran.us.r-project.org")'
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- brew install r
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# - sudo chmod ugo+rw /usr/local/lib/R/site-library
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- R -e 'install.packages(c( "rmarkdown"), repos = "http://cran.us.r-project.org")'
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- R --version
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install:
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install:
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- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
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- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
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- bash miniconda.sh -b -p $HOME/miniconda
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- bash miniconda.sh -b -p $HOME/miniconda
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- source "$HOME/miniconda/etc/profile.d/conda.sh"
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- source "$HOME/miniconda/etc/profile.d/conda.sh"
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- hash -r
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- hash -r
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- conda config --set always_yes yes --set changeps1 no
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- conda config --set always_yes yes --set changeps1 no
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- conda update -q conda
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- conda update -q conda
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- conda info -a
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- conda info -a
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- conda env create -q -n test-environment python=$TRAVIS_PYTHON_VERSION --file environment.yml
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- conda env create -q -n test-environment python=$TRAVIS_PYTHON_VERSION --file environment.yml
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- conda activate test-environment
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- conda activate test-environment
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before_script:
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- snakemake renv_install
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# Install renv and library
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- snakemake renv_init
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- snakemake renv_install
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- snakemake renv_restore
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- snakemake renv_init
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- snakemake renv_restore
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script:
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script:
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- cp -r tests/data/raw/* data/raw
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- cp -r tests/data/raw/* data/raw
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- snakemake --profile tests/settings -R sms_features
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- snakemake --profile tests/settings -R sms_features
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- python -m unittest discover tests/scripts/ -v
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- python -m unittest discover tests/scripts/ -v
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notifications:
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notifications:
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email: false
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email: false
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@ -40,6 +54,9 @@ notifications:
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- "Execution time: *%{duration}*"
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- "Execution time: *%{duration}*"
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- "Message: %{message}"
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- "Message: %{message}"
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cache:
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branches:
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directories:
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except:
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- /usr/local/lib/R
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- master
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only:
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- travis_test
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