2020-05-01 23:17:00 +02:00
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services:
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- mysql
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2020-04-30 00:27:39 +02:00
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language: python
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python:
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2020-05-01 23:17:00 +02:00
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- '3.7'
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2020-04-30 19:02:31 +02:00
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before_install:
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2020-05-01 23:17:00 +02:00
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- sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran40/'
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- sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
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- sudo apt-get install -y r-base r-base-dev
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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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2020-04-30 19:02:31 +02:00
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install:
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2020-05-01 23:17:00 +02:00
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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 $HOME/miniconda
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- source "$HOME/miniconda/etc/profile.d/conda.sh"
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- hash -r
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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 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 activate test-environment
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2020-04-30 23:21:45 +02:00
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before_script:
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2020-05-02 01:46:04 +02:00
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# Install renv and library
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- snakemake renv_install
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- snakemake renv_init
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- snakemake renv_restore
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2020-04-30 00:27:39 +02:00
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script:
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2020-05-01 23:17:00 +02:00
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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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- python -m unittest discover tests/scripts/ -v
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notifications:
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2020-05-01 23:41:57 +02:00
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email: false
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2020-05-01 23:17:00 +02:00
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slack:
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secure: 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on_success: always
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2020-05-01 23:41:57 +02:00
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template:
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- "Repo `%{repository_slug}` *%{result}* build (<%{build_url}|#%{build_number}>) for commit (<%{compare_url}|%{commit}>) on branch `%{branch}`."
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- "Execution time: *%{duration}*"
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- "Message: %{message}"
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cache:
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directories:
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2020-05-02 01:46:04 +02:00
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- /usr/local/lib/R
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