2020-04-30 23:21:45 +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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- "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 20:17:40 +02:00
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# Install Linuxbrew
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- git clone https://github.com/Linuxbrew/brew.git $HOME/.linuxbrew
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- PATH="$HOME/.linuxbrew/bin:$PATH"
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- echo 'export PATH="$HOME/.linuxbrew/bin:$PATH"' >>~/.bash_profile
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- export MANPATH="$(brew --prefix)/share/man:$MANPATH"
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- export INFOPATH="$(brew --prefix)/share/info:$INFOPATH"
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- brew --version
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- brew install r
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- brew install pandoc
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2020-04-30 22:55:48 +02:00
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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 21:59:27 +02:00
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2020-04-30 19:02:31 +02:00
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install:
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2020-04-30 00:27:39 +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 $HOME/miniconda
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2020-04-30 18:30:07 +02:00
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- source "$HOME/miniconda/etc/profile.d/conda.sh"
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2020-04-30 00:27:39 +02:00
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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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# Useful for debugging any issues with conda
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- conda info -a
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2020-04-30 19:02:31 +02:00
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- conda env create -q -n test-environment python=$TRAVIS_PYTHON_VERSION --file environment.yml
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2020-04-30 00:27:39 +02:00
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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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# Install Packrat
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- snakemake packrat_install
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- snakemake packrat_init
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- snakemake packrat_restore
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2020-04-30 00:27:39 +02:00
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script:
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- cp -r tests/data/raw/* data/raw
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2020-05-01 16:28:12 +02:00
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- snakemake --profile tests/settings -R sms_features
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2020-04-30 23:44:51 +02:00
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- python -m unittest discover tests/scripts/ -v
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