43 lines
1.3 KiB
YAML
43 lines
1.3 KiB
YAML
services:
|
|
- mysql
|
|
|
|
language: python
|
|
python:
|
|
- "3.7"
|
|
|
|
before_install:
|
|
# Install Linuxbrew
|
|
- git clone https://github.com/Linuxbrew/brew.git $HOME/.linuxbrew
|
|
- PATH="$HOME/.linuxbrew/bin:$PATH"
|
|
- echo 'export PATH="$HOME/.linuxbrew/bin:$PATH"' >>~/.bash_profile
|
|
- export MANPATH="$(brew --prefix)/share/man:$MANPATH"
|
|
- export INFOPATH="$(brew --prefix)/share/info:$INFOPATH"
|
|
- brew --version
|
|
- brew install r
|
|
- brew install pandoc
|
|
- sudo chmod ugo+rw /usr/local/lib/R/site-library
|
|
- R -e 'install.packages(c( "rmarkdown"), repos = "http://cran.us.r-project.org")'
|
|
|
|
install:
|
|
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
|
|
- bash miniconda.sh -b -p $HOME/miniconda
|
|
- source "$HOME/miniconda/etc/profile.d/conda.sh"
|
|
- hash -r
|
|
- conda config --set always_yes yes --set changeps1 no
|
|
- conda update -q conda
|
|
# Useful for debugging any issues with conda
|
|
- conda info -a
|
|
|
|
- conda env create -q -n test-environment python=$TRAVIS_PYTHON_VERSION --file environment.yml
|
|
- conda activate test-environment
|
|
|
|
before_script:
|
|
# Install Packrat
|
|
- snakemake packrat_install
|
|
- snakemake packrat_init
|
|
- snakemake packrat_restore
|
|
|
|
script:
|
|
- cp -r tests/data/raw/* data/raw
|
|
- snakemake --profile tests/settings -R sms_features
|
|
- python -m unittest discover tests/scripts/ -v |