.gitlab-ci.yml

# The Docker image that will be used to build your app
image: rocker/tidyverse:4.3.2

before_script:
  - apt-get update
  - apt-get install -y --no-install-recommends libcurl4-openssl-dev libxext6 libxtst6 libxt6
  - apt-get install -y --no-install-recommends qpdf pandoc pandoc-citeproc
  - R -e 'install.packages(c("testthat", "rmarkdown"));'
  - R -e "install.packages(c('rsconnect', 'matrix', 'parallel', 'data.table', 'ggplot2', 'gridExtra', 'glmmTMB', 'magrittr', 'MASS', 'reshape2', 'rlang', 'stats', 'utils', 'BiocManager', 'car'))" 
  - R -e "BiocManager::install('S4Vectors', update = FALSE)"
  - R -e "BiocManager::install('DESeq2', update = FALSE)" 
  - R -e 'install.packages(setdiff(desc::desc()$get_deps()$package, c(installed.packages(), "R")));'




pages:
  stage: build
  script:
  - R -e "devtools::document(); pkgdown::build_site(override = list(destination = 'public/'))"
  artifacts:
    paths:
    - public/