.travis.yml

# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
language: R

sudo: required

cache: packages

dist: trusty

before_install:
  - curl -OLs http://eddelbuettel.github.io/r-travis/run.sh && chmod 0755 run.sh
  # optionally add our launchpad repo, but not needed here
  # - sudo add-apt-repository -y ppa:edd/misc
  - Rscript -e 'install.packages(c("covr", "devtools", "roxygen2", "knitr", "testthat", "configr", "RSQLite", "futile.logger", "RMySQL", "data.table", "rmarkdown", "vcfR"))'
  - Rscript -e "source('https://bioconductor.org/biocLite.R'); biocLite(c('AnnotationDbi', 'org.Hs.eg.db'))"
  - Rscript -e 'devtools::install_github("JhuangLab/BioInstaller")'
  - Rscript -e 'devtools::install_github("JhuangLab/ngstk")'
  - ./run.sh bootstrap

install:
  - Rscript -e 'library("devtools");install_github("JhuangLab/annovarR")'

after_failure:
  - ./run.sh dump_logs

after_success:
  - bash <(curl -s https://codecov.io/bash)
  - Rscript -e 'library("covr"); covr::codecov()'