.travis.yml

language: r
pandoc_version: 1.18
r:
  - release
sudo: false
cache:
  packages: yes
  directories:
    - $TRAVIS_BUILD_DIR/_book/_bookdown_files

install:
  - Rscript -e "if (!require('devtools')) install.packages('devtools')"

  - Rscript -e "if (!require('bookdown')) install.packages('bookdown')"
  - Rscript -e "if (!require('knitr')) install.packages('knitr')"
  - Rscript -e "if (!require('BiocInstaller')) {source('https://bioconductor.org/biocLite.R');biocLite('BiocInstaller')}"
  - Rscript -e "if (!require('scRNA.seq.funcs')) devtools::install_github('hemberg-lab/scRNA.seq.funcs')"

  - Rscript -e "if (!require('ggplot2')) install.packages('ggplot2')"
  - Rscript -e "if (!require('pheatmap')) install.packages('pheatmap')"
  - Rscript -e "if (!require('limma')) {source('https://bioconductor.org/biocLite.R');biocLite('limma')}"

  - Rscript -e "if (!require('scater')) {source('https://bioconductor.org/biocLite.R');biocLite('scater')}"
  - Rscript -e "if (!require('statmod')) install.packages('statmod')"
  - Rscript -e "if (!require('mvoutlier')) install.packages('mvoutlier')"
  - Rscript -e "if (!require('Rtsne')) install.packages('Rtsne')"
  - Rscript -e "if (!require('scran')) {source('https://bioconductor.org/biocLite.R');biocLite('scran')}"
  - Rscript -e "if (!require('RUVSeq')) {source('https://bioconductor.org/biocLite.R');biocLite('RUVSeq')}"

  - Rscript -e "if (!require('SC3')) {source('https://bioconductor.org/biocLite.R');biocLite('SC3')}"
  - Rscript -e "if (!require('pcaMethods')) {source('https://bioconductor.org/biocLite.R');biocLite('pcaMethods')}"
  - Rscript -e "if (!require('pcaReduce')) devtools::install_github('JustinaZ/pcaReduce')"
  - Rscript -e "if (!require('lfa')) {source('https://bioconductor.org/biocLite.R');biocLite('lfa')}"
  - Rscript -e "if (!require('Seurat')) devtools::install_github('satijalab/seurat', ref = 'da6cd08')"
  
  - Rscript -e "if (!require('M3Drop')) {source('https://bioconductor.org/biocLite.R');biocLite('M3Drop')}"

  - Rscript -e "if (!require('TSCAN')) {source('https://bioconductor.org/biocLite.R');biocLite('TSCAN')}"
  - Rscript -e "if (!require('monocle')) {source('https://bioconductor.org/biocLite.R');biocLite('monocle')}"
  - Rscript -e "if (!require('destiny')) {source('https://bioconductor.org/biocLite.R');biocLite('destiny')}"

  - Rscript -e "if (!require('ROCR')) install.packages('ROCR')"
  - Rscript -e "if (!require('DESeq2')) {source('https://bioconductor.org/biocLite.R');biocLite('DESeq2')}"
  - Rscript -e "if (!require('edgeR')) {source('https://bioconductor.org/biocLite.R');biocLite('edgeR')}"
  - Rscript -e "if (!require('scde')) devtools::install_github('hms-dbmi/scde', build_vignettes = FALSE)"

before_script:
  - chmod +x ./_build.sh
  - chmod +x ./_deploy.sh

script:
  - ./_build.sh
  - ./_deploy.sh