DiGeST can run on a desktop, or in a distributed environment with a Hadoop cluster back-end.
- R version > 3.2.2
- httr (1.0.0), ggplot2 (1.0.1), shinyjs (0.2.3), shinyBS (0.61), DT (0.1.39), queryBuildR (0.1), RCurl (1.95-4.7), bitops (1.0-6), RJDBC (0.2-5), rJava (0.9-7), plyr (1.8.3), rpivotTable (0.1.5.2), jsonlite (0.9.17), RMySQL (0.10.3), DBI (0.3.1), shiny (0.12.2.9000)
- Clone GitHub repository
git clone https://github.com/Yannael/digest
- In RStudio, open 'digest/code/digest.Rproj'
- Open 'global.R'
- Change 'USE_CLUSTER<-TRUE' to 'USE_CLUSTER<-FALSE'
- Set environment variables to right locations:
SPARK_HOME<-"/path/to/spark/folder" #Where Spark is installed
VARIANTS<-"/path/to/parquet/files" #Where SNPs data are, in parquet format
- Run
library(shiny)
runApp(launch.browser = T)