R/run_ColonyV2.R

In zakrobinson/RSibPurge: A convenient R-interface for COLONY Version 2.0.6.5

#' Run COLONY from R
#'
#' This function will run COLONY , Version 2.0.6.5 Executables (Mac & Linux); Author: Jinliang Wang, Institute of Zoology, Zoological Society of London
#'
#'
#'@param colony_params input file for the program Colony
#'@author Zak Robinson, Contact: zachary.robinson(at)umontana.com
#'@return Output files will be written to file as specified in parameter files
#'@export


run_ColonyV2<-function(colony_params){
  if(Sys.info()["sysname"]=="Windows"){
    stop("This Function Doesn't work on Windows OS")
      }else if(Sys.info()["sysname"]=="Linux"){

        for(i in .libPaths()){
          if(file.exists(paste0(i,"/RSibPurge/bin/linux/colony2s.ifort.out"))){
            colonyV2<-paste0(i,"/RSibPurge/bin/linux/colony2s.ifort.out")
          }
        }
      }else{
        for(i in .libPaths()){
          if(file.exists(paste0(i,"/RSibPurge/bin/mac/colony2s.out"))){
            colonyV2<-paste0(i,"/RSibPurge/bin/mac/colony2s.out")
        }
      }
    }

  system(paste0(colonyV2," ", "IFN:", colony_params))
  return("output file location was specified in param file")
}