Adapted for the specific version of Rsubread

print("I am loading useful packages...")

print(Sys.time())

packages <-c("multidplyr","dplyr","tidyr","reshape2","data.table","optparse","parallel","Rsubread","methods","GenomicRanges","GenomicFeatures","GenomicAlignments","AnnotationDbi","ggplot2","cowplot","tibble")

packages <-c("multidplyr","dplyr","tidyr","reshape2","data.table","optparse","parallel","methods","GenomicRanges","GenomicFeatures","GenomicAlignments","AnnotationDbi","ggplot2","cowplot","tibble")

paks<-lapply(packages, function(x) suppressMessages(require(x, character.only = TRUE)))

rm(paks)

# Check the version of Rsubread

bla<-data.frame(installed.packages()[grep("Rsubread",installed.packages()),c("LibPath","Version")],row.names = NULL)

if(length(grep("Rsubread",installed.packages()))==0){

  print("I did not find Rsubread so I am installing it...")

  install.packages("https://bioarchive.galaxyproject.org/Rsubread_1.26.0.tar.gz", repos = NULL, type = "source")

  library("Rsubread", lib.loc=as.character(bla[bla$Version %in% "1.26.0", "LibPath"]))

}else{

  if(installed.packages()[grep("Rsubread",installed.packages()),"Version"] != "1.26.0"){

    print("I need Rsubread 1.26.0 so I am installing it...")

    install.packages("https://bioarchive.galaxyproject.org/Rsubread_1.26.0.tar.gz", repos = NULL, type = "source")

    library("Rsubread", lib.loc=as.character(bla[bla$Version %in% "1.26.0", "LibPath"]))

  }else{

    print("I am loading Rsubread 1.26.0...")

    library("Rsubread", lib.loc=as.character(bla[bla$Version %in% "1.26.0", "LibPath"]))

  }

}

ncores=opt$cores

bcstart=opt$bcstart

bcend=opt$bcend