Generating xenome genome indexes

This function executes the docker container xenome.2017.01 where xenome is installed.

xenomeIndex(
  group = c("sudo", "docker"),
  xenome.folder = getwd(),
  hg.urlgenome = NULL,
  mm.urlgenome = NULL,
  threads = 8
)

Arguments

group,

a character string. Two options: "sudo" or "docker", depending to which group the user belongs

xenome.folder,

a character string indicating the folder where the indexed reference genomes for xenome will be located

hg.urlgenome,

a character string indicating the URL from uscs download web page for the unmasked human genome sequence of interest

mm.urlgenome,

a character string indicating the URL from uscs download web page for the unmasked mouse genome sequence of interest

threads,

an integer indicating how many threads are used by xenome

Value

The indexed xenome genomes references

Author

Raffaele Calogero

Examples

if (FALSE) {
    #running xenome index
    xenomeIndex(group="docker",xenome.folder="/data/scratch/test", hg.urlgenome=
    "http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz",
    mm.urlgenome="http://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/chromFa.tar.gz")

}