xenomeIndex: Generating xenome genome indexes

In kendomaniac/docker4seq: Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

Generating xenome genome indexes

Description

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

Usage

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(s)

Raffaele Calogero

Examples

## Not run: 
    #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")


## End(Not run)

kendomaniac/docker4seq documentation built on Sept. 3, 2024, 6:42 p.m.