xenomeIndex.Rd
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 )
group, | a character string. Two options: |
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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 |
The indexed xenome genomes references
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") }