indropIndex.Rd
This function executes a docker that produces as output the genome index index for bowtie
indropIndex( group = c("sudo", "docker"), index.folder, ensembl.urlgenome, ensembl.urlgtf )
group, | a character string. Two options: sudo or docker, depending to which group the user belongs |
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index.folder, | a character string indicating the folder where the index will be created. The index will have the prefix genome. |
ensembl.urlgenome, | a character string indicating the URL from ENSEMBL ftp for the unmasked genome sequence of interest |
ensembl.urlgtf, | a character string indicating the URL from ENSEMBL ftp for the GTF for genome of interest |
Raffaele Calogero and Riccardo Panero, raffaele.calogero [at] unito [dot] it, Bioinformatics and Genomics unit, University of Torino Italy
if (FALSE) { library(rCASC) #running indropCounts index build indropIndex(group="docker", index.folder=getwd(), ensembl.urlgenome="ftp://ftp.ensembl.org/pub/release-87/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz", ensembl.urlgtf="ftp://ftp.ensembl.org/pub/release-87/gtf/mus_musculus/Mus_musculus.GRCm38.87.gtf.gz") }