STAR.install: Download and prepare STAR

In Roleren/ORFik: Open Reading Frames in Genomics

Download and prepare STAR

Description

Will not run "make", only use precompiled STAR file.
Can only run on unix systems (Linux and Mac), and requires minimum 30GB memory on genomes like human, rat, zebrafish etc.

Usage

STAR.install(folder = "~/bin", version = "2.7.4a")

Arguments

folder	path to folder for download, fille will be named "STAR-version", where version is version wanted.
version	default "2.7.4a"

Details

ORFik for now only uses precompiled STAR binaries, so if you already have a STAR version it is adviced to redownload the same version, since STAR genome indices usually does not work between STAR versions.

Value

path to runnable STAR

References

https://www.ncbi.nlm.nih.gov/pubmed/23104886

See Also

Other STAR: STAR.align.folder(), STAR.align.single(), STAR.allsteps.multiQC(), STAR.index(), STAR.multiQC(), STAR.remove.crashed.genome(), getGenomeAndAnnotation(), install.fastp()

Examples

## Default folder install:
#STAR.install()
## Manual set folder:
folder <- "/I/WANT/IT/HERE"
#STAR.install(folder, version = "2.7.4a")

Roleren/ORFik documentation built on Oct. 19, 2024, 7:37 a.m.