install.fastp: Download and prepare fastp trimmer

In JokingHero/ORFik: Open Reading Frames in Genomics

Download and prepare fastp trimmer

Description

On Linux, will not run "make", only use precompiled fastp file.
On Mac OS it will use precompiled binaries.
For windows must be installed through WSL (Windows Subsystem Linux)

Usage

install.fastp(folder = "~/bin")

Arguments

folder

path to folder for download, file will be named "fastp", this should be most recent version. On mac it will search for a folder called fastp-master inside folder given. Since there is no precompiled version of fastp for Mac OS.

Value

path to runnable fastp

References

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129281/

See Also

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

Examples

## With default folder:
#install.fastp()

## Or set manual folder:
folder <- "~/I/WANT/IT/HERE/"
#install.fastp(folder)

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.