This is an R packages to generate genomic and bioinformatic pipelines and submit jobs to a HPC running slurm system.

Install

Install devtools first, and then use devtools to install huskeR from github.

#install.packages(devtools)
devtools::install_github("yangjl/huskeR")

# OR specify a path to install
library(devtools)
withr::with_libpaths(new = "/home/jyanglab/jyang21/R/x86_64-pc-linux-gnu-library/3.5", install_github('yangjl/huskeR'))

library(huskeR, lib.loc="/home/jyanglab/jyang21/R/x86_64-pc-linux-gnu-library/3.5")

List all the functions in the package and find help.

## list all the functions
ls(getNamespace("huskeR"), all.names=TRUE)
## help info for a given function
?run_fastq_qc

License

It is a free and open source software, licensed under GPLv3. This is an ongoing research project from Yang Lab. It was intended for internal lab usage. It has not been extensively tested. Use at your own risk.