run_gctb: 'Run GCTB in a wrapper developed by Jinliang Yang Lab at...

In yangjl/huskeR: Genomic and Genetic analysis Pipeline on HPC

Description

you need to download and install GTCB before running this wrapper.

Usage

run_gctb(df, bayes, shid = "run_gtcb", email = NULL,
  runinfo = c(TRUE, "jclarke", "1", "8G", "8:00:00"))

Arguments

df	Input files with all the parameters for the Bayesian alphabet. [data.frame, col: bfile, ... (see examples for more details)]
shid	The prefix of the shell code name in slurm-script folder.
email	Your email address that farm will email to once the job was done or failed.
runinfo	Parameters control the array job partition. A vector of c(TRUE, "batch", "1", "8G", 8:00:00"): 1) run within R or not, 2) -p partition name, 3) –ntasks, 4) –mem and 5) –times.

Details

see more detail about GTCB: http://cnsgenomics.com/software/gctb/#Overview

Value

return a batch of shell scripts to run.

Examples

### build kallisto idex
 kallisto index -i ZmB73_5a_WGS_exons.kallisto.idx ZmB73_5a_WGS_exons.fasta.gz
 kallisto quant -i ~/dbcenter/AGP/AGPv2/ZmB73_5a_WGS_exons.kallisto.idx --plaintext -o .
--single -l 200 -s 20 SRR957415.sra.fastq SRR957416.sra.fastq > test.txt

yangjl/huskeR documentation built on Sept. 2, 2021, 5:38 a.m.