run_fq_dump: 'Run fastq-dump.'

In yangjl/farmeR: Generate pipelines for maize Genomic and Genetic analysis

Description

fastq-dump to dump SRA file.

Usage

run_fq_dump(filepath = "/group/jrigrp4/BS_teo20/WGBS",
  slurmsh = "slurm-script/dump_WGBS.sh", rmsra = TRUE, email = NULL)

run_fq_dump2(filepath = "/group/jrigrp4/BS_teo20/WGBS", rmsra = TRUE,
  gzip = TRUE, email = NULL, run = c(TRUE, "bigmemh", "8196", "1"))

Arguments

filepath	The absolute path of the SRA files.
slurmsh	File name of the output shell command.
rmsra	Remove the original SRA file after dumpping.
email	Your email address that farm will email to once the job was done/failed.
gzip	GZIP the fastq files.
run	Parameters control the array job partition. A vector of c(TRUE, "bigmemh", "8196", "1"): 1) run or not, 2) -p partition name, 3) –mem, adn 4) –ntasks.

Details

see more detail about SRA with Aspera downloading: http://www.ncbi.nlm.nih.gov/books/NBK158899/#SRA_download.downloading_sra_data_using

Value

return a single shell script to run.

Examples

## run a single node job:
run_fq_dump(filepath="/group/jrigrp4/BS_teo20/WGBS",
            slurmsh="slurm-script/dump_WGBS.sh", rmsra=TRUE, email=NULL)

##  run array job:
run_fq_dump2(filepath="test", rmsra=TRUE, gzip=TRUE, email=NULL, run=c(TRUE, "bigmemh", "8196", "1"))

yangjl/farmeR documentation built on May 4, 2019, 2:28 p.m.