run_iput: 'Run iget and iput to get/put data from/to iPlant.'

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

Description

Downloading SRA using 'ascp' utility or Aspera Connect.

Usage

run_iput(files, jobs1cpu = 1, localpwd = "largedata/gatk_vcf",
  email = NULL, runinfo = c(FALSE, "bigmemh", 1))

Arguments

email	Your email address that farm will email to once the job was done/failed.
sra	An input data.frame for SRA ids. Must contains column: SRR.
maxspeed	The max speed for downloading.
outdir	The output directory.
arrayjobs	A character specify the number of array you try to run, i.e. 1-100.
jobid	The job name show up in your sq NAME column.

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 batch of shell scripts.

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