run_aspera: 'Run Aspera Connect to download from SRA.'
In yangjl/huskeR: Genomic and Genetic analysis Pipeline on HPC

Description Usage Arguments Details Value Examples

Downloading SRA using 'ascp' utility or Aspera Connect. How to download and install 'ascp': http://downloads.asperasoft.com/en/downloads/8?list

run_aspera(sradf, maxspeed = "100m", outdir = ".", cmdno = 1,
  email = NULL, runinfo)

set_aspera(sradf, srow, erow, j, maxspeed, outdir)

`sradf`	An input data.frame for SRA ids. Must contains column: SRR. [df["SRR"]]
`maxspeed`	The max speed for downloading. [chr, =200m]
`outdir`	The output directory. [chr, ="."]
`cmdno`	Number of commands to excute in each array job. [num, =1]
`email`	Your email address that farm will email to once the job was done/failed. [chr, =NULL]
`runinfo`	[vector, = c(FALSE, "bigmemh", 5, "5G", "16:00:00")]
`srow`	Start row of the df. [num, 1]
`erow`	End row of the df. [num, 10]

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

return a batch of shell scripts.

sra <- data.frame(SRR=c("ERR877647", "ERR877648"),
SRX=c( "ERX957210", "ERX957211"),
pid=c( "1_Base1_Bbreve-sc-2188486", "P1_ECvsrS_1-sc-2201977"))
run_aspera(sra, maxspeed="200m", outdir=".", arrayjobs="1-2", jobid="aspera", email=NULL)