fastGeoSubmission: Submit data files to GEO database by sftp in a fast way,...

In paodan/SRRDownloader: Download Raw Fastq Files from SRA Database.

Submit data files to GEO database by sftp in a fast way, using ncft.

Description

The detailed submission process can be found in GEO File Transfer Protocol: https://www.ncbi.nlm.nih.gov/geo/info/submissionftp.html.

Usage

fastGeoSubmission(
  fileNames,
  destDir,
  geoFTP = "ftp-private.ncbi.nlm.nih.gov",
  geoPassword = "33%9uyj_fCh?M16H",
  nPerBatch = 10,
  sleepSecond = 100
)

Arguments

fileNames	a vector of filenames with full path name to submit
destDir	the directory in GEO FTP server. This directory must be created in advance (in shell): sftp [e-mail] password: 33 mkdir destDir More detailes can be found in GEO File Transfer Protocol
geoFTP	GEO FTP server address. Default is "ftp-private.ncbi.nlm.nih.gov". This password can be found in GEO File Transfer Protocol.
geoPassword	GEO FTP server password. Default is "33 This password can be found in GEO File Transfer Protocol.
nPerBatch	the number of uploading process in each batch. Default is 10.
sleepSecond	the time (in second) to wait after each batch. Default is 100 (seconds).

Examples

{
## Not run: 
# Upload files in "./tmp" folder to "ftpDir"
files = dir("./tmp", full.names = T)
fastGeoSubmission(files, "ftpDir")

## End(Not run)
}

paodan/SRRDownloader documentation built on Aug. 25, 2023, 3:23 a.m.