ascpR: Fasp file downloading using the ascp command line program
In zhujack/SRAdb: A compilation of metadata from NCBI SRA and tools

ascpR

R Documentation

Fasp file downloading using the ascp command line program

Description

This function downloads files by fasp protocol using Aspera's ascp command line program, which is include in Aspera Connect software (http://www.asperasoft.com/).

Usage

ascpR( ascpCMD, ascpSource, destDir = getwd() )

Arguments

`ascpCMD`	ascp main commands, which should be constructed by a user according to the actual installation of Aspera Connect in the system, with proper options to be used. Example commands: "ascp -QT -l 300m -i /usr/local/aspera/connect/etc/asperaweb_id_dsa.putty" (Linux) or "'/Applications/Aspera Connect.app/Contents/Resources/ascp' -QT -l 300m -i '/Applications/Aspera Connect.app/Contents/Resources/asperaweb_id_dsa.putty'" (Mac OS X). More about ascp please see the help ('ascp -h' in a shell).
`ascpSource`	character vector of fasp file sources for the ascp command, e.g. era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR000/SRR000648/SRR000648.fastq.gz (EBI), anonftp@ftp-trace.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByExp/sra/SRX/SRX000/SRX000122/SRR000657/SRR000657.sra (NCBI).
`destDir`	destination directory to save downloaded files.

Details

The function takes advatage of Aspera's fasp transport technology (http://www.asperasoft.com/), which provides high-speed transfering large files over the Internet. Due to complexity with options with ascp and installation difference between different systems, this funciton asks users to supply main ascp comands. Users who are not familiar with ascp command line program should have IT support personnel to install the software and constrct main ascp comands.

Value

A data.frame containing all matched SRA accessions and ftp or fasp addresses.

Author(s)

Jack Zhu <zhujack@mail.nih.gov>

References

http://www.asperasoft.com/

Examples

## Using the SRAmetadb demo database
## Not run: 
	library( SRAdb )
	sra_dbname <- file.path(system.file('extdata', package='SRAdb'), 'SRAmetadb_demo.sqlite')	
	sra_con <- dbConnect(dbDriver("SQLite"), sra_dbname)
	rs <- getFASTQinfo (in_acc=c("SRR000648","SRR000657"), sra_con, srcType='fasp')
	
	ascpSource <- rs$fasp
	ascpCMD <- 'ascp -QT -l 300m -i /usr/local/aspera/connect/etc/asperaweb_id_dsa.putty'
	## common ascpCMD in Mac OS X:
	#ascpCMD = "'/Applications/Aspera Connect.app/Contents/Resources/ascp' -QT -l 300m -i '/Applications/Aspera Connect.app/Contents/Resources/asperaweb_id_dsa.putty'"
	
	ascpR( ascpCMD, ascpSource, destDir = getwd() )
	dbDisconnect( sra_con )
    
## End(Not run)

## The actual SRAmetadb sqlite database can be downloaded using function: getSRAdbFile. Warning: the actual SRAmetadb sqlite database is pretty large (> 35GB as of May, 2018) after uncompression. So, downloading and uncompressing of the actual SRAmetadb sqlite could take quite a few minutes depending on your network bandwidth. Direct links for downloading the SRAmetadb sqlite database:  https://s3.amazonaws.com/starbuck1/sradb/SRAmetadb.sqlite.gz https://gbnci-abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz

zhujack/SRAdb documentation built on Oct. 26, 2022, 7:32 a.m.