Description Usage Arguments Details Value Author(s) References See Also Examples
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/).
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).
character vector of fasp file sources for the ascp command, e.g. email@example.com:vol1/fastq/SRR000/SRR000648/SRR000648.fastq.gz (EBI), firstname.lastname@example.org:/sra/sra-instant/reads/ByExp/sra/SRX/SRX000/SRX000122/SRR000657/SRR000657.sra (NCBI).
destination directory to save downloaded files.
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.
A data.frame containing all matched SRA accessions and ftp or fasp addresses.
Jack Zhu <email@example.com>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
## 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
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.