查看服務(wù)器版本
lsb_release -a
#LSB Version: :core-4.1-amd64:core-4.1-noarch:cxx-4.1-amd64:cxx-4.1-noarch:desktop-4.1-amd64:desktop-4.1-noarch:languages-4.1-amd64:languages-4.1-noarch:printing-4.1-amd64:printing-4.1-noarch
#Distributor ID: NFSServer
#Description: NFS Server release 3.2 (RTM1)
#Release: 3.2
#Codename: RTM1
rpm --version
# RPM version 4.11.3
注：RPM為Centos系統(tǒng)
下載并解壓安裝包
wget -c https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/3.1.1/sratoolkit.3.1.1-centos_linux64.tar.gz
tar -zxvf sratoolkit.3.1.1-centos_linux64.tar.gz
加入環(huán)境變量或每次運(yùn)行前運(yùn)行命令
export PATH=/work/home/acwnw4bl7y/sratoolkit.3.1.1-centos_linux64/bin/:$PATH
測試
prefetch -h
Usage:
prefetch [options] <SRA accession> [...]
Download SRA files and their dependencies
prefetch [options] --perm <JWT cart file> <SRA accession> [...]
Download SRA files and their dependencies from JWT cart
prefetch [options] --cart <kart file>
Download cart file
prefetch [options] <URL> --output-file <FILE>
Download URL to FILE
prefetch [options] <URL> [...] --output-directory <DIRECTORY>
Download URL or URL-s to DIRECTORY
prefetch [options] <SRA file> [...]
Check SRA file for missed dependencies and download them
Options:
-T|--type <value> Specify file type to download. Default: sra
-t|--transport <http|fasp|both> Transport: one of: fasp; http; both
[default]. (fasp only; http only; first try
fasp (ascp), use http if cannot download
using fasp).
--location <value> Location of data.
-N|--min-size <size> Minimum file size to download in KB
(inclusive).
-X|--max-size <size> Maximum file size to download in KB
(exclusive). Default: 20G
-f|--force <yes|no|all|ALL> Force object download: one of: no, yes,
all, ALL. no [default]: skip download if the
object if found and complete; yes: download
it even if it is found and is complete; all:
ignore lock files (stale locks or it is
being downloaded by another process use
at your own risk!); ALL: ignore lock files,
restart download from beginning.
-r|--resume <yes|no> Resume partial downloads: one of: no, yes
[default].
-C|--verify <yes|no> Verify after download: one of: no, yes
[default].
-p|--progress Show progress.
-H|--heartbeat <value> Time period in minutes to display download
progress. (0: no progress), default: 1
--eliminate-quals Download SRA Lite files with simplified
base quality scores, or fail if not
available.
-c|--check-all Double-check all refseqs.
-S|--check-rs <yes|no|smart> Check for refseqs in downloaded files: one
of: no, yes, smart [default]. Smart: skip
check for large encrypted non-sra files.
-o|--order <kart|size> Kart prefetch order when downloading
kart: one of: kart, size. (in kart order, by
file size: smallest first), default: size.
-R|--rows <rows> Kart rows to download (default all). Row
list should be ordered.
--perm <PATH> PATH to jwt cart file.
--ngc <PATH> PATH to ngc file.
--cart <PATH> To read kart file.
-a|--ascp-path <ascp-binary|private-key-file> Path to ascp program and
private key file (asperaweb_id_dsa.putty)
--ascp-options <value> Arbitrary options to pass to ascp command
line.
-o|--output-file <FILE> Write file to FILE when downloading
single file.
-O|--output-directory <DIRECTORY> Save files to DIRECTORY/
-h|--help Output brief explanation for the program.
-V|--version Display the version of the program then
quit.
-L|--log-level <level> Logging level as number or enum string. One
of (fatal|sys|int|err|warn|info|debug) or
(0-6) Current/default is warn.
-v|--verbose Increase the verbosity of the program
status messages. Use multiple times for more
verbosity. Negates quiet.
-q|--quiet Turn off all status messages for the
program. Negated by verbose.
--option-file <file> Read more options and parameters from the
file.
prefetch : 3.1.1
