国内高速下载测序SRA数据

# 下载
wget wget https://download.asperasoft.com/download/sw/connect/3.9.9/ibm-aspera-connect-3.9.9.177872-linux-g2.12-64.tar.gz 
# 解压
tar -zxvf ibm-aspera-connect-3.9.9.177872-linux-g2.12-64.tar.gz
# 安装 软件安装路径是用户根目录的 .aspera/
./ibm-aspera-connect-3.9.9.177872-linux-g2.12-64.sh 

# 下载&解压
wget　https://github.com/enasequence/enaBrowserTools/archive/v1.6.tar.gz
tar -zxvf v1.6.tar.gz
​
# 配置别名 方便查看脚本位置信息
alias enaDataGet=/disk/share/toolkits/enaBrowserTools/python3-1.6/enaDataGet
alias enaGroupGet=/disk/share/toolkits/enaBrowserTools/python3-1.6/enaGroupGet

# 配置许可(这一步需要账户有root权限，普通用户无法设置，也可以不需要设置)
sudo cp ~/.aspera/connect/etc/aspera-license /usr/local/bin/
# 添加环境变量
echo 'export PATH=~/.aspera/connect/bin:$PATH' >> ~/.bashrc
source ~/.bashrc 
#  配置秘钥
mkdir /home/zouhua/.aspera/config/ 
# 复制到配置目录
cp ~/.aspera/connect/etc/asperaweb_id_dsa.openssh /home/zouhua/.aspera/config/

# step1 配置aspera_settings.ini
cd /disk/share/toolkits/enaBrowserTools-1.6 & vi aspera_settings.ini

[aspera]
ASPERA_BIN = /path/to/ascp
ASPERA_PRIVATE_KEY = /path/to/aspera_dsa.openssh
ASPERA_OPTIONS =
ASPERA_SPEED = 100M

[aspera]
ASPERA_BIN = /home/zouhua/.aspera/connect/bin/ascp
ASPERA_PRIVATE_KEY = /home/zouhua/.aspera/connect/etc/asperaweb_id_dsa.openssh
ASPERA_OPTIONS =
ASPERA_SPEED = 500M

# step2 配置aspera
export ENA_ASPERA_INIFILE="/disk/share/toolkits/enaBrowserTools-1.6/aspera_settings.ini"

usage: enaDataGet [-h] [-f {embl,fasta,submitted,fastq,sra}] [-d DEST] [-w]
                  [-m] [-i] [-a] [-as ASPERA_SETTINGS] [-v]
                  accession
​
Download data for a given accession
​
positional arguments:
  accession             Sequence, coding, assembly, run, experiment or
                        analysis accession or WGS prefix (LLLLVV) to download
​
optional arguments:
  -h, --help            show this help message and exit
  -f {embl,fasta,submitted,fastq,sra}, --format {embl,fasta,submitted,fastq,sra}
                        File format required. Format requested must be
                        permitted for data type selected. sequence, assembly
                        and wgs accessions: embl(default) and fasta formats.
                        read group: submitted, fastq and sra formats. analysis
                        group: submitted only.
  -d DEST, --dest DEST  Destination directory (default is current running
                        directory)
  -w, --wgs             Download WGS set for each assembly if available
                        (default is false)
  -e, --extract-wgs     Extract WGS scaffolds for each assembly if available
                        (default is false)
  -exp, --expanded      Expand CON scaffolds when downloading embl format
                        (default is false)
  -m, --meta            Download read or analysis XML in addition to data
                        files (default is false)
  -i, --index           Download CRAM index files with submitted CRAM files,
                        if any (default is false). This flag is ignored for
                        fastq and sra format options.
  -a, --aspera          Use the aspera command line client to download,
                        instead of FTP.
  -as ASPERA_SETTINGS, --aspera-settings ASPERA_SETTINGS
                        Use the provided settings file, will otherwise check
                        for environment variable or default settings file
                        location.
  -v, --version         show program's version number and exit
 
############################################################################
usage: enaGroupGet [-h] [-g {sequence,wgs,assembly,read,analysis}]
                   [-f {embl,fasta,submitted,fastq,sra}] [-d DEST] [-w] [-m]
                   [-i] [-a] [-as ASPERA_SETTINGS] [-t] [-v]
                   accession
​
Download data for a given study or sample, or (for sequence and assembly) taxon
​
positional arguments:
  accession             Study or sample accession or NCBI tax ID to fetch data
                        for
​
optional arguments:
  -h, --help            show this help message and exit
  -g {sequence,wgs,assembly,read,analysis}, --group {sequence,wgs,assembly,read,analysis}
                        Data group to be downloaded for this
                        study/sample/taxon (default is read)
  -f {embl,fasta,submitted,fastq,sra}, --format {embl,fasta,submitted,fastq,sra}
                        File format required. Format requested must be
                        permitted for data group selected. sequence, assembly
                        and wgs groups: embl and fasta formats. read group:
                        submitted, fastq and sra formats. analysis group:
                        submitted only.
  -d DEST, --dest DEST  Destination directory (default is current running
                        directory)
  -w, --wgs             Download WGS set for each assembly if available
                        (default is false)
  -e, --extract-wgs     Extract WGS scaffolds for each assembly if available
                        (default is false)
  -exp, --expanded      Expand CON scaffolds when downloading embl format
                        (default is false)
  -m, --meta            Download read or analysis XML in addition to data
                        files (default is false)
  -i, --index           Download CRAM index files with submitted CRAM files,
                        if any (default is false). This flag is ignored for
                        fastq and sra format options.
  -a, --aspera          Use the aspera command line client to download,
                        instead of FTP.
  -as ASPERA_SETTINGS, --aspera-settings ASPERA_SETTINGS
                        Use the provided settings file, will otherwise check
                        for environment variable or default settings file
                        location.
  -t, --subtree         Include subordinate taxa (taxon subtree) when querying
                        with NCBI tax ID (default is false)
  -v, --version         show program's version number and exit

/disk/share/toolkits/enaBrowserTools-1.6/python3/enaDataGet -f sra -a SRR212430 -d ./sra
# /disk/share/toolkits/enaBrowserTools-1.6/python3/enaDataGet -f sra SRR212430 -d ./sra