Question: How to change the default fold of the downloading sra data using prefetch ?
0
gravatar for zengxi.hada
2.0 years ago by
zengxi.hada70
Hong Kong
zengxi.hada70 wrote:

Hi, 

I am trying to use "prefetch" to download sra data. But I found the default output folder is /home/[USER]/ncbi/public/sra/, which is not big enough. I check the mannual file for sra-toolkit, but didn't find a option to set the output directory. Can anyone tell me how to change the default fold of the downloading for prefetch ? Thanks a lot.

 

Best,

Michael

 

sequencing next-gen • 2.6k views
ADD COMMENTlink modified 22 months ago by Shicheng Guo4.6k • written 2.0 years ago by zengxi.hada70
6
gravatar for Shicheng Guo
22 months ago by
Shicheng Guo4.6k
Shicheng Guo4.6k wrote:

Set the vdb-config as the way I mentioned.

1, come to bin directory, such as: /home/sratoolkit.2.5.5-centos_linux64/bin 
2, run it in the terminal:    ./vdb-config -i
3, change the fold of Workspace Name to a big harddisk.
4, by the way, use Tab to move

Re-run fastq-dump, the cache files will come to new setted directory.

ADD COMMENTlink modified 14 months ago • written 22 months ago by Shicheng Guo4.6k

thank you very much!

ADD REPLYlink written 21 months ago by zengxi.hada70
2
gravatar for h.mon
2.0 years ago by
h.mon11k
Brazil
h.mon11k wrote:

See this install and config guide: there is a tools called ./vdb-config to configure sra-tools.

ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by h.mon11k

Thank you very much !

ADD REPLYlink written 21 months ago by zengxi.hada70
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