How to change the default fold of the downloading sra data using prefetch ?

Question

[zengxi.hada]

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 manual 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

Answer 1

[Shicheng Guo]

Set the vdb-config as the way I mentioned.

1. Go 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 set directory.

[zengxi.hada]

thank you very much!

Answer 2

[h.mon]

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

[zengxi.hada]

Thank you very much !