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

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

next-gen-sequencing
• 14,462 views • link
updated by Ram Ram • written by zengxi.hada zengxi.hada

2 answers

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.

• 1 views • link
updated by Ram Ram • written by Shicheng Guo Shicheng Guo

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

• 1 views • link
written by h.mon h.mon

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