Question: SRA toolkit not installed
0
gravatar for izzy.yichao.cai
21 months ago by
izzy.yichao.cai130 wrote:

Hi all, I tried to use SRA toolkit to down and convert .sra file to fastq file in Linux. However, I have problem using SRA toolkit.

After I wget SRA toolkit and extract it, I tried to run the test command as stated on the official website "fastq-dump -X 5 -Z SRR390728" in the directory of /home/[user_name]/sratoolkit[version]/bin. The error is that: "The program 'fastq-dump' is currently not installed. To run 'fastq-dump' please ask your administrator to install the package 'sra-toolkit'" What may be wrong?

Also, if I want to use SRA toolkit on a server that I have no root. How do I download and use SRA toolkit(cause I have the same error when I do the previous on the server)?

software error • 1.6k views
ADD COMMENTlink modified 21 months ago by Sukhdeep Singh9.2k • written 21 months ago by izzy.yichao.cai130
1
gravatar for Sukhdeep Singh
21 months ago by
Sukhdeep Singh9.2k
Netherlands
Sukhdeep Singh9.2k wrote:

Follow the instructions here

https://github.com/ncbi/sra-tools/wiki/HowTo:-Binary-Installation

ADD COMMENTlink written 21 months ago by Sukhdeep Singh9.2k
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