Question: How can I change the default path to which SRA files are downloaded?
3
gravatar for cacaucenturion2
21 months ago by
Canada
cacaucenturion2360 wrote:

By default, SRA files will be download to ~/ncbi/ncbi_public/sra by using sratoolkit from ncbi

However, there is limited space. So I want to change the path.

Is there a way to download SRA files using sratoolkit (fastq-dump) or can I download the SRA files directly without parsing converting it into fastq files?

rna-seq • 3.3k views
ADD COMMENTlink modified 5 months ago by caritogandini10 • written 21 months ago by cacaucenturion2360
4
gravatar for sunhanice
21 months ago by
sunhanice170
United States
sunhanice170 wrote:

I always downloaded SRA files directly using wget, and then converted them to fastq.tar.gz locally with fastq-dump.

The file address for SRA file is like this format:

/sra/sra-instant/reads/ByRun/sra/{SRR|ERR|DRR}/<first 6 characters of accession>/<accession>/<accession>.sra

For example:

ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR119/SRR1192353/SRR1192353.sra

ADD COMMENTlink written 21 months ago by sunhanice170

This is simple! Thanks!

ADD REPLYlink written 15 months ago by cacaucenturion2360
4
gravatar for piet
21 months ago by
piet1.3k
planet earth
piet1.3k wrote:

Yes, one of the shortcomings of sratoolkit is, that it stores huge temporary files in your home directory, which may have limited space and my be mounted via NFS.

The official way for changing several settings is to use 'vdb-config'. This program simply creates a config file named '$HOME/.ncbi/user-settings.mkfg'. But its much easier to create and edit this file with a text editor or on the command line.

The following will change the cache directory to '/tmp':

echo '/repository/user/main/public/root = "/tmp"' > $HOME/.ncbi/user-settings.mkfg
ADD COMMENTlink modified 21 months ago • written 21 months ago by piet1.3k
1
gravatar for caritogandini
5 months ago by
caritogandini10 wrote:

Check out this!

https://github.com/ncbi/sra-tools/wiki/Toolkit-Configuration

ADD COMMENTlink written 5 months ago by caritogandini10
0
gravatar for Tao
15 months ago by
Tao110
Tao110 wrote:

You will find the anwser here: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=dbgap_use and here: http://www.ncbi.nlm.nih.gov/books/NBK36439/#Download.Download_Procedure

ADD COMMENTlink written 15 months ago by Tao110

So complicated! Thanks!

ADD REPLYlink written 15 months ago by cacaucenturion2360
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