Question: How can I change the default path to which SRA files are downloaded?
3
gravatar for Cacau
2.1 years ago by
Cacau390
Canada
Cacau390 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 • 4.2k views
ADD COMMENTlink modified 9 months ago by caritogandini10 • written 2.1 years ago by Cacau390
5
gravatar for sunhanice
2.1 years ago by
sunhanice180
United States
sunhanice180 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 2.1 years ago by sunhanice180

This is simple! Thanks!

ADD REPLYlink written 19 months ago by Cacau390
5
gravatar for piet
2.1 years ago by
piet1.4k
planet earth
piet1.4k 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 2.1 years ago • written 2.1 years ago by piet1.4k
1
gravatar for caritogandini
9 months ago by
caritogandini10 wrote:

Check out this!

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

ADD COMMENTlink written 9 months ago by caritogandini10
0
gravatar for Tao
19 months ago by
Tao120
Tao120 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 19 months ago by Tao120

So complicated! Thanks!

ADD REPLYlink written 19 months ago by Cacau390
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