Question: Failure to download data from EBI-SRA to a local Galaxy instance
1
gravatar for yu.1.wang
3.6 years ago by
yu.1.wang20
Germany
yu.1.wang20 wrote:

Hi, I find that the galaxy downloading link from EBI-SRA doesn't work on my local galaxy instance. When I try it directly on the EBI website, it sent me to the main Galaxy instance at PSU. Do I miss some configurations here? When I click the link of the EBI-SRA files for galaxy in my local galaxy instance, nothing happens. Thanks a lot.

Best,

Yu Wang

 

 

 

download sra ebi • 1.2k views
ADD COMMENTlink modified 12 months ago by mohancm890 • written 3.6 years ago by yu.1.wang20
0
gravatar for Jennifer Hillman Jackson
3.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hi,

The links for "Send to Galaxy" at this web site will always load into Galaxy Main (http://usegalaxy.org). However, if you copy the link and then paste it into the Upload tool as a URL, the data will load into your local.

Please give this a try and let us know if it doesn't work, Jen, Galaxy team

ADD COMMENTlink written 3.6 years ago by Jennifer Hillman Jackson25k
0
gravatar for mohancm89
12 months ago by
mohancm890
mohancm890 wrote:

Hi, I am also facing the same problem and tried as suggested by Jackson. Still the problem not solved. I want to download the dataset SRR1029672, so I used first get data option "EBI SRA ENA SRA". With this tool I got the following error

Dataset Error

An error occured while running the tool ebi_sra_main.

Tool execution generated the following messages:

The remote data source application may be off line, please try again later. Error:

Then I saw this suggestions and tried.

The URL I used is "ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR102/002/SRR1029672/SRR1029672.fastq.gz"

This time I got something new problem

Unable to fetch ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR102/002/SRR1029672/SRR1029672.fastq.gz <urlopen error="" ftp="" error:="" &gt;<="" p="">

Note: I am working in an institute network which asks for proxy authentication. I have sorted this by using setproxy.sh code.

Kindly help Thank you

ADD COMMENTlink written 12 months ago by mohancm890

Hi, I am also facing the same problem and tried as suggested by Jackson. Still the problem not solved. I want to download the dataset SRR1029672, so I used first get data option "EBI SRA ENA SRA". With this tool I got the following error

Dataset Error

An error occured while running the tool ebi_sra_main.

Tool execution generated the following messages:

The remote data source application may be off line, please try again later. Error:

Then I saw this suggestions and tried.

The URL I used is "ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR102/002/SRR1029672/SRR1029672.fastq.gz"

This time I got something new problem

Unable to fetch ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR102/002/SRR1029672/SRR1029672.fastq.gz <urlopen error="" ftp="" error:="" &gt;<="" p="">

Note: I am working in an institute network which asks for proxy authentication. I have sorted this by using setproxy.sh code.

Kindly help Thank you

ADD REPLYlink written 12 months ago by mohancm890
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