Question: Failure to download data from EBI-SRA to a local Galaxy instance
1
gravatar for yu.1.wang
2.6 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 • 870 views
ADD COMMENTlink modified 25 days ago by mohancm890 • written 2.6 years ago by yu.1.wang20
0
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson23k 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 2.6 years ago by Jennifer Hillman Jackson23k
0
gravatar for mohancm89
25 days 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 25 days 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 25 days ago by mohancm890
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 95 users visited in the last hour