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Question: Inability to upload SRR file from website
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gravatar for h.stotz
5 months ago by
h.stotz • 20
European Union
h.stotz • 20 wrote:

I am trying to upload SRA or SRR files from ENA, but Galaxy fails and my files are red. The info says "The uploaded file contains invalid HTML content". Can you help me with this? For instance, I like to upload SRR3134040.

Many thanks,

Henrik
get-data sra ebi-sra galaxy srr • 168 views
ADD COMMENT • link •
modified 5 months ago by Jennifer Hillman Jackson ♦ 25k • written 5 months ago by h.stotz • 20
0
gravatar for Jennifer Hillman Jackson
5 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Are you using the links labeled with (Galaxy)?

I just retested this at Galaxy Main https://usegalaxy.org and it worked (was a problem before, but not with this specific error): https://github.com/galaxyproject/usegalaxy-playbook/issues/117

I'll retest with your accession. Also please try again making sure to use the Galaxy link and let us know how that turns out. Warnings about HTML content usually means that the data is in an unexpected format (looks like code/html and isn't specifically whitelisted to permit display). This is a security function and properly formatted sra datasets shouldn't trigger the error.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 5 months ago by Jennifer Hillman Jackson ♦ 25k

Oh, ok, I've seen this before.

If you want to capture the URL for use in the Upload tool, use the links labeled with (FTP). Yours would be: 

NCBI SRA file (FTP): ftp://ftp.sra.ebi.ac.uk/vol1/srr/SRR313/000/SRR3134040

The (Galaxy) links actually point to a script, not data: 

NCBI SRA file (Galaxy): javascript:;

Or, you can use the tool Get Data > EBI SRA tool from within Galaxy and use the (Galaxy) links for a direct import. The tests completed and both the fastq and sra data for this accession load fine.

FAQ, the graphic needs an update but the usage help is still current: https://galaxyproject.org/support/loading-data/#get-data-ebi-sra

ADD REPLY • link modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson ♦ 25k
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