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Question: bulk data transfer from ENA
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gravatar for i b
21 months ago by
i b • 330
i b • 330 wrote:

hi, is there a way to transfer in bulk data from the ENA website to galaxy? rather then doing one sample at the time...

thanks ibseq
galaxy • 749 views
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modified 21 months ago by Jennifer Hillman Jackson ♦ 25k • written 21 months ago by i b • 330
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gravatar for Jennifer Hillman Jackson
21 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Not at this time through the data retrieval tool. Also, there are ongoing issues with this tool, please see: https://biostar.usegalaxy.org/p/21066/#21709

It might be possible to copy the links from multiple datasets, save that in a text file, then paste those into the Upload tool. I have not tested that yet today. Will post back to the other post as another workaround if this works.

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 21 months ago • written 21 months ago by Jennifer Hillman Jackson ♦ 25k

Loading with the Upload tool using URLs results in the same sort of failure ("Connection reset by peer"). These are green, empty, datasets, not red - but the problem is declared in the dataset's box.

Once the problems with the data provider are resolved, I would definitely suggest that you test this out as a way to load data in batch. URLs from any server that supports public data retrieval via HTTP or FTP are a valid way to load data into Galaxy with the Upload tool.

As an aside, I did have one transfer with the EBI SRA tool work today when I ran several in batch. Yet that is how this problem has been manifesting - some retrievals are successful, some fail, for the same query, for different queries, at the same time, or different times. This is the root of the problem and what we are hoping to get resolved.

ADD REPLY • link written 21 months ago by Jennifer Hillman Jackson ♦ 25k
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