downloading to a local machine in bulk

Question: downloading to a local machine in bulk

21 months ago by

ib7 • 0

United Kingdom

ib7 • 0 wrote:

hello, how can i download to my local machine from galaxy without clicking on the save icon for each dataset? I know about the "export to file" option but this is to save to another galaxy server? is this to save to my local amchine as well? the wget/curl option doesnt seem to work on the full history

thanks for the help ib7

download export-import galaxy history dataset • 724 views

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modified 21 months ago by Jennifer Hillman Jackson ♦ 25k • written 21 months ago by ib7 • 0

Try 'export history to file' history option. It will give you link to a tarball with all your datasets in it.

ADD REPLY • link written 21 months ago by Martin Čech ♦♦ 4.9k

Correct, forgot that can be another alternative for some. Thanks Martin!

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

hi martin, doesn't work always somehow. I have managed to download one history, but now, I cannot any longer. The link cannot be opened on the teminal as a directory containing data.

any advice? thanks ib7

ADD REPLY • link written 21 months ago by i b • 330

Did you download the archive? Or what link in terminal do you mean?

ADD REPLY • link written 21 months ago by Martin Čech ♦♦ 4.9k

HI Martin, A link was created when I “export to file” I copied the link on a terminal and used wget <link> (with/without quotes), but it is a not a tar that’s it’s being downloaded. If I open it, it looks like a script.

ADD REPLY • link written 21 months ago by i b • 330

21 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Dataset download as a batch operation is a current enhancement request under review. Please see: https://github.com/galaxyproject/galaxy/issues/3195

And yes, the other functions (import/export to file) are for transferring entire histories from one Galaxy to another. This includes moving data from Galaxy Main into a local Galaxy. There are some issues with this functionality (but not for all cases), please see: https://github.com/galaxyproject/galaxy/issues/3235

Multiple mget/curl requests could be placed into a script, but the URL for each dataset would have to be obtained through the UI or using the API. But once that script is launched, it could run while you are doing other things. https://docs.galaxyproject.org/en/master/api_doc.html

Thanks! Jen, Galaxy team

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

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