Export data as compressed file

usegalaxy.org support
, , ,
#1

Hi,
Is it possible to download multiple data-sets as a compressed file into my workstation? an R object would work too.
I don’t intent to create a link and access the data from a different server, I basically want to do the same as selecting a object and clicking the 3.5 diskette icon to download the file, but with multiple objects at once.

thanks

1 Like
#2

Hi @AgustinGV

Try this:

  • History menu > Copy Datasets – By putting just the datasets you want to download into a new history, this will make the overall history size smaller and the next step will go faster. But you could also download the entire history these data are in. The bigger the history, the more time archive creation will take.
    • Note: Copying datasets does not consume more quota space.
  • History menu > Export History to file – Create and download an archive of that new history.
  • Uncompress that history archive and all of the datasets will be inside it.

For others reading, that history archive can also be imported into other Galaxy servers (the original uncompressed version) – including a simple local Galaxy – as a way of backing up data in context.

Alternative:

  • Use curl or wget. FAQ: Downloading Data
  • Note: This does require capturing each dataset’s disc icon URL. But is faster than downloading via a web browser.

Some discussion (and linked discussion) about ways to improve data download (using FTP was one idea). All of this is still pending a final solution: https://github.com/galaxyproject/galaxy/issues/2968

Thanks!

1 Like
#3

Thanks, I tried that, but I received the following message:

Exporting History ‘pseudoalignment Export’. You will need to make this history ‘accessible’ in order to import this to another galaxy sever.
Use this link to download the archive or import it to another Galaxy server: https://usegalaxy.org/history/export_archive?id=da43b74d2ed1eb76

If I open the link in a new tab I get to the same page, and

If I click “make this history accessible” I’ve got this:

Internal Server Error

The server has either erred or is incapable of performing the requested operation.

Finally, the history should be accessible as I set it from the “Share or Publish” menu

Share or Publish History pseudoalignment Export

Make History Accessible via Link and Publish It

This history is currently accessible via link .

Anyone can view and import this history by visiting the following URL:

1 Like
#4

Correct, histories need to be in a “shared by link” state.

Do this in a way that also shares the datasets, like this (check the box before generating the link). You can unshare to check if you did this already, then regenerate the link:

exmaple-share-by-link-plus-datasets
exmaple-share-by-link-plus-datasets.png1270×352 36.9 KB

I would suggest starting over. Not sure why the server errored, but perhaps because of the “objects” (datasets) were not shared originally, or because of opening the link in a new tab (?).

You might need to create the archive again. Enough time has passed that the prior archive has likely cleared by now. That will be important.

I’ll also test to see if not sharing objects is the problem. If I can reproduce it, will report it to our developers so we can make the usage clearer.

Thanks!

1 Like
#5

I just try it and it work,
thanks!

1 Like
#6

Hey @AgustinGV – super!! Glad that worked out :slight_smile: