Question: Downloading data? option gone?
0
gravatar for Elizabeth Clare
5 months ago by
Elizabeth Clare20 wrote:

Hi,

I want to perform a bulk download from my galaxy history. There used to be an option to export to a file. It's still listed on the Galaxy instruction page here https://galaxyproject.org/support/download-data/

but no such option is available in my galaxy history options (in fact lots of old options seem to be gone).

How do I download my datasets now? one at a time is going to be hundreds of files.

Thanks Beth

ADD COMMENTlink modified 5 months ago • written 5 months ago by Elizabeth Clare20
0
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Two options for data download (explained in the FAQ with more details):

  • Disc icon within a dataset. If working with dataset collections, you'll need to click into the collection to access the disc icon for the entire collection (near the top) and/or click into the individual datasets of the collection to find this icon (and others: job details, etc). Clicking on the icon will download each directly, or you can capture the URL and use wget or curl.

  • Export History to File. This option is listed under the gear icon > History menu near the top of the right panel. This exports everything in the history. If you just need some of the data but still want to do this in batch, copy that subset of data into a new history and export that instead. The larger the history, the longer it takes to compress it into an archive and later download it. Uncompress the archive once you have it locally to access individual datasets. Archives can also be used with the option Import from File - using the Galaxy URL for the archive or your downloaded archive to load it up somewhere else (your own local Galaxy or any Galaxy that has the option available/activated).

This is how Galaxy is configured by default. If working at a server where these options were for some reason disabled, you'll need to contact the administrators of that server directly for help. Known Public Galaxy servers often have contact information on the welcome page of the server with additional information here: https://galaxyproject.org/public-galaxy-servers/

Note: If your browser window is small, elements in the History menu list can be cut-off at the bottom. Make your window bigger to see all if you think this might be your specific problem. This menu should scroll but isn't right now at https://usegalaxy.org. I'll ask the developers about it.

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson25k
0
gravatar for Elizabeth Clare
5 months ago by
Elizabeth Clare20 wrote:

Hi,

I know it’s supposed to be under the gear icon in history… but I can’t see any export to file option?

I can see it in your tutorial movies but I can’t see it in my options. That is what I was posting about.

Under the gear icon I have three categories of options.

History Lists

Curren History

Dataset Actions

Each has a few options but none is to export my history to file. I am using the main galaxy server I think. ".org"

Beth

ADD COMMENTlink written 5 months ago by Elizabeth Clare20
0
gravatar for Elizabeth Clare
5 months ago by
Elizabeth Clare20 wrote:

AH! it is the window size. I am on a small computer and it does not fit even when the window is maximized. I had to actually change the text size in my browser and it does appear down at the bottom.

So it's there but the lack of scrolling hides it.

Thanks!

Beth

ADD COMMENTlink written 5 months ago by Elizabeth Clare20

That's what happened to me, too :) Glad this was worked out. We'll fix the scroll on the menu for the longer term solution.

ADD REPLYlink written 5 months ago by Jennifer Hillman Jackson25k

Ticket for the scrolling fix, please follow for updates if interested: https://github.com/galaxyproject/galaxy/issues/6284

ADD REPLYlink written 5 months ago by Jennifer Hillman Jackson25k
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