Question: download Galaxy history
0
gravatar for biofilia
10 months ago by
biofilia0
biofilia0 wrote:

Hi,

As recommended by https://biostar.usegalaxy.org/p/3965/ , in order to download my entire Results history, I have used 'wget' followed by the weblink provided when I choose "Export History" from the pull-down menu. Although no error is given, the only thing that downloads is an 'export archive,' not the data itself. Does anyone know whether the problem is that the exported files are too large (they tally ~ 8Gb)? If so, is there any other convenient way to download 20+ result files?

Thanks, Merwin

galaxy • 474 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by biofilia0
1
gravatar for Jennifer Hillman Jackson
10 months ago by
United States
Jennifer Hillman Jackson24k wrote:

Hi Merwin,

The server was busy today. The data might not have been fully compressed when you downloaded. Please try again and let us know if this is still a problem now (this the usual solution). If still a problem, I'll do some testing.

The individual files could be downloaded with curl/wget command lines put into a simple shell script, but you would still need to capture the URL for each (copy/paste). For 20, it could get tedious, but it is an option. For 100, it would probably not be, unless using the API.

There is an enhancement request to enable download through FTP. No decisions yet, but you can follow it here if interested: https://github.com/galaxyproject/galaxy/issues/2968

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 10 months ago • written 10 months ago by Jennifer Hillman Jackson24k
0
gravatar for biofilia
10 months ago by
biofilia0
biofilia0 wrote:

Hi Jen,

I tried again with the same result. I ended up downloading the files individually, as you suggest. I'd still be interested, though, in knowing the source of the problem, in case a similar issue arises the next time I want to download the entire history.

Thanks, Merwin

ADD COMMENTlink written 10 months ago by biofilia0

Hi Merwin, Would you share a link to the history you are trying to download? Send it in an email using your registered account address. Including a link to this post would help connect it all together. Thanks! Jen

ADD REPLYlink written 10 months ago by Jennifer Hillman Jackson24k

The problem with downloading entire histories is a known and I confirmed that is what the problem is with your use-case.

I replied direct, but for others, batch download of datasets by URL is the workaround (as described above). Placing this option with the user interface is an enhancement request:

Batch download for datasets https://github.com/galaxyproject/galaxy/issues/3195

ADD REPLYlink written 10 months ago by Jennifer Hillman Jackson24k
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