I am trying to import a history from another Galaxy server. When I download the history from the other server, I receive a URL, which I can click to download the tar.gz file. I have tried to copy that URL into the Users > Import interface on usegalaxy.org, but it ends in an error, screen capture below. I also tried to upload the local file (both as tar.gz and the extracted file). No action happens when I click on “Import History”. (I read a post dated approximately 10 months ago with a similar issue, and I have made the history accessible by link to try the export again, but I am still getting the error.) Please let me know what I am doing wrong. Thank you!
Hi @jclaudio
it seems some restrictions were introduced to data sharing recently. On “source” Galaxy server go to history menu (small triangle icon at the top right corner of the history panel) > Share or publish > make history accessible. This should address the import history error. You can you the old link.
Kind regards,
Igor
Thanks for the response. My link was “accessible” on the sending side, and I also tried toggling on the Public share, then creating a new link. Those still didn’t work for an import by URL, but I did find I was able to download the file then upload it afterward.
Hi @jclaudio
I am glad you’ve found the solution.
I reproduced the history import issue. It was resolved by making the history accessible. What do you mean by “link was accessible”? You can copy the link or your history status(?) was changed to “accessible”?
Kind regards,
Igor
Yes, I clicked on this option (screenshot) to make the history accessible, then used the Export to File function to generate the URL for the archive download.
Hi @jclaudio
I am sorry for being too pedantic, but the description says the history is restricted to you and users listed below. Have you clicked at Make History Accessible via Link?
It seems you use an old version of Galaxy. A similar page on Galaxy Australia looks somewhat different:
I have not included the link in the screenshot. Note that the description says it is available to anyone with link.
Kind regards,
Igor
I apologize – in my screenshot, I show the buttons prior to actually clicking on the submit button, so you are correct in that the description in my screenshot says “restricted to you and users listed below”, but I did use the link created in order to generate the archive file. (Sorry about that misclarity on my part!)
I have a related question. Most of my histories are able to be imported by using the file upload, but not all. Do you know why this might be the case?
Is the server where the history archive was generated exposed publicly? Meaning, any URL needs to be publicly accessible for a Galaxy server to read it. Servers are not “aware” of accounts at other servers by default (or ever) unless some special configuration was involved – and that wouldn’t be available at many public servers, including UseGalaxy.org.
If the server is not hosted publicly, then other servers outside of your local network (or maybe just your computer?) cannot read in data via URL. Instead, you’ll need to download the archive, then upload it to other servers. Transfer entire histories from one Galaxy server to another
Maybe I’m misunderstanding and you can clarify more?
What is the URL of the “from” server?
And please confirm that the “to” server is UseGalaxy.org?
Hard to say. Some file systems do not support big files, at least it was the case in the past. In this situation big files might be truncated, creating a broken archive. Personally, I found history export very slow, at least on Galaxy Australia, and rarely use it for big histories. I transfer big files individually. New version of Galaxy provides link to files (chain icon). Copy and paste it into target Galaxy upload menu, Get/Fetch data section. It works like a charm between usegalaxy.* servers (with small number of files).
@igor Thank you for the link, and I was able to import correctly from that link. @jennaj Based on this, I believe what you wrote is the case. I toggled the history to public & share for two histories, and although it still returned the error, I think that there are some other custom permissions set. Thank you both for your responses and helping me with sorting this out.
